Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: cc336f61c09eac6c3dd9dba706b08481dc5bd709
https://github.com/galaxyproject/galaxy/commit/cc336f61c09eac6c3dd9dba706b0…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-06-03 (Fri, 03 Jun 2016)
Changed paths:
M .ci/py3_sources.txt
M contrib/galaxy_config_merger.py
M contrib/nagios/check_galaxy.py
M cron/build_chrom_db.py
M cron/parse_builds.py
M cron/parse_builds_3_sites.py
M lib/galaxy/config.py
M lib/galaxy_utils/sequence/fastq.py
M lib/tool_shed/util/container_util.py
M scripts/cleanup_datasets/admin_cleanup_datasets.py
M scripts/cleanup_datasets/cleanup_datasets.py
M test/api/test_workflows_from_yaml.py
M test/base/interactor.py
M test/base/twilltestcase.py
M test/unit/tools/test_actions.py
M test/unit/workflows/test_run_parameters.py
M tool_list.py
M tools/data_source/data_source.py
M tools/data_source/fetch.py
M tools/data_source/genbank.py
M tools/data_source/hbvar_filter.py
M tools/data_source/import.py
M tools/data_source/microbial_import.py
M tools/data_source/microbial_import_code.py
M tools/data_source/upload.py
Log Message:
-----------
Make some files compatible with Python3
Also enlarge the set of files tested with flake8 under Python3
Commit: e2f21933553208da44ac7a189ef45c9f9ad8c82b
https://github.com/galaxyproject/galaxy/commit/e2f21933553208da44ac7a189ef4…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-06-06 (Mon, 06 Jun 2016)
Changed paths:
M .ci/py3_sources.txt
M contrib/galaxy_config_merger.py
M contrib/nagios/check_galaxy.py
M cron/build_chrom_db.py
M cron/parse_builds.py
M cron/parse_builds_3_sites.py
M lib/galaxy/config.py
M lib/galaxy_utils/sequence/fastq.py
M lib/tool_shed/util/container_util.py
M scripts/cleanup_datasets/admin_cleanup_datasets.py
M scripts/cleanup_datasets/cleanup_datasets.py
M test/api/test_workflows_from_yaml.py
M test/base/interactor.py
M test/base/twilltestcase.py
M test/unit/tools/test_actions.py
M test/unit/workflows/test_run_parameters.py
M tool_list.py
M tools/data_source/data_source.py
M tools/data_source/fetch.py
M tools/data_source/genbank.py
M tools/data_source/hbvar_filter.py
M tools/data_source/import.py
M tools/data_source/microbial_import.py
M tools/data_source/microbial_import_code.py
M tools/data_source/upload.py
Log Message:
-----------
Merge pull request #2453 from nsoranzo/python3
Python3: Make some files compatible with Python3
Compare: https://github.com/galaxyproject/galaxy/compare/7b3e5369f8d6...e2f219335532
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: afc8bdc81d9feb9d2b6e523fd37a945c83e22a2a
https://github.com/galaxyproject/galaxy/commit/afc8bdc81d9feb9d2b6e523fd37a…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-03-15 (Tue, 15 Mar 2016)
Changed paths:
M .gitignore
A config/job_conf_k8s.xml
A lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Initial commit for collaboration on the k8s runner/job configuration.
Commit: fa3da5a5194cc5317d658a1bab36f824e2b73b93
https://github.com/galaxyproject/galaxy/commit/fa3da5a5194cc5317d658a1bab36…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-03-15 (Tue, 15 Mar 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Adds imports for pykube
Commit: eff6d21a516174e619bc3d12b7b78b378dff6526
https://github.com/galaxyproject/galaxy/commit/eff6d21a516174e619bc3d12b7b7…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-03-15 (Tue, 15 Mar 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Changes import to handle missing dependency
Commit: 9c4ef02e9ff50a173b8531668ab042bf8cbc9ed1
https://github.com/galaxyproject/galaxy/commit/9c4ef02e9ff50a173b8531668ab0…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-03-15 (Tue, 15 Mar 2016)
Changed paths:
M config/job_conf_k8s.xml
Log Message:
-----------
Sample config file for k8s based execution.
Commit: f2ef8de953930906913dbff88561e98b6800fe90
https://github.com/galaxyproject/galaxy/commit/f2ef8de953930906913dbff88561…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-03-15 (Tue, 15 Mar 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
First trial at the __init__
Commit: 97af6466cdfc148e4c1f1424d24319a18e29f8bd
https://github.com/galaxyproject/galaxy/commit/97af6466cdfc148e4c1f1424d243…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-06 (Wed, 06 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Configures pykube to use the kubernetes config file path set in the job_conf.xml, imports Job instead of Pod.
Commit: 63842580dc62070128637ea3bde261040e78e4ac
https://github.com/galaxyproject/galaxy/commit/63842580dc62070128637ea3bde2…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-07 (Thu, 07 Apr 2016)
Changed paths:
M config/job_conf_k8s.xml
Log Message:
-----------
Adds persistent volume claim name example in config.
Commit: d5abfb6eb5182c4aa7e48427c2440edd771c3ff3
https://github.com/galaxyproject/galaxy/commit/d5abfb6eb5182c4aa7e48427c244…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-07 (Thu, 07 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Initial commit of queue_job plus required helper methods (not finished).
Commit: 2c485d768057ca6e80eb1650fe93fad5b7e0e371
https://github.com/galaxyproject/galaxy/commit/2c485d768057ca6e80eb1650fe93…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-07 (Thu, 07 Apr 2016)
Changed paths:
M config/job_conf_k8s.xml
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Adds pieces for PersistentVolume and PersistentVolumesClaims
Commit: 2607be1810a5b95cab863d715efe8e889918c2fd
https://github.com/galaxyproject/galaxy/commit/2607be1810a5b95cab863d715efe…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-13 (Wed, 13 Apr 2016)
Changed paths:
M config/job_conf_k8s.xml
Log Message:
-----------
Adds namespace and port proposal for job_conf file.
Commit: ac2a82c47cffceb4eeb18d201f4f48887828ca55
https://github.com/galaxyproject/galaxy/commit/ac2a82c47cffceb4eeb18d201f4f…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-13 (Wed, 13 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Minor formatting
Commit: af03b96ac13038aab81f2301f213a2a710c7520d
https://github.com/galaxyproject/galaxy/commit/af03b96ac13038aab81f2301f213…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-13 (Wed, 13 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Job name and correct spec.
Commit: c16fe1618fe535a92cb4ee97432e4675010741fa
https://github.com/galaxyproject/galaxy/commit/c16fe1618fe535a92cb4ee97432e…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-13 (Wed, 13 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Adds async jobs to monitor queue
Commit: f6dc05f57cda5f510eaaec6ec978360b918fd73b
https://github.com/galaxyproject/galaxy/commit/f6dc05f57cda5f510eaaec6ec978…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-13 (Wed, 13 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Improves job name, prepending string to make it URLable as required by kubernetes
Commit: 0d21b52d52469300917fe7ea83d6f1100987878e
https://github.com/galaxyproject/galaxy/commit/0d21b52d52469300917fe7ea83d6…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-13 (Wed, 13 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Comments ports usage (we leave this feature for later) and other minor formatting.
Commit: 6cbbbfe161003c4a595eba4c10dc358a920a26ab
https://github.com/galaxyproject/galaxy/commit/6cbbbfe161003c4a595eba4c10dc…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-13 (Wed, 13 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
changes way that 'command' option is passed to k8s on the Job object to cater for multi line commands.
Commit: 96d86de6cf519b39c3c85cfd9d05b52894897f78
https://github.com/galaxyproject/galaxy/commit/96d86de6cf519b39c3c85cfd9d05…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-13 (Wed, 13 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Implements stop job.
Commit: 820d33c7645c546cd341054fc18981fcf80a59c6
https://github.com/galaxyproject/galaxy/commit/820d33c7645c546cd341054fc189…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-15 (Fri, 15 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Minor correction of message.
Commit: 820913c2d641c38d279903e07d2008cd864390bc
https://github.com/galaxyproject/galaxy/commit/820913c2d641c38d279903e07d20…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-15 (Fri, 15 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Adds some todo's
Commit: ef70f0edfad324a0887d53084d38414d110ac1b4
https://github.com/galaxyproject/galaxy/commit/ef70f0edfad324a0887d53084d38…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-18 (Mon, 18 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Implements watch_item and replaces the watched_items, to use the parent logic.
Commit: f80242069b4e4eed455e5ac2a4f37f3e2404c6a0
https://github.com/galaxyproject/galaxy/commit/f80242069b4e4eed455e5ac2a4f3…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-18 (Mon, 18 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Changes stop job to scale job to zero replicas instead of deleting the job (for logging purposes)
Commit: 000259512057592909b459ff609742d1ae26a35e
https://github.com/galaxyproject/galaxy/commit/000259512057592909b459ff6097…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-18 (Mon, 18 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Minor documentation improvement.
Commit: 25f422290e2b2a5a48b84b872efa3d1f15d50a66
https://github.com/galaxyproject/galaxy/commit/25f422290e2b2a5a48b84b872efa…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-18 (Mon, 18 Apr 2016)
Changed paths:
M config/job_conf_k8s.xml
Log Message:
-----------
Adds pods retrials for per installation and individual docker destination.
Commit: bdf283edb0a4ef49349f58a6b2df4014d0e3ae00
https://github.com/galaxyproject/galaxy/commit/bdf283edb0a4ef49349f58a6b2df…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-18 (Mon, 18 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Removes unnecessary __get_job_states
Commit: 8ff8c1c4f591d2ae1d61f8ce76b4758f47cff305
https://github.com/galaxyproject/galaxy/commit/8ff8c1c4f591d2ae1d61f8ce76b4…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-18 (Mon, 18 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Uses k8s pod log as stdout/stderr.
Commit: 9fbf03dd7d45e3c06b66b98a562063284e28b8ed
https://github.com/galaxyproject/galaxy/commit/9fbf03dd7d45e3c06b66b98a5620…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-19 (Tue, 19 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Removes unnecessary get CLI plugins method.
Commit: f686253ca7715e509c74778f3e78ab96358ccc92
https://github.com/galaxyproject/galaxy/commit/f686253ca7715e509c74778f3e78…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-19 (Tue, 19 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
PEP8 compliant formatting
Commit: 58c969723264fb8fec5e837c9483c7ad401d3fae
https://github.com/galaxyproject/galaxy/commit/58c969723264fb8fec5e837c9483…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-19 (Tue, 19 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Clean up for queue method.
Commit: e50ed67ced41554856498246f5d5fa3004e40b63
https://github.com/galaxyproject/galaxy/commit/e50ed67ced41554856498246f5d5…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-19 (Tue, 19 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Removes apparently unnecessary parse_destination_params...
Commit: daf8ccbf0473872cb288267f23150cdcd2f80e84
https://github.com/galaxyproject/galaxy/commit/daf8ccbf0473872cb288267f2315…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-19 (Tue, 19 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Removes url_to_destination, as this is only for legacy destinations (which I guess our's isn't, wouldn't have any URL to transform either)
Commit: 258c2812b9c15be5101856ae0b4a33d51f087015
https://github.com/galaxyproject/galaxy/commit/258c2812b9c15be5101856ae0b4a…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-19 (Tue, 19 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Adds some logging plus job state changes.
Commit: 0c08228349a88f92d044bc903056cf3ad7b4e0cc
https://github.com/galaxyproject/galaxy/commit/0c08228349a88f92d044bc903056…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-20 (Wed, 20 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Fixes initial handling of runner params.
Commit: 43ff13d005aa8c7192837df2e33c559fbdf8d42d
https://github.com/galaxyproject/galaxy/commit/43ff13d005aa8c7192837df2e33c…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-20 (Wed, 20 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Starts monitor thread and worker threads.
Commit: e3d239a484c4e04395a29dc8c030c30856a1f942
https://github.com/galaxyproject/galaxy/commit/e3d239a484c4e04395a29dc8c030…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-22 (Fri, 22 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Changes k8s job api path to extensions/v1beta1 as pykube doesn't support the other one yet.
Commit: ffdc08bbc1cef98b3e10130b5763b8bd794ca9c8
https://github.com/galaxyproject/galaxy/commit/ffdc08bbc1cef98b3e10130b5763…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-22 (Fri, 22 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Fixes labels and faulty spec hierarchy.
Commit: cabfd83ad2a747382d613585c0e040e4506b217b
https://github.com/galaxyproject/galaxy/commit/cabfd83ad2a747382d613585c0e0…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-22 (Fri, 22 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Fixes volumes and containers to be as expected json arrays.
Commit: ec97296ba8990bda593bd78bbd9e79f02e62d31b
https://github.com/galaxyproject/galaxy/commit/ec97296ba8990bda593bd78bbd9e…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-22 (Fri, 22 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Fixes non-DNS persistent volume claim.
Commit: 943fb128f1a8445ce8e79784b32ec71a625ec24a
https://github.com/galaxyproject/galaxy/commit/943fb128f1a8445ce8e79784b32e…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-25 (Mon, 25 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Improves formatting (PEP suggestions).
Commit: a55afa51aa41198b027dfe757b9037890da97e9a
https://github.com/galaxyproject/galaxy/commit/a55afa51aa41198b027dfe757b90…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-25 (Mon, 25 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Handles correctly error and output files.
Commit: 74a4772e77dadddd4da7bbbce8164e5b5bbdd41b
https://github.com/galaxyproject/galaxy/commit/74a4772e77dadddd4da7bbbce816…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-04-25 (Mon, 25 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Removes some unneeded imports.
Commit: 94f38e79572ee44a2b5c7c4108d18a0aa2716bd0
https://github.com/galaxyproject/galaxy/commit/94f38e79572ee44a2b5c7c4108d1…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-05-03 (Tue, 03 May 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Missing os environment functionality import (forgot to include in commit).
Commit: 7abd09e38509e7668c2440a6c6fe5e6931bdc9d7
https://github.com/galaxyproject/galaxy/commit/7abd09e38509e7668c2440a6c6fe…
Author: Pablo Moreno <pcm32(a)users.noreply.github.com>
Date: 2016-05-03 (Tue, 03 May 2016)
Changed paths:
M .ci/flake8_wrapper.sh
M .ci/py3_sources.txt
M .gitignore
M CONTRIBUTORS.md
M Makefile
M README.rst
R buildbot_setup.sh
M client/README.md
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/mvc/citation/citation-model.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-parameters.js
R client/galaxy/scripts/mvc/form/form-select-content.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folder-view.js
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-library-view.js
M client/galaxy/scripts/mvc/library/library-librarylist-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/mvc/library/library-model.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/ui/ui-list.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-options.js
A client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/scripts/utils/localization.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/library.less
M client/galaxy/style/less/ui.less
M client/galaxy/style/less/upload.less
M client/grunt-tasks/style.js
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
A config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample
M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample
M config/plugins/interactive_environments/jupyter/templates/jupyter.mako
A config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample
M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
M config/plugins/tours/core.galaxy_ui.yaml
M config/plugins/tours/core.scratchbook.yaml
M config/reports.ini.sample
M config/tool_data_table_conf.xml.sample
M config/tool_shed.ini.sample
M contrib/galaxy.debian-init
M contrib/galaxy.fedora-init
A contrib/galaxy_reports.fedora-init
A contrib/galaxy_supervisor.conf
A display_applications/biom/biom_simple.xml
A display_applications/iobio/bam.xml
A display_applications/iobio/vcf.xml
M doc/source/admin/framework_dependencies.rst
M doc/source/lib/modules.rst
R doc/source/lib/pulsar.client.rst
R doc/source/lib/pulsar.client.staging.rst
R doc/source/lib/pulsar.client.transport.rst
R doc/source/lib/pulsar.rst
M doc/source/releases/index.rst
R install_and_test_tool_shed_repositories.sh
M lib/galaxy/app.py
M lib/galaxy/config.py
A lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml
A lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml
A lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml
A lib/galaxy/datatypes/converters/cml_to_smi_converter.xml
A lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml
A lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml
A lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml
A lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml
A lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml
A lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml
A lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml
A lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml
A lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml
A lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml
A lib/galaxy/datatypes/converters/mol_to_cml_converter.xml
A lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml
A lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml
A lib/galaxy/datatypes/converters/mol_to_smi_converter.xml
A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml
A lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml
A lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml
A lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml
A lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml
A lib/galaxy/datatypes/converters/smi_to_cml_converter.xml
A lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml
A lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml
A lib/galaxy/datatypes/converters/smi_to_mol_converter.xml
A lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml
A lib/galaxy/datatypes/converters/smi_to_smi_converter.xml
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/display_applications/application.py
A lib/galaxy/datatypes/molecules.py
A lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
A lib/galaxy/datatypes/test/5e5z.pdb
A lib/galaxy/datatypes/test/drugbank_drugs.cml
A lib/galaxy/datatypes/test/drugbank_drugs.inchi
A lib/galaxy/datatypes/test/drugbank_drugs.mol2
A lib/galaxy/datatypes/test/drugbank_drugs.sdf
A lib/galaxy/datatypes/test/drugbank_drugs.smi
A lib/galaxy/datatypes/test/issue1818.tabular
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.axes
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.filter
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.freq
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.lower.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.map
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.oligos
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.otu
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.pair.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.quan
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.ref.taxonomy
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.sabund
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.shared
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.square.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.axes
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.filter
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.freq
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.lower.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.map
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.oligos
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.otu
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.pair.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.quan
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.ref.taxonomy
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.sabund
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.shared
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.square.dist
A lib/galaxy/datatypes/test/q.fps
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/pbs.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
M lib/galaxy/jobs/runners/util/job_script/__init__.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/context.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/history_contents.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/custom_types.py
A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
R lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py
M lib/galaxy/model/util.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/runtime_actions.py
A lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/commands.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/errors.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/lint.py
M lib/galaxy/tools/linters/__init__.py
M lib/galaxy/tools/linters/citations.py
M lib/galaxy/tools/linters/command.py
A lib/galaxy/tools/linters/general.py
M lib/galaxy/tools/linters/help.py
M lib/galaxy/tools/linters/inputs.py
M lib/galaxy/tools/linters/outputs.py
M lib/galaxy/tools/linters/stdio.py
M lib/galaxy/tools/linters/tests.py
R lib/galaxy/tools/linters/top_level.py
M lib/galaxy/tools/linters/xml_order.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parameters/wrapped_json.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/util/__init__.py
R lib/galaxy/util/dictobj.py
M lib/galaxy/util/jstree.py
M lib/galaxy/util/log/fluent_log.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/util/validation.py
M lib/galaxy/version.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/helpers/__init__.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/middleware/statsd.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/datatypes.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/metrics.py
M lib/galaxy/webapps/galaxy/api/quotas.py
M lib/galaxy/webapps/galaxy/api/remote_files.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/tool_runner.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
M lib/galaxy/webapps/tool_shed/api/users.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/webapps/tool_shed/model/mapping.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/scheduling_manager.py
R lib/pulsar/__init__.py
R lib/pulsar/client/__init__.py
R lib/pulsar/client/action_mapper.py
R lib/pulsar/client/amqp_exchange.py
R lib/pulsar/client/amqp_exchange_factory.py
R lib/pulsar/client/client.py
R lib/pulsar/client/config_util.py
R lib/pulsar/client/decorators.py
R lib/pulsar/client/destination.py
R lib/pulsar/client/interface.py
R lib/pulsar/client/job_directory.py
R lib/pulsar/client/manager.py
R lib/pulsar/client/object_client.py
R lib/pulsar/client/path_mapper.py
R lib/pulsar/client/setup_handler.py
R lib/pulsar/client/staging/__init__.py
R lib/pulsar/client/staging/down.py
R lib/pulsar/client/staging/up.py
R lib/pulsar/client/transport/__init__.py
R lib/pulsar/client/transport/curl.py
R lib/pulsar/client/transport/poster.py
R lib/pulsar/client/transport/requests.py
R lib/pulsar/client/transport/ssh.py
R lib/pulsar/client/transport/standard.py
R lib/pulsar/client/util.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/repository/relation_builder.py
M lib/tool_shed/galaxy_install/dependency_display.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/util.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/repository_registry.py
R lib/tool_shed/scripts/api/add_repository_registry_entry.py
R lib/tool_shed/scripts/api/common.py
R lib/tool_shed/scripts/api/create_categories.py
R lib/tool_shed/scripts/api/create_users.py
R lib/tool_shed/scripts/api/export.py
R lib/tool_shed/scripts/api/get_filtered_repository_revisions.py
R lib/tool_shed/scripts/api/import_capsule.py
R lib/tool_shed/scripts/api/remove_repository_registry_entry.py
R lib/tool_shed/scripts/api/reset_metadata_on_repositories.py
R lib/tool_shed/scripts/api/tool_shed_repository_revision_update.py
R lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh
R lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py
R lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py
R lib/tool_shed/scripts/bootstrap_tool_shed/parse_run_sh_args.sh
R lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample
R lib/tool_shed/scripts/check_filesystem_for_empty_tool_dependency_installation_paths.py
R lib/tool_shed/scripts/check_repositories_for_functional_tests.py
R lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py
R lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py
R lib/tool_shed/scripts/clean_up_tool_dependency_directory.py
R lib/tool_shed/scripts/deprecate_repositories_without_metadata.py
R lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py
M lib/tool_shed/tool_shed_registry.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/metadata_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/utility_containers/__init__.py
M lib/tool_shed/utility_containers/utility_container_manager.py
M run.sh
M run_reports.sh
M run_tests.sh
M run_tool_shed.sh
M scripts/bootstrap_history.py
M scripts/common_startup.sh
M scripts/functional_tests.py
M scripts/summarize_timings.py
A scripts/tool_shed/api/add_repository_registry_entry.py
A scripts/tool_shed/api/common.py
A scripts/tool_shed/api/create_categories.py
A scripts/tool_shed/api/create_users.py
A scripts/tool_shed/api/export.py
A scripts/tool_shed/api/get_filtered_repository_revisions.py
A scripts/tool_shed/api/import_capsule.py
A scripts/tool_shed/api/remove_repository_registry_entry.py
A scripts/tool_shed/api/reset_metadata_on_repositories.py
A scripts/tool_shed/api/tool_shed_repository_revision_update.py
A scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh
A scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py
A scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py
A scripts/tool_shed/bootstrap_tool_shed/parse_run_sh_args.sh
A scripts/tool_shed/bootstrap_tool_shed/user_info.xml.sample
A scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py
A scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py
A scripts/tool_shed/clean_up_tool_dependency_directory.py
A scripts/tool_shed/deprecate_repositories_without_metadata.py
A scripts/tool_shed/show_tool_dependency_installation_dir_contents.py
M static/maps/layout/masthead.js.map
M static/maps/layout/menu.js.map
M static/maps/layout/page.js.map
M static/maps/mvc/citation/citation-model.js.map
M static/maps/mvc/form/form-input.js.map
M static/maps/mvc/form/form-parameters.js.map
R static/maps/mvc/form/form-select-content.js.map
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/history-model.js.map
M static/maps/mvc/history/history-view.js.map
M static/maps/mvc/history/multi-panel.js.map
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-folder-view.js.map
M static/maps/mvc/library/library-folderlist-view.js.map
M static/maps/mvc/library/library-folderrow-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/library/library-library-view.js.map
M static/maps/mvc/library/library-librarylist-view.js.map
M static/maps/mvc/library/library-librarytoolbar-view.js.map
M static/maps/mvc/library/library-model.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/ui/ui-list.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/ui/ui-options.js.map
A static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/maps/mvc/workflow/workflow-terminals.js.map
M static/maps/utils/localization.js.map
M static/maps/utils/utils.js.map
M static/maps/viz/trackster/tracks.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/layout/masthead.js
M static/scripts/layout/menu.js
M static/scripts/layout/page.js
M static/scripts/mvc/citation/citation-model.js
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/form/form-parameters.js
R static/scripts/mvc/form/form-select-content.js
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/history/history-view.js
M static/scripts/mvc/history/multi-panel.js
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-folder-view.js
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/library/library-library-view.js
M static/scripts/mvc/library/library-librarylist-view.js
M static/scripts/mvc/library/library-librarytoolbar-view.js
M static/scripts/mvc/library/library-model.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/ui/ui-list.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-options.js
A static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/workflow/workflow-terminals.js
M static/scripts/utils/localization.js
M static/scripts/utils/utils.js
M static/scripts/viz/trackster/tracks.js
M static/style/blue/base.css
M static/style/blue/library.css
A templates/admin/tool_shed_repository/browse_categories.mako
A templates/admin/tool_shed_repository/browse_category.mako
M templates/admin/tool_shed_repository/initiate_repository_installation.mako
A templates/admin/tool_shed_repository/preview_repository.mako
M templates/base/base_panels.mako
M templates/display_base.mako
M templates/sharing_base.mako
A templates/slug_editing_js.mako
M templates/webapps/galaxy/admin/index.mako
A templates/webapps/galaxy/admin/toolsheds.mako
M templates/webapps/galaxy/galaxy.masthead.mako
M templates/webapps/galaxy/galaxy.panels.mako
M templates/webapps/galaxy/history/display.mako
M templates/webapps/galaxy/library/common/browse_library.mako
M templates/webapps/galaxy/library/common/ldda_info.mako
M templates/webapps/galaxy/library/common/library_info.mako
A templates/webapps/galaxy/visualization/gie.mako
M templates/webapps/galaxy/workflow/display.mako
R templates/webapps/galaxy/workflow/export.mako
M templates/webapps/galaxy/workflow/list.mako
M templates/webapps/galaxy/workflow/run.mako
M templates/webapps/galaxy/workflow/sharing.mako
M templates/webapps/tool_shed/index.mako
M templates/webapps/tool_shed/repository/common.mako
M templates/webapps/tool_shed/repository/manage_repository.mako
M templates/webapps/tool_shed/repository/view_changeset.mako
M test/api/test_tools.py
A test/base/driver_util.py
A test/base/integration_util.py
M test/base/interactor.py
M test/base/twilltestcase.py
M test/casperjs/casperjs_runner.py
R test/functional/test_admin_features.py
R test/functional/test_data_security.py
R test/functional/test_dataset_features.py
R test/functional/test_get_data.py
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R test/functional/test_sample_tracking.py
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M test/functional/test_toolbox.py
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R test/install_and_test_tool_shed_repositories/__init__.py
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R test/install_and_test_tool_shed_repositories/base/twilltestcase.py
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R test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py
R test/install_and_test_tool_shed_repositories/repositories_with_tools/__init__.py
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R test/install_and_test_tool_shed_repositories/tool_dependency_definitions/__init__.py
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A test/integration/__init__.py
A test/integration/embedded_pulsar_job_conf.xml
A test/integration/test_pulsar_embedded.py
A test/manual/launch_and_run.sh
A test/manual/workflow_job_conf.xml
M test/manual/workflows_scaling.py
M test/qunit/test-app.js
A test/qunit/tests/form_tests.html
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A test/shed_functional/__init__.py
A test/shed_functional/base/__init__.py
A test/shed_functional/base/common.py
A test/shed_functional/base/test_db_util.py
A test/shed_functional/base/twilltestcase.py
A test/shed_functional/functional/__init__.py
A test/shed_functional/functional/test_0000_basic_repository_features.py
A test/shed_functional/functional/test_0010_repository_with_tool_dependencies.py
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A test/shed_functional/functional/test_0030_repository_dependency_revisions.py
A test/shed_functional/functional/test_0040_repository_circular_dependencies.py
A test/shed_functional/functional/test_0050_circular_dependencies_4_levels.py
A test/shed_functional/functional/test_0060_workflows.py
A test/shed_functional/functional/test_0070_invalid_tool.py
A test/shed_functional/functional/test_0080_advanced_circular_dependencies.py
A test/shed_functional/functional/test_0090_tool_search.py
A test/shed_functional/functional/test_0100_complex_repository_dependencies.py
A test/shed_functional/functional/test_0110_invalid_simple_repository_dependencies.py
A test/shed_functional/functional/test_0120_simple_repository_dependency_multiple_owners.py
A test/shed_functional/functional/test_0130_datatype_converters.py
A test/shed_functional/functional/test_0140_tool_help_images.py
A test/shed_functional/functional/test_0150_prior_installation_required.py
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A test/shed_functional/functional/test_0170_complex_prior_installation_required.py
A test/shed_functional/functional/test_0300_reset_all_metadata.py
A test/shed_functional/functional/test_0310_hg_api_features.py
A test/shed_functional/functional/test_0400_repository_component_reviews.py
A test/shed_functional/functional/test_0410_repository_component_review_access_control.py
A test/shed_functional/functional/test_0420_citable_urls_for_repositories.py
A test/shed_functional/functional/test_0430_browse_utilities.py
A test/shed_functional/functional/test_0440_deleting_dependency_definitions.py
A test/shed_functional/functional/test_0460_upload_to_repository.py
A test/shed_functional/functional/test_0470_tool_dependency_repository_type.py
A test/shed_functional/functional/test_0480_tool_dependency_xml_verification.py
A test/shed_functional/functional/test_0490_export_import_repositories.py
A test/shed_functional/functional/test_0500_export_repository_simple_dependency.py
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A test/shed_functional/functional/test_0540_get_all_metadata_from_api.py
A test/shed_functional/functional/test_0550_metadata_updated_dependencies.py
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A test/shed_functional/functional/test_1300_reset_all_metadata.py
A test/shed_functional/functional/test_1400_review_migration_stages.py
A test/shed_functional/functional/test_1410_update_manager.py
A test/shed_functional/functional/test_1420_tool_dependency_environment_inheritance.py
A test/shed_functional/functional/test_1430_repair_installed_repository.py
A test/shed_functional/functional/test_1440_missing_env_sh_files.py
A test/shed_functional/functional/test_1450_installing_datatypes_sniffers.py
A test/shed_functional/functional/test_1460_data_managers.py
A test/shed_functional/functional/test_1470_updating_installed_repositories.py
A test/shed_functional/functional_tests.py
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A test/shed_functional/test_data/bismark/bismark.tar
A test/shed_functional/test_data/bismark/bismark_methylation_extractor.xml
A test/shed_functional/test_data/blast/blast_datatypes.tar
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A test/shed_functional/test_data/bwa/bwa_base.tar
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A test/shed_functional/test_data/bwa/complex/tool_dependencies.xml
A test/shed_functional/test_data/column_maker/column_maker.tar
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A test/shed_functional/test_data/emboss/0470_files/emboss_complex_dependency.tar
A test/shed_functional/test_data/emboss/0470_files/tool_dependencies.xml
A test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml
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A test/shed_functional/test_data/emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml
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A test/shed_functional/test_data/emboss/libx11_proto/first_tool_dependency/tool_dependencies.xml
A test/shed_functional/test_data/emboss/libx11_proto/second_tool_dependency/tool_dependencies.xml
A test/shed_functional/test_data/filtering/README
A test/shed_functional/test_data/filtering/filtering_0000.txt
A test/shed_functional/test_data/filtering/filtering_1.1.0.tar
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A test/shed_functional/test_data/filtering/filtering_test_data.tar
A test/shed_functional/test_data/filtering/readme.txt
A test/shed_functional/test_data/filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga
A test/shed_functional/test_data/freebayes/freebayes.tar
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A test/shed_functional/test_data/htseq_count/htseq_count.tar
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A test/shed_functional/test_data/package_matplotlib/tool_dependencies.xml
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A test/shed_functional/test_data/proteomics_datatypes/proteomics_datatypes.tar
A test/shed_functional/test_data/readme.txt
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A test/shed_functional/test_data/repository_capsules/0510_trans_proteomic_pipeline.tar.gz
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R test/tool_shed/__init__.py
R test/tool_shed/base/__init__.py
R test/tool_shed/base/common.py
R test/tool_shed/base/test_db_util.py
R test/tool_shed/base/twilltestcase.py
R test/tool_shed/functional/__init__.py
R test/tool_shed/functional/test_0000_basic_repository_features.py
R test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py
R test/tool_shed/functional/test_0020_basic_repository_dependencies.py
R test/tool_shed/functional/test_0030_repository_dependency_revisions.py
R test/tool_shed/functional/test_0040_repository_circular_dependencies.py
R test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py
R test/tool_shed/functional/test_0060_workflows.py
R test/tool_shed/functional/test_0070_invalid_tool.py
R test/tool_shed/functional/test_0080_advanced_circular_dependencies.py
R test/tool_shed/functional/test_0090_tool_search.py
R test/tool_shed/functional/test_0100_complex_repository_dependencies.py
R test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py
R test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py
R test/tool_shed/functional/test_0130_datatype_converters.py
R test/tool_shed/functional/test_0140_tool_help_images.py
R test/tool_shed/functional/test_0150_prior_installation_required.py
R test/tool_shed/functional/test_0160_circular_prior_installation_required.py
R test/tool_shed/functional/test_0170_complex_prior_installation_required.py
R test/tool_shed/functional/test_0300_reset_all_metadata.py
R test/tool_shed/functional/test_0310_hg_push_from_api.py
R test/tool_shed/functional/test_0400_repository_component_reviews.py
R test/tool_shed/functional/test_0410_repository_component_review_access_control.py
R test/tool_shed/functional/test_0420_citable_urls_for_repositories.py
R test/tool_shed/functional/test_0430_browse_utilities.py
R test/tool_shed/functional/test_0440_deleting_dependency_definitions.py
R test/tool_shed/functional/test_0450_skip_tool_tests.py
R test/tool_shed/functional/test_0460_upload_to_repository.py
R test/tool_shed/functional/test_0470_tool_dependency_repository_type.py
R test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py
R test/tool_shed/functional/test_0490_export_import_repositories.py
R test/tool_shed/functional/test_0500_export_repository_simple_dependency.py
R test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py
R test/tool_shed/functional/test_0520_import_export_circular_dependencies.py
R test/tool_shed/functional/test_0530_repository_admin_feature.py
R test/tool_shed/functional/test_0540_get_all_metadata_from_api.py
R test/tool_shed/functional/test_1000_install_basic_repository.py
R test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py
R test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py
R test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py
R test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py
R test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py
R test/tool_shed/functional/test_1060_install_repository_with_workflow.py
R test/tool_shed/functional/test_1070_invalid_tool.py
R test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py
R test/tool_shed/functional/test_1090_repository_dependency_handling.py
R test/tool_shed/functional/test_1100_install_updated_repository_dependencies.py
R test/tool_shed/functional/test_1110_install_tool_from_tool_search.py
R test/tool_shed/functional/test_1120_install_repository_with_complex_dependencies.py
R test/tool_shed/functional/test_1130_install_repository_with_invalid_repository_dependency.py
R test/tool_shed/functional/test_1140_simple_repository_dependency_multiple_owners.py
R test/tool_shed/functional/test_1150_datatype_converters.py
R test/tool_shed/functional/test_1160_tool_help_images.py
R test/tool_shed/functional/test_1170_prior_installation_required.py
R test/tool_shed/functional/test_1180_circular_prior_installation_required.py
R test/tool_shed/functional/test_1190_complex_prior_installation_required.py
R test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py
R test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
R test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py
R test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py
R test/tool_shed/functional/test_1300_reset_all_metadata.py
R test/tool_shed/functional/test_1400_review_migration_stages.py
R test/tool_shed/functional/test_1410_update_manager.py
R test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py
R test/tool_shed/functional/test_1430_repair_installed_repository.py
R test/tool_shed/functional/test_1440_missing_env_sh_files.py
R test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py
R test/tool_shed/functional/test_1460_data_managers.py
R test/tool_shed/functional/test_1470_updating_installed_repositories.py
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R test/tool_shed/test_data/0460_files/repository_dependencies.xml
R test/tool_shed/test_data/0460_files/repository_dependencies_in_root.tar
R test/tool_shed/test_data/0460_files/repository_dependencies_in_subfolder.tar
R test/tool_shed/test_data/0460_files/tool_dependencies.xml
R test/tool_shed/test_data/0460_files/tool_dependencies_in_root.tar
R test/tool_shed/test_data/0460_files/tool_dependencies_in_subfolder.tar
R test/tool_shed/test_data/0480_files/tool_dependencies.xml
R test/tool_shed/test_data/0540_files/column_maker/column_maker.tar
R test/tool_shed/test_data/0540_files/column_maker/repository_dependencies.xml
R test/tool_shed/test_data/0540_files/convert_chars/convert_chars.tar
R test/tool_shed/test_data/0540_files/convert_chars/tool_dependencies.xml
R test/tool_shed/test_data/0540_files/package_bwa/tool_dependencies.xml
R test/tool_shed/test_data/1420_files/binary_tarballs/atlas.tar
R test/tool_shed/test_data/1420_files/binary_tarballs/boost.tar
R test/tool_shed/test_data/1420_files/binary_tarballs/bzlib.tar
R test/tool_shed/test_data/1420_files/binary_tarballs/lapack.tar
R test/tool_shed/test_data/1420_files/binary_tarballs/numpy.tar
R test/tool_shed/test_data/1420_files/binary_tarballs/rdkit.tar
R test/tool_shed/test_data/1420_files/package_atlas_3_10_1420/tool_dependencies.xml
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R test/tool_shed/test_data/1460_files/data_manager_files/test_data_manager.tar
R test/tool_shed/test_data/bed_to_gff_converter/bed_to_gff_converter.tar
R test/tool_shed/test_data/bismark/bismark.tar
R test/tool_shed/test_data/bismark/bismark_methylation_extractor.xml
R test/tool_shed/test_data/blast/blast_datatypes.tar
R test/tool_shed/test_data/blast/blastxml_to_top_descr.tar
R test/tool_shed/test_data/bwa/bwa_base.tar
R test/tool_shed/test_data/bwa/bwa_color.tar
R test/tool_shed/test_data/bwa/complex/bwa_base.tar
R test/tool_shed/test_data/bwa/complex/readme/tool_dependencies.xml
R test/tool_shed/test_data/bwa/complex/tool_dependencies.xml
R test/tool_shed/test_data/column_maker/column_maker.tar
R test/tool_shed/test_data/convert_chars/convert_chars.tar
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R test/tool_shed/test_data/emboss/0470_files/tool_dependencies.xml
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R test/tool_shed/test_data/emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml
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R test/tool_shed/test_data/filtering/filtering_1.1.0.tar
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R test/tool_shed/test_data/filtering/filtering_test_data.tar
R test/tool_shed/test_data/filtering/readme.txt
R test/tool_shed/test_data/filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga
R test/tool_shed/test_data/freebayes/freebayes.tar
R test/tool_shed/test_data/freebayes/freebayes.xml
R test/tool_shed/test_data/freebayes/invalid_tool_dependencies/tool_dependencies.xml
R test/tool_shed/test_data/freebayes/malformed_tool_dependencies/tool_dependencies.xml
R test/tool_shed/test_data/freebayes/sam_fa_indices.loc.sample
R test/tool_shed/test_data/freebayes/tool_data_table_conf.xml.sample
R test/tool_shed/test_data/freebayes/tool_dependencies.xml
R test/tool_shed/test_data/htseq_count/htseq_count.tar
R test/tool_shed/test_data/package_matplotlib/package_matplotlib_1_2.tar
R test/tool_shed/test_data/package_matplotlib/tool_dependencies.xml
R test/tool_shed/test_data/package_numpy/package_numpy_1_7.tar
R test/tool_shed/test_data/proteomics_datatypes/proteomics_datatypes.tar
R test/tool_shed/test_data/readme.txt
R test/tool_shed/test_data/repository_capsules/0490_filtering.tar.gz
R test/tool_shed/test_data/repository_capsules/0500_emboss_5.tar.gz
R test/tool_shed/test_data/repository_capsules/0510_trans_proteomic_pipeline.tar.gz
R test/tool_shed/test_data/repository_capsules/0520_filtering.tar.gz
M test/unit/jobs/test_command_factory.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/test_HistoryContentsManager.py
A test/unit/shed_unit/__init__.py
A test/unit/shed_unit/test_fabric_util.py
A test/unit/shed_unit/test_td_common_util.py
A test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/test_lazy_process.py
M test/unit/test_objectstore.py
R test/unit/tool_shed_unit_tests/__init__.py
R test/unit/tool_shed_unit_tests/test_fabric_util.py
R test/unit/tool_shed_unit_tests/test_td_common_util.py
R test/unit/tool_shed_unit_tests/test_tool_panel_manager.py
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_select_parameters.py
A tool-data/bam_iobio.loc.sample
A tool-data/biom_simple_display.loc.sample
A tool-data/vcf_iobio.loc.sample
M tools/data_source/biomart.xml
M tools/data_source/upload.py
M tools/filters/trimmer.xml
M tools/stats/grouping.py
M tools/stats/grouping.xml
Log Message:
-----------
Merge pull request #1 from galaxyproject/dev
Staying up to date with galaxy dev
Commit: 70091517c889c7ec27f6cccdf08df39cfcd319ac
https://github.com/galaxyproject/galaxy/commit/70091517c889c7ec27f6cccdf08d…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-05-04 (Wed, 04 May 2016)
Changed paths:
M .ci/flake8_wrapper.sh
M .ci/py3_sources.txt
M .gitignore
M CONTRIBUTORS.md
M Makefile
M README.rst
R buildbot_setup.sh
M client/README.md
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/mvc/citation/citation-model.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-parameters.js
R client/galaxy/scripts/mvc/form/form-select-content.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folder-view.js
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-library-view.js
M client/galaxy/scripts/mvc/library/library-librarylist-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/mvc/library/library-model.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/ui/ui-list.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-options.js
A client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/scripts/utils/localization.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/library.less
M client/galaxy/style/less/ui.less
M client/galaxy/style/less/upload.less
M client/grunt-tasks/style.js
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
A config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample
M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample
M config/plugins/interactive_environments/jupyter/templates/jupyter.mako
A config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample
M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
M config/plugins/tours/core.galaxy_ui.yaml
M config/plugins/tours/core.scratchbook.yaml
M config/reports.ini.sample
M config/tool_data_table_conf.xml.sample
M config/tool_shed.ini.sample
M contrib/galaxy.debian-init
M contrib/galaxy.fedora-init
A contrib/galaxy_reports.fedora-init
A contrib/galaxy_supervisor.conf
A display_applications/biom/biom_simple.xml
A display_applications/iobio/bam.xml
A display_applications/iobio/vcf.xml
M doc/source/admin/framework_dependencies.rst
M doc/source/lib/modules.rst
R doc/source/lib/pulsar.client.rst
R doc/source/lib/pulsar.client.staging.rst
R doc/source/lib/pulsar.client.transport.rst
R doc/source/lib/pulsar.rst
M doc/source/releases/index.rst
R install_and_test_tool_shed_repositories.sh
M lib/galaxy/app.py
M lib/galaxy/config.py
A lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml
A lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml
A lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml
A lib/galaxy/datatypes/converters/cml_to_smi_converter.xml
A lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml
A lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml
A lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml
A lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml
A lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml
A lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml
A lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml
A lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml
A lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml
A lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml
A lib/galaxy/datatypes/converters/mol_to_cml_converter.xml
A lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml
A lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml
A lib/galaxy/datatypes/converters/mol_to_smi_converter.xml
A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml
A lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml
A lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml
A lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml
A lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml
A lib/galaxy/datatypes/converters/smi_to_cml_converter.xml
A lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml
A lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml
A lib/galaxy/datatypes/converters/smi_to_mol_converter.xml
A lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml
A lib/galaxy/datatypes/converters/smi_to_smi_converter.xml
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/display_applications/application.py
A lib/galaxy/datatypes/molecules.py
A lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
A lib/galaxy/datatypes/test/5e5z.pdb
A lib/galaxy/datatypes/test/drugbank_drugs.cml
A lib/galaxy/datatypes/test/drugbank_drugs.inchi
A lib/galaxy/datatypes/test/drugbank_drugs.mol2
A lib/galaxy/datatypes/test/drugbank_drugs.sdf
A lib/galaxy/datatypes/test/drugbank_drugs.smi
A lib/galaxy/datatypes/test/issue1818.tabular
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.axes
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.filter
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.freq
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.lower.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.map
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.oligos
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.otu
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.pair.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.quan
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.ref.taxonomy
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.sabund
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.shared
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.square.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.axes
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.filter
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.freq
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.lower.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.map
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.oligos
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.otu
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.pair.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.quan
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.ref.taxonomy
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.sabund
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.shared
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.square.dist
A lib/galaxy/datatypes/test/q.fps
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/pbs.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
M lib/galaxy/jobs/runners/util/job_script/__init__.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/context.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/history_contents.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/custom_types.py
A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
R lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py
M lib/galaxy/model/util.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/runtime_actions.py
A lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/commands.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/errors.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/lint.py
M lib/galaxy/tools/linters/__init__.py
M lib/galaxy/tools/linters/citations.py
M lib/galaxy/tools/linters/command.py
A lib/galaxy/tools/linters/general.py
M lib/galaxy/tools/linters/help.py
M lib/galaxy/tools/linters/inputs.py
M lib/galaxy/tools/linters/outputs.py
M lib/galaxy/tools/linters/stdio.py
M lib/galaxy/tools/linters/tests.py
R lib/galaxy/tools/linters/top_level.py
M lib/galaxy/tools/linters/xml_order.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parameters/wrapped_json.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/util/__init__.py
R lib/galaxy/util/dictobj.py
M lib/galaxy/util/jstree.py
M lib/galaxy/util/log/fluent_log.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/util/validation.py
M lib/galaxy/version.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/helpers/__init__.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/middleware/statsd.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/datatypes.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/metrics.py
M lib/galaxy/webapps/galaxy/api/quotas.py
M lib/galaxy/webapps/galaxy/api/remote_files.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/tool_runner.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
M lib/galaxy/webapps/tool_shed/api/users.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/webapps/tool_shed/model/mapping.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/scheduling_manager.py
R lib/pulsar/__init__.py
R lib/pulsar/client/__init__.py
R lib/pulsar/client/action_mapper.py
R lib/pulsar/client/amqp_exchange.py
R lib/pulsar/client/amqp_exchange_factory.py
R lib/pulsar/client/client.py
R lib/pulsar/client/config_util.py
R lib/pulsar/client/decorators.py
R lib/pulsar/client/destination.py
R lib/pulsar/client/interface.py
R lib/pulsar/client/job_directory.py
R lib/pulsar/client/manager.py
R lib/pulsar/client/object_client.py
R lib/pulsar/client/path_mapper.py
R lib/pulsar/client/setup_handler.py
R lib/pulsar/client/staging/__init__.py
R lib/pulsar/client/staging/down.py
R lib/pulsar/client/staging/up.py
R lib/pulsar/client/transport/__init__.py
R lib/pulsar/client/transport/curl.py
R lib/pulsar/client/transport/poster.py
R lib/pulsar/client/transport/requests.py
R lib/pulsar/client/transport/ssh.py
R lib/pulsar/client/transport/standard.py
R lib/pulsar/client/util.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/repository/relation_builder.py
M lib/tool_shed/galaxy_install/dependency_display.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/util.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/repository_registry.py
R lib/tool_shed/scripts/api/add_repository_registry_entry.py
R lib/tool_shed/scripts/api/common.py
R lib/tool_shed/scripts/api/create_categories.py
R lib/tool_shed/scripts/api/create_users.py
R lib/tool_shed/scripts/api/export.py
R lib/tool_shed/scripts/api/get_filtered_repository_revisions.py
R lib/tool_shed/scripts/api/import_capsule.py
R lib/tool_shed/scripts/api/remove_repository_registry_entry.py
R lib/tool_shed/scripts/api/reset_metadata_on_repositories.py
R lib/tool_shed/scripts/api/tool_shed_repository_revision_update.py
R lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh
R lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py
R lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py
R lib/tool_shed/scripts/bootstrap_tool_shed/parse_run_sh_args.sh
R lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample
R lib/tool_shed/scripts/check_filesystem_for_empty_tool_dependency_installation_paths.py
R lib/tool_shed/scripts/check_repositories_for_functional_tests.py
R lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py
R lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py
R lib/tool_shed/scripts/clean_up_tool_dependency_directory.py
R lib/tool_shed/scripts/deprecate_repositories_without_metadata.py
R lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py
M lib/tool_shed/tool_shed_registry.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/metadata_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/utility_containers/__init__.py
M lib/tool_shed/utility_containers/utility_container_manager.py
M run.sh
M run_reports.sh
M run_tests.sh
M run_tool_shed.sh
M scripts/bootstrap_history.py
M scripts/common_startup.sh
M scripts/functional_tests.py
M scripts/summarize_timings.py
A scripts/tool_shed/api/add_repository_registry_entry.py
A scripts/tool_shed/api/common.py
A scripts/tool_shed/api/create_categories.py
A scripts/tool_shed/api/create_users.py
A scripts/tool_shed/api/export.py
A scripts/tool_shed/api/get_filtered_repository_revisions.py
A scripts/tool_shed/api/import_capsule.py
A scripts/tool_shed/api/remove_repository_registry_entry.py
A scripts/tool_shed/api/reset_metadata_on_repositories.py
A scripts/tool_shed/api/tool_shed_repository_revision_update.py
A scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh
A scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py
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A scripts/tool_shed/bootstrap_tool_shed/parse_run_sh_args.sh
A scripts/tool_shed/bootstrap_tool_shed/user_info.xml.sample
A scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py
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A scripts/tool_shed/clean_up_tool_dependency_directory.py
A scripts/tool_shed/deprecate_repositories_without_metadata.py
A scripts/tool_shed/show_tool_dependency_installation_dir_contents.py
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M static/scripts/utils/localization.js
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M templates/webapps/galaxy/history/display.mako
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M templates/webapps/galaxy/workflow/run.mako
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M templates/webapps/tool_shed/index.mako
M templates/webapps/tool_shed/repository/common.mako
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M test/api/test_tools.py
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M test/casperjs/casperjs_runner.py
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R test/functional/test_data_security.py
R test/functional/test_dataset_features.py
R test/functional/test_get_data.py
R test/functional/test_library_features.py
R test/functional/test_library_security.py
R test/functional/test_metadata_editing.py
R test/functional/test_sample_tracking.py
R test/functional/test_tags.py
M test/functional/test_toolbox.py
R test/functional/test_ucsc_table_browser.py
R test/functional/test_user_info.py
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R test/install_and_test_tool_shed_repositories/__init__.py
R test/install_and_test_tool_shed_repositories/base/__init__.py
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R test/install_and_test_tool_shed_repositories/base/twilltestcase.py
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R test/install_and_test_tool_shed_repositories/functional/__init__.py
R test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py
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A test/integration/embedded_pulsar_job_conf.xml
A test/integration/test_pulsar_embedded.py
A test/manual/launch_and_run.sh
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M test/qunit/test-app.js
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A test/shed_functional/__init__.py
A test/shed_functional/base/__init__.py
A test/shed_functional/base/common.py
A test/shed_functional/base/test_db_util.py
A test/shed_functional/base/twilltestcase.py
A test/shed_functional/functional/__init__.py
A test/shed_functional/functional/test_0000_basic_repository_features.py
A test/shed_functional/functional/test_0010_repository_with_tool_dependencies.py
A test/shed_functional/functional/test_0020_basic_repository_dependencies.py
A test/shed_functional/functional/test_0030_repository_dependency_revisions.py
A test/shed_functional/functional/test_0040_repository_circular_dependencies.py
A test/shed_functional/functional/test_0050_circular_dependencies_4_levels.py
A test/shed_functional/functional/test_0060_workflows.py
A test/shed_functional/functional/test_0070_invalid_tool.py
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A test/shed_functional/functional/test_0090_tool_search.py
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A test/shed_functional/functional/test_0110_invalid_simple_repository_dependencies.py
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A test/shed_functional/functional/test_0400_repository_component_reviews.py
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A test/shed_functional/functional/test_1070_invalid_tool.py
A test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py
A test/shed_functional/functional/test_1090_repository_dependency_handling.py
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A test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py
A test/shed_functional/functional/test_1150_datatype_converters.py
A test/shed_functional/functional/test_1160_tool_help_images.py
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A test/shed_functional/functional/test_1300_reset_all_metadata.py
A test/shed_functional/functional/test_1400_review_migration_stages.py
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A test/shed_functional/test_data/column_maker/column_maker.tar
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R test/tool_shed/__init__.py
R test/tool_shed/base/__init__.py
R test/tool_shed/base/common.py
R test/tool_shed/base/test_db_util.py
R test/tool_shed/base/twilltestcase.py
R test/tool_shed/functional/__init__.py
R test/tool_shed/functional/test_0000_basic_repository_features.py
R test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py
R test/tool_shed/functional/test_0020_basic_repository_dependencies.py
R test/tool_shed/functional/test_0030_repository_dependency_revisions.py
R test/tool_shed/functional/test_0040_repository_circular_dependencies.py
R test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py
R test/tool_shed/functional/test_0060_workflows.py
R test/tool_shed/functional/test_0070_invalid_tool.py
R test/tool_shed/functional/test_0080_advanced_circular_dependencies.py
R test/tool_shed/functional/test_0090_tool_search.py
R test/tool_shed/functional/test_0100_complex_repository_dependencies.py
R test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py
R test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py
R test/tool_shed/functional/test_0130_datatype_converters.py
R test/tool_shed/functional/test_0140_tool_help_images.py
R test/tool_shed/functional/test_0150_prior_installation_required.py
R test/tool_shed/functional/test_0160_circular_prior_installation_required.py
R test/tool_shed/functional/test_0170_complex_prior_installation_required.py
R test/tool_shed/functional/test_0300_reset_all_metadata.py
R test/tool_shed/functional/test_0310_hg_push_from_api.py
R test/tool_shed/functional/test_0400_repository_component_reviews.py
R test/tool_shed/functional/test_0410_repository_component_review_access_control.py
R test/tool_shed/functional/test_0420_citable_urls_for_repositories.py
R test/tool_shed/functional/test_0430_browse_utilities.py
R test/tool_shed/functional/test_0440_deleting_dependency_definitions.py
R test/tool_shed/functional/test_0450_skip_tool_tests.py
R test/tool_shed/functional/test_0460_upload_to_repository.py
R test/tool_shed/functional/test_0470_tool_dependency_repository_type.py
R test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py
R test/tool_shed/functional/test_0490_export_import_repositories.py
R test/tool_shed/functional/test_0500_export_repository_simple_dependency.py
R test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py
R test/tool_shed/functional/test_0520_import_export_circular_dependencies.py
R test/tool_shed/functional/test_0530_repository_admin_feature.py
R test/tool_shed/functional/test_0540_get_all_metadata_from_api.py
R test/tool_shed/functional/test_1000_install_basic_repository.py
R test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py
R test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py
R test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py
R test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py
R test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py
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M test/unit/jobs/test_command_factory.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/test_HistoryContentsManager.py
A test/unit/shed_unit/__init__.py
A test/unit/shed_unit/test_fabric_util.py
A test/unit/shed_unit/test_td_common_util.py
A test/unit/shed_unit/test_tool_panel_manager.py
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M test/unit/tools/test_select_parameters.py
A tool-data/bam_iobio.loc.sample
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M tools/data_source/biomart.xml
M tools/data_source/upload.py
M tools/filters/trimmer.xml
M tools/stats/grouping.py
M tools/stats/grouping.xml
Log Message:
-----------
Merge branch 'dev' into feature/k8s_job_runner
# Conflicts:
# .gitignore
Commit: 3347713198940111c553676e3982bb96338707b5
https://github.com/galaxyproject/galaxy/commit/3347713198940111c553676e3982…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-05-04 (Wed, 04 May 2016)
Changed paths:
M config/job_conf.xml.sample_advanced
Log Message:
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Adds job_conf documentation for Kubernetes runner on the job_conf.xml.sample_advanced file.
Commit: 951a9319f6c54e4a279868e60e6065b4924b7091
https://github.com/galaxyproject/galaxy/commit/951a9319f6c54e4a279868e60e60…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-05-05 (Thu, 05 May 2016)
Changed paths:
M config/job_conf.xml.sample_advanced
Log Message:
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Describes scenario with <interpreter> <script> inside assumed working directories in containers.
Commit: 401ded6b7e4e5f21bff95d58d8188699dc390ee2
https://github.com/galaxyproject/galaxy/commit/401ded6b7e4e5f21bff95d58d818…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-05-05 (Thu, 05 May 2016)
Changed paths:
R config/job_conf_k8s.xml
Log Message:
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Removes job_conf_k8s.xml file
Commit: b2cf8b5a9f7ca330e2c2b10051e0d19416534be6
https://github.com/galaxyproject/galaxy/commit/b2cf8b5a9f7ca330e2c2b10051e0…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-05-05 (Thu, 05 May 2016)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
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Adds temporary dependency on my version of pykube, until changes on pykube are pulled and a new release is available.
Commit: 33109d192b870e89769792ceeafbae3563c14f70
https://github.com/galaxyproject/galaxy/commit/33109d192b870e89769792ceeafb…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-05-05 (Thu, 05 May 2016)
Changed paths:
M config/job_conf.xml.sample_advanced
Log Message:
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Fixes typo on comment of runner documentation.
Commit: 8cb13de22fa0876f53471c433e987e44c3b53e8b
https://github.com/galaxyproject/galaxy/commit/8cb13de22fa0876f53471c433e98…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-05-05 (Thu, 05 May 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
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Fixes other errors spotted by travis.
Commit: b46b4915bbd93fd75a025c745a7ac2047fe7c507
https://github.com/galaxyproject/galaxy/commit/b46b4915bbd93fd75a025c745a7a…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-05-06 (Fri, 06 May 2016)
Changed paths:
M config/job_conf.xml.sample_advanced
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Small typos/issues fixed for travis.
Commit: 0016c51cfe146361401beb5922665d1e356894d4
https://github.com/galaxyproject/galaxy/commit/0016c51cfe146361401beb592266…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-05-13 (Fri, 13 May 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Adheres to pykube new logs method instead of previous get_logs
Commit: c6da8ebe8bff3ac0e985bf91684f236d3733ba07
https://github.com/galaxyproject/galaxy/commit/c6da8ebe8bff3ac0e985bf91684f…
Author: Pablo Moreno <pcm32(a)users.noreply.github.com>
Date: 2016-05-20 (Fri, 20 May 2016)
Changed paths:
M CONTRIBUTORS.md
M Makefile
M README.rst
M client/bower.json
M client/galaxy/scripts/libs/backbone.js
M client/galaxy/scripts/libs/bootstrap-tour.js
M client/galaxy/scripts/libs/d3.js
M client/galaxy/scripts/libs/jquery/jquery.js
M client/galaxy/scripts/libs/jquery/jquery.migrate.js
M client/galaxy/scripts/libs/raven.js
M client/galaxy/scripts/libs/require.js
M client/galaxy/scripts/libs/tracekit.js
M client/galaxy/scripts/libs/underscore.js
M client/galaxy/scripts/mvc/collection/collection-li.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/dataset/dataset-model.js
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view-annotated.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.js
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M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form.js
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M client/galaxy/scripts/mvc/ui/popup-menu.js
M client/galaxy/scripts/mvc/ui/ui-drilldown.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
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M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/ui/ui-select.js
M client/galaxy/scripts/ui/hoverhighlight.js
M client/galaxy/scripts/ui/loading-indicator.js
M client/galaxy/scripts/ui/mode-button.js
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M config/plugins/visualizations/charts/static/views/group.js
R config/plugins/visualizations/graphview/config/graphview.xml
R config/plugins/visualizations/graphview/static/graphview.css
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M contrib/nagios/check_galaxy.py
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M doc/source/releases/16.01.rst
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M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/ngsindex.py
M lib/galaxy/datatypes/registry.py
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M lib/galaxy/jobs/transfer_manager.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/folders.py
M lib/galaxy/managers/hdas.py
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M lib/galaxy/managers/libraries.py
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M lib/galaxy/managers/users.py
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M lib/galaxy/model/migrate/versions/0080_quota_tables.py
M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0085_add_task_info.py
M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
M lib/galaxy/model/migrate/versions/0095_hda_subsets.py
M lib/galaxy/model/migrate/versions/0096_openid_provider.py
M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
M lib/galaxy/model/tool_shed_install/mapping.py
M lib/galaxy/openid/providers.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/commands.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/errors.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
M lib/galaxy/tools/lint.py
M lib/galaxy/tools/linters/general.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/sanitize.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/tools/test.py
M lib/galaxy/tools/util/maf_utilities.py
R lib/galaxy/util/backports/importlib/__init__.py
M lib/galaxy/util/directory_hash.py
M lib/galaxy/util/inflection.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/visualization/plugins/resource_parser.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/web/proxy/js/package.json
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/group_roles.py
M lib/galaxy/webapps/galaxy/api/group_users.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/api/quotas.py
M lib/galaxy/webapps/galaxy/api/remote_files.py
M lib/galaxy/webapps/galaxy/api/search.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
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M lib/galaxy/webapps/galaxy/api/workflows.py
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M lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py
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M lib/galaxy/webapps/tool_shed/model/migrate/versions/0006_add_email_alerts_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0009_add_malicious_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0011_add_tool_versions_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0012_add_downloadable_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0014_add_deprecated_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py
M lib/galaxy/webapps/tool_shed/util/hgweb_config.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy_ext/metadata/set_metadata.py
M lib/galaxy_utils/sequence/fastq.py
M lib/galaxy_utils/sequence/vcf.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/galaxy_install/dependency_display.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/installed_repository_manager.py
M lib/tool_shed/galaxy_install/migrate/common.py
M lib/tool_shed/galaxy_install/repair_repository_manager.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M lib/tool_shed/galaxy_install/utility_containers/__init__.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/repository_registry.py
M lib/tool_shed/tool_shed_registry.py
M lib/tool_shed/tools/data_table_manager.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/util/basic_util.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_dependency_util.py
M lib/tool_shed/util/tool_util.py
M lib/tool_shed/util/xml_util.py
M lib/tool_shed/utility_containers/__init__.py
M lib/tool_shed/utility_containers/utility_container_manager.py
M scripts/api/data_manager_example_execute.py
A scripts/api/filter_failed_datasets_from_collection.py
M scripts/api/search.py
M scripts/api/upload_to_history.py
M scripts/bootstrap_history.py
M scripts/check_galaxy.py
M scripts/cleanup_datasets/cleanup_datasets.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/cleanup_datasets/populate_uuid.py
M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py
M scripts/cleanup_datasets/rename_purged_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
M scripts/cleanup_datasets/update_metadata.py
M scripts/common_startup.sh
M scripts/data_libraries/build_lucene_index.py
M scripts/data_libraries/build_whoosh_index.py
M scripts/drmaa_external_killer.py
M scripts/drmaa_external_runner.py
M scripts/extract_dataset_part.py
M scripts/microbes/BeautifulSoup.py
M scripts/microbes/harvest_bacteria.py
M scripts/others/incorrect_gops_jobs.py
M scripts/others/incorrect_gops_join_jobs.py
M scripts/runtime_stats.py
M scripts/tool_shed/api/common.py
M scripts/tool_shed/api/create_categories.py
M scripts/tool_shed/api/create_users.py
M scripts/tool_shed/api/import_capsule.py
M scripts/tool_shed/api/reset_metadata_on_repositories.py
M scripts/tool_shed/build_ts_whoosh_index.py
M scripts/tool_shed/check_download_urls.py
M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py
M scripts/tool_shed/deprecate_repositories_without_metadata.py
M scripts/tools/maf/check_loc_file.py
M scripts/transfer.py
M static/maps/libs/backbone.js.map
M static/maps/libs/bootstrap-tour.js.map
M static/maps/libs/d3.js.map
M static/maps/libs/jquery/jquery.js.map
M static/maps/libs/jquery/jquery.migrate.js.map
M static/maps/libs/raven.js.map
M static/maps/libs/require.js.map
M static/maps/libs/tracekit.js.map
M static/maps/libs/underscore.js.map
M static/maps/mvc/collection/collection-li.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/maps/mvc/dataset/dataset-model.js.map
M static/maps/mvc/form/form-data.js.map
M static/maps/mvc/form/form-input.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/history-model.js.map
M static/maps/mvc/history/history-view-annotated.js.map
M static/maps/mvc/history/history-view-edit-current.js.map
M static/maps/mvc/history/history-view.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/ui/popup-menu.js.map
M static/maps/mvc/ui/ui-drilldown.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/ui/ui-options.js.map
M static/maps/mvc/ui/ui-portlet.js.map
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/maps/mvc/ui/ui-select.js.map
M static/maps/ui/hoverhighlight.js.map
M static/maps/ui/loading-indicator.js.map
M static/maps/ui/mode-button.js.map
M static/maps/ui/pagination.js.map
M static/maps/ui/peek-column-selector.js.map
M static/maps/utils/metrics-logger.js.map
M static/maps/utils/utils.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/libs/backbone.js
M static/scripts/libs/bootstrap-tour.js
M static/scripts/libs/d3.js
M static/scripts/libs/jquery/jquery.js
M static/scripts/libs/jquery/jquery.migrate.js
M static/scripts/libs/raven.js
M static/scripts/libs/require.js
M static/scripts/libs/tracekit.js
M static/scripts/libs/underscore.js
M static/scripts/mvc/collection/collection-li.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/dataset/dataset-model.js
M static/scripts/mvc/form/form-data.js
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/history/history-view-annotated.js
M static/scripts/mvc/history/history-view-edit-current.js
M static/scripts/mvc/history/history-view.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/ui/popup-menu.js
M static/scripts/mvc/ui/ui-drilldown.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-options.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/ui/ui-select.js
M static/scripts/ui/hoverhighlight.js
M static/scripts/ui/loading-indicator.js
M static/scripts/ui/mode-button.js
M static/scripts/ui/pagination.js
M static/scripts/ui/peek-column-selector.js
M static/scripts/utils/metrics-logger.js
M static/scripts/utils/utils.js
M static/style/blue/base.css
M templates/show_params.mako
M templates/webapps/galaxy/data_manager/view_job.mako
A test-data/composite_output_expected_log
M test/api/test_datasets.py
M test/api/workflows_format_2/converter.py
M test/api/workflows_format_2/interface.py
M test/api/workflows_format_2/main.py
M test/base/asserts/__init__.py
M test/base/asserts/xml.py
M test/base/driver_util.py
M test/base/twilltestcase.py
M test/casperjs/casperjs_runner.py
M test/casperjs/server_env.py
M test/functional/test_data_managers.py
M test/functional/test_toolbox.py
M test/functional/tools/composite_output.xml
M test/qunit/test-app.js
M test/qunit/test-common.js
M test/qunit/test-data/fakeserver.js
R test/qunit/test-libs/qunit-1.14.0.css
R test/qunit/test-libs/qunit-1.14.0.js
A test/qunit/test-libs/qunit-1.23.1.css
A test/qunit/test-libs/qunit-1.23.1.js
A test/qunit/test-libs/sinon-1.17.3.js
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M test/qunit/tests/modal_tests.js
M test/qunit/tests/page_tests.js
M test/qunit/tests/ui_tests.js
M test/qunit/tests/workflow_editor_tests.js
M test/shed_functional/base/twilltestcase.py
M test/shed_functional/functional/test_0060_workflows.py
M test/shed_functional/functional/test_0100_complex_repository_dependencies.py
M test/shed_functional/functional/test_0170_complex_prior_installation_required.py
M test/shed_functional/functional/test_0300_reset_all_metadata.py
M test/shed_functional/functional/test_0310_hg_api_features.py
M test/shed_functional/functional/test_1060_install_repository_with_workflow.py
M test/shed_functional/functional/test_1120_install_repository_with_complex_dependencies.py
M test/shed_functional/functional/test_1190_complex_prior_installation_required.py
M test/shed_functional/functional/test_1300_reset_all_metadata.py
M test/shed_functional/functional/test_1420_tool_dependency_environment_inheritance.py
M test/shed_functional/functional_tests.py
M test/unit/managers/test_CollectionManager.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_select_parameters.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/base/test_HookPluginManager.py
M test/unit/web/base/test_PageServingPluginManager.py
M test/unit/web/base/test_PluginManager.py
M test/unit/web/framework/test_webapp.py
M tools/data_source/data_source.py
M tools/data_source/fetch.py
M tools/data_source/hbvar_filter.py
M tools/data_source/microbial_import.py
M tools/data_source/upload.py
M tools/evolution/add_scores.py
M tools/extract/extract_genomic_dna.py
M tools/extract/liftOver_wrapper.py
M tools/filters/axt_to_lav.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/joinWrapper.py
M tools/filters/lav_to_bed.py
M tools/filters/mergeCols.py
M tools/filters/sff_extract.py
M tools/filters/sorter.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_fasta_concat.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/metag_tools/blat_wrapper.py
M tools/metag_tools/shrimp_color_wrapper.py
M tools/metag_tools/shrimp_wrapper.py
M tools/next_gen_conversion/fastq_conversions.py
M tools/next_gen_conversion/fastq_gen_conv.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velveth_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
Log Message:
-----------
Merge pull request #2 from galaxyproject/dev
Stays up-to-date with galaxy dev branch
Commit: a54a2e068d1bc1c9fc1bc56b9fd3194925f4d213
https://github.com/galaxyproject/galaxy/commit/a54a2e068d1bc1c9fc1bc56b9fd3…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-05-20 (Fri, 20 May 2016)
Changed paths:
M CONTRIBUTORS.md
M Makefile
M README.rst
M client/bower.json
M client/galaxy/scripts/libs/backbone.js
M client/galaxy/scripts/libs/bootstrap-tour.js
M client/galaxy/scripts/libs/d3.js
M client/galaxy/scripts/libs/jquery/jquery.js
M client/galaxy/scripts/libs/jquery/jquery.migrate.js
M client/galaxy/scripts/libs/raven.js
M client/galaxy/scripts/libs/require.js
M client/galaxy/scripts/libs/tracekit.js
M client/galaxy/scripts/libs/underscore.js
M client/galaxy/scripts/mvc/collection/collection-li.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/dataset/dataset-model.js
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view-annotated.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form.js
R client/galaxy/scripts/mvc/tool/tool-template.js
M client/galaxy/scripts/mvc/ui/popup-menu.js
M client/galaxy/scripts/mvc/ui/ui-drilldown.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-options.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/ui/ui-select.js
M client/galaxy/scripts/ui/hoverhighlight.js
M client/galaxy/scripts/ui/loading-indicator.js
M client/galaxy/scripts/ui/mode-button.js
M client/galaxy/scripts/ui/pagination.js
M client/galaxy/scripts/ui/peek-column-selector.js
M client/galaxy/scripts/utils/metrics-logger.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/ui.less
M client/grunt-tasks/scripts.js
M client/grunt-tasks/style.js
M config/job_conf.xml.sample_advanced
M config/plugins/visualizations/charts/static/views/group.js
R config/plugins/visualizations/graphview/config/graphview.xml
R config/plugins/visualizations/graphview/static/graphview.css
R config/plugins/visualizations/graphview/static/graphview.js
R config/plugins/visualizations/graphview/static/jquery.rdfquery.core.js
R config/plugins/visualizations/graphview/templates/graphview.mako
M contrib/nagios/check_galaxy.py
M cron/build_chrom_db.py
M doc/source/releases/16.01.rst
A doc/source/releases/16.04.rst
M doc/source/releases/16.04_announce.rst
A doc/source/releases/16.07_announce.rst
M doc/source/releases/index.rst
M lib/galaxy/config.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
M lib/galaxy/datatypes/converters/gff_to_bed_converter.py
M lib/galaxy/datatypes/converters/lped_to_fped_converter.py
M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/ngsindex.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/deferred/__init__.py
M lib/galaxy/jobs/deferred/data_transfer.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/jobs/splitters/multi.py
M lib/galaxy/jobs/transfer_manager.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/folders.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/libraries.py
M lib/galaxy/managers/roles.py
M lib/galaxy/managers/sharable.py
M lib/galaxy/managers/users.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/migrate/versions/0001_initial_tables.py
M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py
M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0009_request_table.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0014_pages.py
M lib/galaxy/model/migrate/versions/0015_tagging.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0019_request_library_folder.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0021_user_prefs.py
M lib/galaxy/model/migrate/versions/0025_user_info.py
M lib/galaxy/model/migrate/versions/0027_request_events.py
M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
M lib/galaxy/model/migrate/versions/0029_user_actions.py
M lib/galaxy/model/migrate/versions/0030_history_slug_column.py
M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0037_samples_library.py
M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0040_page_annotations.py
M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
M lib/galaxy/model/migrate/versions/0049_api_keys_table.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0053_item_ratings.py
M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
M lib/galaxy/model/migrate/versions/0057_request_notify.py
M lib/galaxy/model/migrate/versions/0058_history_import_export.py
M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
M lib/galaxy/model/migrate/versions/0060_history_archive_import.py
M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
M lib/galaxy/model/migrate/versions/0063_sequencer_table.py
M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
M lib/galaxy/model/migrate/versions/0080_quota_tables.py
M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0085_add_task_info.py
M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
M lib/galaxy/model/migrate/versions/0095_hda_subsets.py
M lib/galaxy/model/migrate/versions/0096_openid_provider.py
M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
M lib/galaxy/model/tool_shed_install/mapping.py
M lib/galaxy/openid/providers.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/commands.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/errors.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
M lib/galaxy/tools/lint.py
M lib/galaxy/tools/linters/general.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/sanitize.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/tools/test.py
M lib/galaxy/tools/util/maf_utilities.py
R lib/galaxy/util/backports/importlib/__init__.py
M lib/galaxy/util/directory_hash.py
M lib/galaxy/util/inflection.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/visualization/plugins/resource_parser.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/web/proxy/js/package.json
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/group_roles.py
M lib/galaxy/webapps/galaxy/api/group_users.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/api/quotas.py
M lib/galaxy/webapps/galaxy/api/remote_files.py
M lib/galaxy/webapps/galaxy/api/search.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/visualizations.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/async.py
M lib/galaxy/webapps/galaxy/controllers/biostar.py
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/requests_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/tool_runner.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0002_add_tool_suite_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0006_add_email_alerts_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0009_add_malicious_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0011_add_tool_versions_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0012_add_downloadable_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0014_add_deprecated_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py
M lib/galaxy/webapps/tool_shed/util/hgweb_config.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy_ext/metadata/set_metadata.py
M lib/galaxy_utils/sequence/fastq.py
M lib/galaxy_utils/sequence/vcf.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/galaxy_install/dependency_display.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/installed_repository_manager.py
M lib/tool_shed/galaxy_install/migrate/common.py
M lib/tool_shed/galaxy_install/repair_repository_manager.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M lib/tool_shed/galaxy_install/utility_containers/__init__.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/repository_registry.py
M lib/tool_shed/tool_shed_registry.py
M lib/tool_shed/tools/data_table_manager.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/util/basic_util.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_dependency_util.py
M lib/tool_shed/util/tool_util.py
M lib/tool_shed/util/xml_util.py
M lib/tool_shed/utility_containers/__init__.py
M lib/tool_shed/utility_containers/utility_container_manager.py
M scripts/api/data_manager_example_execute.py
A scripts/api/filter_failed_datasets_from_collection.py
M scripts/api/search.py
M scripts/api/upload_to_history.py
M scripts/bootstrap_history.py
M scripts/check_galaxy.py
M scripts/cleanup_datasets/cleanup_datasets.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/cleanup_datasets/populate_uuid.py
M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py
M scripts/cleanup_datasets/rename_purged_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
M scripts/cleanup_datasets/update_metadata.py
M scripts/common_startup.sh
M scripts/data_libraries/build_lucene_index.py
M scripts/data_libraries/build_whoosh_index.py
M scripts/drmaa_external_killer.py
M scripts/drmaa_external_runner.py
M scripts/extract_dataset_part.py
M scripts/microbes/BeautifulSoup.py
M scripts/microbes/harvest_bacteria.py
M scripts/others/incorrect_gops_jobs.py
M scripts/others/incorrect_gops_join_jobs.py
M scripts/runtime_stats.py
M scripts/tool_shed/api/common.py
M scripts/tool_shed/api/create_categories.py
M scripts/tool_shed/api/create_users.py
M scripts/tool_shed/api/import_capsule.py
M scripts/tool_shed/api/reset_metadata_on_repositories.py
M scripts/tool_shed/build_ts_whoosh_index.py
M scripts/tool_shed/check_download_urls.py
M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py
M scripts/tool_shed/deprecate_repositories_without_metadata.py
M scripts/tools/maf/check_loc_file.py
M scripts/transfer.py
M static/maps/libs/backbone.js.map
M static/maps/libs/bootstrap-tour.js.map
M static/maps/libs/d3.js.map
M static/maps/libs/jquery/jquery.js.map
M static/maps/libs/jquery/jquery.migrate.js.map
M static/maps/libs/raven.js.map
M static/maps/libs/require.js.map
M static/maps/libs/tracekit.js.map
M static/maps/libs/underscore.js.map
M static/maps/mvc/collection/collection-li.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/maps/mvc/dataset/dataset-model.js.map
M static/maps/mvc/form/form-data.js.map
M static/maps/mvc/form/form-input.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/history-model.js.map
M static/maps/mvc/history/history-view-annotated.js.map
M static/maps/mvc/history/history-view-edit-current.js.map
M static/maps/mvc/history/history-view.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/ui/popup-menu.js.map
M static/maps/mvc/ui/ui-drilldown.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/ui/ui-options.js.map
M static/maps/mvc/ui/ui-portlet.js.map
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/maps/mvc/ui/ui-select.js.map
M static/maps/ui/hoverhighlight.js.map
M static/maps/ui/loading-indicator.js.map
M static/maps/ui/mode-button.js.map
M static/maps/ui/pagination.js.map
M static/maps/ui/peek-column-selector.js.map
M static/maps/utils/metrics-logger.js.map
M static/maps/utils/utils.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/libs/backbone.js
M static/scripts/libs/bootstrap-tour.js
M static/scripts/libs/d3.js
M static/scripts/libs/jquery/jquery.js
M static/scripts/libs/jquery/jquery.migrate.js
M static/scripts/libs/raven.js
M static/scripts/libs/require.js
M static/scripts/libs/tracekit.js
M static/scripts/libs/underscore.js
M static/scripts/mvc/collection/collection-li.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/dataset/dataset-model.js
M static/scripts/mvc/form/form-data.js
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/history/history-view-annotated.js
M static/scripts/mvc/history/history-view-edit-current.js
M static/scripts/mvc/history/history-view.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/ui/popup-menu.js
M static/scripts/mvc/ui/ui-drilldown.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-options.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/ui/ui-select.js
M static/scripts/ui/hoverhighlight.js
M static/scripts/ui/loading-indicator.js
M static/scripts/ui/mode-button.js
M static/scripts/ui/pagination.js
M static/scripts/ui/peek-column-selector.js
M static/scripts/utils/metrics-logger.js
M static/scripts/utils/utils.js
M static/style/blue/base.css
M templates/show_params.mako
M templates/webapps/galaxy/data_manager/view_job.mako
A test-data/composite_output_expected_log
M test/api/test_datasets.py
M test/api/workflows_format_2/converter.py
M test/api/workflows_format_2/interface.py
M test/api/workflows_format_2/main.py
M test/base/asserts/__init__.py
M test/base/asserts/xml.py
M test/base/driver_util.py
M test/base/twilltestcase.py
M test/casperjs/casperjs_runner.py
M test/casperjs/server_env.py
M test/functional/test_data_managers.py
M test/functional/test_toolbox.py
M test/functional/tools/composite_output.xml
M test/qunit/test-app.js
M test/qunit/test-common.js
M test/qunit/test-data/fakeserver.js
R test/qunit/test-libs/qunit-1.14.0.css
R test/qunit/test-libs/qunit-1.14.0.js
A test/qunit/test-libs/qunit-1.23.1.css
A test/qunit/test-libs/qunit-1.23.1.js
A test/qunit/test-libs/sinon-1.17.3.js
R test/qunit/test-libs/sinon-1.9.1.js
M test/qunit/tests/form_tests.js
M test/qunit/tests/list-of-pairs-collection-creator.js
M test/qunit/tests/metrics-logger.js
M test/qunit/tests/modal_tests.js
M test/qunit/tests/page_tests.js
M test/qunit/tests/ui_tests.js
M test/qunit/tests/workflow_editor_tests.js
M test/shed_functional/base/twilltestcase.py
M test/shed_functional/functional/test_0060_workflows.py
M test/shed_functional/functional/test_0100_complex_repository_dependencies.py
M test/shed_functional/functional/test_0170_complex_prior_installation_required.py
M test/shed_functional/functional/test_0300_reset_all_metadata.py
M test/shed_functional/functional/test_0310_hg_api_features.py
M test/shed_functional/functional/test_1060_install_repository_with_workflow.py
M test/shed_functional/functional/test_1120_install_repository_with_complex_dependencies.py
M test/shed_functional/functional/test_1190_complex_prior_installation_required.py
M test/shed_functional/functional/test_1300_reset_all_metadata.py
M test/shed_functional/functional/test_1420_tool_dependency_environment_inheritance.py
M test/shed_functional/functional_tests.py
M test/unit/managers/test_CollectionManager.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_select_parameters.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/base/test_HookPluginManager.py
M test/unit/web/base/test_PageServingPluginManager.py
M test/unit/web/base/test_PluginManager.py
M test/unit/web/framework/test_webapp.py
M tools/data_source/data_source.py
M tools/data_source/fetch.py
M tools/data_source/hbvar_filter.py
M tools/data_source/microbial_import.py
M tools/data_source/upload.py
M tools/evolution/add_scores.py
M tools/extract/extract_genomic_dna.py
M tools/extract/liftOver_wrapper.py
M tools/filters/axt_to_lav.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/joinWrapper.py
M tools/filters/lav_to_bed.py
M tools/filters/mergeCols.py
M tools/filters/sff_extract.py
M tools/filters/sorter.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_fasta_concat.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/metag_tools/blat_wrapper.py
M tools/metag_tools/shrimp_color_wrapper.py
M tools/metag_tools/shrimp_wrapper.py
M tools/next_gen_conversion/fastq_conversions.py
M tools/next_gen_conversion/fastq_gen_conv.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velveth_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
Log Message:
-----------
Merge branch 'dev' into feature/k8s_job_runner
Commit: 46fb489cb4165fbeb198e2305cf27d4faa35367e
https://github.com/galaxyproject/galaxy/commit/46fb489cb4165fbeb198e2305cf2…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-05-20 (Fri, 20 May 2016)
Changed paths:
M lib/galaxy/tools/deps/containers.py
Log Message:
-----------
Adds the ability to build container ids for pieces for the centralised galaxy containers class and takes into account the default and override modes, suggested by jmchilton.
Commit: 8e176d4318ee934cbfce924a5f65dbefc196b4a0
https://github.com/galaxyproject/galaxy/commit/8e176d4318ee934cbfce924a5f65…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-05-20 (Fri, 20 May 2016)
Changed paths:
M config/job_conf.xml.sample_advanced
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Moves the kubernetes runner to use the centralised galaxy way of picking containers, allowing destinations to override a tool, use a tool, or have a default container if the tool doesn't provide one.
Commit: f06d8a01b01093033500ad5e69771302dab31b09
https://github.com/galaxyproject/galaxy/commit/f06d8a01b01093033500ad5e6977…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-05-20 (Fri, 20 May 2016)
Changed paths:
M config/job_conf.xml.sample_advanced
Log Message:
-----------
Additional new required parameter for destinations (that will be used with the kubernetes runner) to play nicely with existing galaxy handling of containers.
Commit: 84a9ae36e3061d8911fcdfea63773ff31bbc57d3
https://github.com/galaxyproject/galaxy/commit/84a9ae36e3061d8911fcdfea6377…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-05-20 (Fri, 20 May 2016)
Changed paths:
M config/job_conf.xml.sample_advanced
Log Message:
-----------
Removes quotes to docker_enabled paramter value in documentation of destination associated with Kubernetes.
Commit: c484ab37eefa6906be549bbe559fe17754d0b7ec
https://github.com/galaxyproject/galaxy/commit/c484ab37eefa6906be549bbe559f…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-05-20 (Fri, 20 May 2016)
Changed paths:
M lib/galaxy/tools/deps/containers.py
Log Message:
-----------
Adds missing parenthesis for string formatting.
Commit: 4a908141e3a954582676d5e924fb3c4b41032356
https://github.com/galaxyproject/galaxy/commit/4a908141e3a954582676d5e924fb…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-05-20 (Fri, 20 May 2016)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Fixes use of container object returned by underlying galaxy methods.
Commit: c7929f882e07a9d9d42e0250dfee2bb487f7ee94
https://github.com/galaxyproject/galaxy/commit/c7929f882e07a9d9d42e0250dfee…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-05-20 (Fri, 20 May 2016)
Changed paths:
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Introduces additional parameter to avoid having the command-line modified for kubernetes.
Commit: c0b4119c5efff89c39245eda280d0a155d797423
https://github.com/galaxyproject/galaxy/commit/c0b4119c5efff89c39245eda280d…
Author: Pablo Moreno <pcm32(a)users.noreply.github.com>
Date: 2016-06-01 (Wed, 01 Jun 2016)
Changed paths:
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/ui/ui-frames.js
M client/galaxy/style/less/frame.less
M doc/source/dev/faq.rst
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
A lib/galaxy/datatypes/checkers.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/qualityscore.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/datatypes/triples.py
M lib/galaxy/datatypes/xml.py
M lib/galaxy/external_services/actions.py
M lib/galaxy/external_services/parameters.py
M lib/galaxy/external_services/service.py
M lib/galaxy/forms/forms.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/metrics/collectl/processes.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/managers/citations.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/tags.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
M lib/galaxy/model/migrate/versions/0046_post_job_actions.py
M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py
M lib/galaxy/model/migrate/versions/0061_tasks.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/commands.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/docker_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/toolbox/watcher.py
A lib/galaxy/tools/verify/__init__.py
A lib/galaxy/tools/verify/asserts/__init__.py
A lib/galaxy/tools/verify/asserts/tabular.py
A lib/galaxy/tools/verify/asserts/text.py
A lib/galaxy/tools/verify/asserts/xml.py
A lib/galaxy/tools/verify/test_data.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/checkers.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/plugins/config_parser.py
M lib/galaxy/visualization/plugins/registry.py
M lib/galaxy/visualization/plugins/resource_parser.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/base/pluginframework.py
M lib/galaxy/webapps/galaxy/api/datatypes.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/external_services.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/tool_shed/security/__init__.py
M lib/galaxy/workflow/extract.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/repository_types/metadata.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/tool_dependency_util.py
M scripts/bootstrap_history.py
M scripts/common_startup.sh
M static/maps/layout/scratchbook.js.map
M static/maps/mvc/history/history-model.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/ui/ui-frames.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/scratchbook.js
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/ui/ui-frames.js
M static/style/blue/base.css
M templates/show_params.mako
M templates/webapps/galaxy/workflow/editor_tool_form.mako
M templates/webapps/galaxy/workflow/run.mako
M test/api/test_tools.py
M test/api/test_workflows.py
R test/base/asserts/__init__.py
R test/base/asserts/tabular.py
R test/base/asserts/text.py
R test/base/asserts/xml.py
R test/base/test_data.py
M test/base/twilltestcase.py
M test/functional/test_toolbox.py
A test/functional/tools/checksum.xml
A test/functional/tools/composite_output_tests.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/tools/simple_constructs.yml
M test/shed_functional/base/twilltestcase.py
M test/unit/managers/test_HistoryManager.py
M test/unit/tools/test_select_parameters.py
M tools/filters/axt_to_concat_fasta.xml
M tools/filters/axt_to_fasta.xml
M tools/filters/axt_to_lav.py
M tools/filters/axt_to_lav.xml
M tools/filters/bed2gff.xml
M tools/filters/bed_to_bigbed.xml
M tools/filters/gff2bed.xml
M tools/filters/gtf2bedgraph.xml
M tools/stats/filtering.xml
M tools/stats/gsummary.xml
Log Message:
-----------
Merge pull request #3 from galaxyproject/dev
Updates to current galaxy dev
Commit: 64ade008ffa832d3537e915a91e1b50813900065
https://github.com/galaxyproject/galaxy/commit/64ade008ffa832d3537e915a91e1…
Author: Pablo Moreno <pablo.a.moreno(a)gmail.com>
Date: 2016-06-01 (Wed, 01 Jun 2016)
Changed paths:
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/ui/ui-frames.js
M client/galaxy/style/less/frame.less
M doc/source/dev/faq.rst
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
A lib/galaxy/datatypes/checkers.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/qualityscore.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/datatypes/triples.py
M lib/galaxy/datatypes/xml.py
M lib/galaxy/external_services/actions.py
M lib/galaxy/external_services/parameters.py
M lib/galaxy/external_services/service.py
M lib/galaxy/forms/forms.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/metrics/collectl/processes.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/managers/citations.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/tags.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
M lib/galaxy/model/migrate/versions/0046_post_job_actions.py
M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py
M lib/galaxy/model/migrate/versions/0061_tasks.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/commands.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/docker_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/toolbox/watcher.py
A lib/galaxy/tools/verify/__init__.py
A lib/galaxy/tools/verify/asserts/__init__.py
A lib/galaxy/tools/verify/asserts/tabular.py
A lib/galaxy/tools/verify/asserts/text.py
A lib/galaxy/tools/verify/asserts/xml.py
A lib/galaxy/tools/verify/test_data.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/checkers.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/plugins/config_parser.py
M lib/galaxy/visualization/plugins/registry.py
M lib/galaxy/visualization/plugins/resource_parser.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/base/pluginframework.py
M lib/galaxy/webapps/galaxy/api/datatypes.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/external_services.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/tool_shed/security/__init__.py
M lib/galaxy/workflow/extract.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/repository_types/metadata.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/tool_dependency_util.py
M scripts/bootstrap_history.py
M scripts/common_startup.sh
M static/maps/layout/scratchbook.js.map
M static/maps/mvc/history/history-model.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/ui/ui-frames.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/scratchbook.js
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/ui/ui-frames.js
M static/style/blue/base.css
M templates/show_params.mako
M templates/webapps/galaxy/workflow/editor_tool_form.mako
M templates/webapps/galaxy/workflow/run.mako
M test/api/test_tools.py
M test/api/test_workflows.py
R test/base/asserts/__init__.py
R test/base/asserts/tabular.py
R test/base/asserts/text.py
R test/base/asserts/xml.py
R test/base/test_data.py
M test/base/twilltestcase.py
M test/functional/test_toolbox.py
A test/functional/tools/checksum.xml
A test/functional/tools/composite_output_tests.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/tools/simple_constructs.yml
M test/shed_functional/base/twilltestcase.py
M test/unit/managers/test_HistoryManager.py
M test/unit/tools/test_select_parameters.py
M tools/filters/axt_to_concat_fasta.xml
M tools/filters/axt_to_fasta.xml
M tools/filters/axt_to_lav.py
M tools/filters/axt_to_lav.xml
M tools/filters/bed2gff.xml
M tools/filters/bed_to_bigbed.xml
M tools/filters/gff2bed.xml
M tools/filters/gtf2bedgraph.xml
M tools/stats/filtering.xml
M tools/stats/gsummary.xml
Log Message:
-----------
Merge branch 'dev' into feature/k8s_job_runner
Commit: a931b4b37dbdea5df238a8b7079d5dd64c8fb6aa
https://github.com/galaxyproject/galaxy/commit/a931b4b37dbdea5df238a8b7079d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-06-05 (Sun, 05 Jun 2016)
Changed paths:
M config/job_conf.xml.sample_advanced
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/runners/__init__.py
A lib/galaxy/jobs/runners/kubernetes.py
M lib/galaxy/tools/deps/containers.py
Log Message:
-----------
Merge pull request #2314 from phnmnl/feature/k8s_job_runner
Kubernetes job runner
Compare: https://github.com/galaxyproject/galaxy/compare/037d88f29b54...a931b4b37dbd
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: c78c2796d3ad40f61f817b4487e7710a0571f17b
https://github.com/galaxyproject/galaxy/commit/c78c2796d3ad40f61f817b4487e7…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-06-03 (Fri, 03 Jun 2016)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/style/less/library.less
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/style/blue/base.css
M static/style/blue/library.css
Log Message:
-----------
isolate the data libraries css to affect only the libraries app
Commit: 037d88f29b54eebfce95393678befca657142eb7
https://github.com/galaxyproject/galaxy/commit/037d88f29b54eebfce95393678be…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-06-03 (Fri, 03 Jun 2016)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/style/less/library.less
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/style/blue/base.css
M static/style/blue/library.css
Log Message:
-----------
Merge pull request #2444 from martenson/isolate-lib-css
isolate the data libraries css to affect only the libraries app
Compare: https://github.com/galaxyproject/galaxy/compare/789c3009369c...037d88f29b54
Branch: refs/heads/master
Home: https://github.com/galaxyproject/infrastructure-playbook
Commit: 9e8c599db611325a7edfd2ceb6d83256e0540274
https://github.com/galaxyproject/infrastructure-playbook/commit/9e8c599db61…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-06-03 (Fri, 03 Jun 2016)
Changed paths:
M ansible.cfg
M common_roles
A galaxyenv/group_vars/cvmfsstratum0servers.yml
M galaxyenv/group_vars/cvmfsstratum1servers.yml
M galaxyenv/inventory
A galaxyenv/secret_host_vars/cvmfs1-iu0.galaxyproject.org.yml
A galaxyenv/secret_host_vars/cvmfs1-psu0.galaxyproject.org.yml
A galaxyenv/secret_host_vars/cvmfs1-tacc0.galaxyproject.org.yml
M roles/cvmfs/defaults/main.yml
A roles/cvmfs/files/cvmfs_wipecache.c
A roles/cvmfs/files/cvmfs_wipecache.centos_6
M roles/cvmfs/tasks/client.yml
M roles/cvmfs/tasks/stratum0.yml
M roles/cvmfs/tasks/stratum1.yml
A roles/cvmfs/templates/01-manage-units.rules.j2
M taccenv/group_vars/galaxyservers.yml
Log Message:
-----------
Unprivileged CVMFS updating for Test/Main