galaxy-commits June 2016

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[galaxyproject/galaxy] cc336f: Make some files compatible with Python3
by GitHub 06 Jun '16

06 Jun '16

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

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[galaxyproject/galaxy] 1d7ce3: Fix usage of super() in the mothur datatypes.
by GitHub 05 Jun '16

05 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1d7ce30fbbae350ca3e75e384fce848f947d33b7 https://github.com/galaxyproject/galaxy/commit/1d7ce30fbbae350ca3e75e384fce… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-06-05 (Sun, 05 Jun 2016) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- Fix usage of super() in the mothur datatypes. Commit: 7b3e5369f8d66db6139edbf3f863efdf5e1c0d3b https://github.com/galaxyproject/galaxy/commit/7b3e5369f8d66db6139edbf3f863… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-05 (Sun, 05 Jun 2016) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- Merge pull request #2457 from bgruening/mothur_fix Fix usage of super() in the mothur datatypes. Compare: https://github.com/galaxyproject/galaxy/compare/a97cae3e8b6e...7b3e5369f8d6

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[galaxyproject/galaxy] 69879a: Merge _complete_terminal_job() from BaseJobRunner ...
by GitHub 05 Jun '16

05 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 69879af87e72e7d0ba679c7ff2785a8f1e75b3c2 https://github.com/galaxyproject/galaxy/commit/69879af87e72e7d0ba679c7ff278… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Merge _complete_terminal_job() from BaseJobRunner into DRMAAJobRunner Commit: ca12c37451b6541d62f958928dd55cea874b0c5d https://github.com/galaxyproject/galaxy/commit/ca12c37451b6541d62f958928dd5… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Clarify _complete_terminal_job() return value Commit: 301f7dbbda272da764f3796b02e35a6eab587df2 https://github.com/galaxyproject/galaxy/commit/301f7dbbda272da764f3796b02e3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- SLURM: when scontrol fails, try to get job state with sacct Commit: 63e28efed3f4e8afde91c609ce3744f4fde66457 https://github.com/galaxyproject/galaxy/commit/63e28efed3f4e8afde91c609ce37… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-02 (Thu, 02 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Log SLURM accounting storage error Commit: a97cae3e8b6e0969ed3dacb557863bc2c4cd3ad3 https://github.com/galaxyproject/galaxy/commit/a97cae3e8b6e0969ed3dacb55786… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-06-05 (Sun, 05 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2403 from nsoranzo/slurm SLURM: when scontrol fails, try to get job state with sacct Compare: https://github.com/galaxyproject/galaxy/compare/a931b4b37dbd...a97cae3e8b6e

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[galaxyproject/galaxy] afc8bd: Initial commit for collaboration on the k8s runner...
by GitHub 05 Jun '16

05 Jun '16

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 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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: ----------- 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: ----------- 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: ----------- 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: ----------- 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: ----------- 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: ----------- 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. 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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: 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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. 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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

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[galaxyproject/galaxy] c78c27: isolate the data libraries css to affect only the ...
by GitHub 03 Jun '16

03 Jun '16

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

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[galaxyproject/usegalaxy-playbook] ade523: Update Galaxy in CVMFS
by GitHub 03 Jun '16

03 Jun '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ade5239f76c58f21d9a3e8f6512ce6dd6e2b781c https://github.com/galaxyproject/usegalaxy-playbook/commit/ade5239f76c58f21… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-03 (Fri, 03 Jun 2016) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M galaxy.yml M galaxy_static.yml A stage/galaxy_version.yml M stage/group_vars/all.yml M stage/group_vars/galaxyservers.yml M stage/inventory M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Update Galaxy in CVMFS

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[galaxyproject/infrastructure-playbook] 6b30c2: Fix group membership on stratum 1s
by GitHub 03 Jun '16

03 Jun '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 6b30c2af50ad8a7e1d5fcd7c2906661ea9aaf910 https://github.com/galaxyproject/infrastructure-playbook/commit/6b30c2af50a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-03 (Fri, 03 Jun 2016) Changed paths: M common_roles M galaxyenv/group_vars/cvmfsstratum1servers.yml M galaxyenv/secret_host_vars/cvmfs0-tacc0.galaxyproject.org.yml Log Message: ----------- Fix group membership on stratum 1s

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[galaxyproject/galaxy] 2e6317: Add support to pdbqt datatype
by GitHub 03 Jun '16

03 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2e6317e777608a831d1ad0ae500ab8416f3d5a87 https://github.com/galaxyproject/galaxy/commit/2e6317e777608a831d1ad0ae500a… Author: leobiscassi <leo.biscassi(a)gmail.com> Date: 2016-06-03 (Fri, 03 Jun 2016) Changed paths: M lib/galaxy/datatypes/molecules.py A lib/galaxy/datatypes/test/NuBBE_1_obabel_3D.pdbqt Log Message: ----------- Add support to pdbqt datatype Commit: c21317551331964a9cf3e1fa1cf47940b334fdf9 https://github.com/galaxyproject/galaxy/commit/c21317551331964a9cf3e1fa1cf4… Author: leobiscassi <leo.biscassi(a)gmail.com> Date: 2016-06-03 (Fri, 03 Jun 2016) Changed paths: M lib/galaxy/datatypes/molecules.py Log Message: ----------- Adjust set_peek method of the pdbqt class Commit: e428a801db1ab97763a0482c0c84b938a931402b https://github.com/galaxyproject/galaxy/commit/e428a801db1ab97763a0482c0c84… Author: leobiscassi <leo.biscassi(a)gmail.com> Date: 2016-06-03 (Fri, 03 Jun 2016) Changed paths: M lib/galaxy/datatypes/molecules.py Log Message: ----------- fix pep8 errors Commit: 6abcbb84a839ca881b9e925d50e9913568c78325 https://github.com/galaxyproject/galaxy/commit/6abcbb84a839ca881b9e925d50e9… Author: leobiscassi <leo.biscassi(a)gmail.com> Date: 2016-06-03 (Fri, 03 Jun 2016) Changed paths: M lib/galaxy/datatypes/molecules.py Log Message: ----------- Adjust sniff function Commit: 789c3009369c0f3712cc140d404ad0a8b1151f48 https://github.com/galaxyproject/galaxy/commit/789c3009369c0f3712cc140d404a… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-06-03 (Fri, 03 Jun 2016) Changed paths: M lib/galaxy/datatypes/molecules.py A lib/galaxy/datatypes/test/NuBBE_1_obabel_3D.pdbqt Log Message: ----------- Merge pull request #2452 from leobiscassi/add_pdbqt_datatype Add support to PDBQT molecule datatype Compare: https://github.com/galaxyproject/galaxy/compare/30fd1d679b16...789c3009369c

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[galaxyproject/infrastructure-playbook] 9e8c59: Unprivileged CVMFS updating for Test/Main
by GitHub 03 Jun '16

03 Jun '16

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

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[galaxyproject/galaxy] 110f0f: add mothur.tre datatype (subclass)
by GitHub 03 Jun '16

03 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 110f0fe23d8ee28dbd6937b77aa4cac5d17474dc https://github.com/galaxyproject/galaxy/commit/110f0fe23d8ee28dbd6937b77aa4… Author: shiltemann <zazkia(a)gmail.com> Date: 2016-05-23 (Mon, 23 May 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- add mothur.tre datatype (subclass) Commit: f63ab5c38446a2a43dd6532ec064f52eb8445f54 https://github.com/galaxyproject/galaxy/commit/f63ab5c38446a2a43dd6532ec064… Author: shiltemann <zazkia(a)gmail.com> Date: 2016-05-23 (Mon, 23 May 2016) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- scan entire file when setting metadata for large group files this would not find all groups Commit: b83f1b8d24536fc79625cc11da9e47d90e47752a https://github.com/galaxyproject/galaxy/commit/b83f1b8d24536fc79625cc11da9e… Author: shiltemann <zazkia(a)gmail.com> Date: 2016-05-27 (Fri, 27 May 2016) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- add otulabels metadata to mothur.otu datatype Commit: 61589b378ace13a853a952b892cae4d8ceaea92b https://github.com/galaxyproject/galaxy/commit/61589b378ace13a853a952b892ca… Author: shiltemann <zazkia(a)gmail.com> Date: 2016-05-31 (Tue, 31 May 2016) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- minimize number of lines read in set_meta functions Commit: abdae9539b2e2c7fc4b11973d13fd3148c49db2f https://github.com/galaxyproject/galaxy/commit/abdae9539b2e2c7fc4b11973d13f… Author: shiltemann <zazkia(a)gmail.com> Date: 2016-06-02 (Thu, 02 Jun 2016) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- update superclass accessing Commit: 30fd1d679b1603f32b39ab7ff3ae5b927044150e https://github.com/galaxyproject/galaxy/commit/30fd1d679b1603f32b39ab7ff3ae… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-06-03 (Fri, 03 Jun 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/mothur.py Log Message: ----------- Merge pull request #2429 from shiltemann/mothur_datatypes small updates to Mothur datatypes Compare: https://github.com/galaxyproject/galaxy/compare/697b01c211f0...30fd1d679b16

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