- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 82811d: Bump version of sqlite3 in nodejs proxy
by GitHub 07 Oct '15

07 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 82811dd9217824946723ab54638da80ae40f2b54 https://github.com/galaxyproject/galaxy/commit/82811dd9217824946723ab54638d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M lib/galaxy/web/proxy/js/package.json Log Message: ----------- Bump version of sqlite3 in nodejs proxy @nitesh1989 and I tested this this morning and it let him install the nodejs proxy on OSX Commit: cd9c13ab495fa946724e5a67cd70d0d6342bafba https://github.com/galaxyproject/galaxy/commit/cd9c13ab495fa946724e5a67cd70… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M lib/galaxy/web/proxy/js/package.json Log Message: ----------- Merge pull request #866 from erasche/gie-nodejs-proxy-sqlite Bump version of sqlite3 in nodejs proxy Compare: https://github.com/galaxyproject/galaxy/compare/a5e75e8bbe6e...cd9c13ab495f

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[galaxyproject/galaxy] 22a565: Try harder to verify script integrity before runni...
by GitHub 07 Oct '15

07 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 22a565d1a25a5eda466d49b69df3c3ab436e8b82 https://github.com/galaxyproject/galaxy/commit/22a565d1a25a5eda466d49b69df3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Try harder to verify script integrity before running job scripts. These "Text file busy" errors are occasionally encountered in the wild in production settings and more commonly when running Galaxy in Docker containers. Simply sycning the file system has proven insufficient to prevent the problem and I do not want to add an arbitrary sleep. So this new strategy is used. - Inject special functionality into each job script that when executed with a certain environment variable set causes the script to exit with a specific return code. - Have Galaxy rerun this script in that configuration until it can succeed in executing the script. - In between each iteration sleep for a small amount of time and try to cause a file system sync. This entire is ... insane ... so I have added a configuration option to disable it entirely check_job_script_integrity=False. Commit: c53aeaef7737ff897dd2a754b16a9e077273e776 https://github.com/galaxyproject/galaxy/commit/c53aeaef7737ff897dd2a754b16a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Simplify shell expression thanks to suggestion by @nsoranzo. Commit: a5e75e8bbe6e465327c7ef783e7236ea2e467b53 https://github.com/galaxyproject/galaxy/commit/a5e75e8bbe6e465327c7ef783e72… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Merge pull request #865 from jmchilton/script_integrity Try harder to verify script integrity before running job scripts. Compare: https://github.com/galaxyproject/galaxy/compare/495e3db97fdc...a5e75e8bbe6e

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[galaxyproject/galaxy] 1fa7c1: Populate env.sh files with X_ROOT_DIR.
by GitHub 07 Oct '15

07 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1fa7c103865d12d76e7450ed4eb4404498d04d71 https://github.com/galaxyproject/galaxy/commit/1fa7c103865d12d76e7450ed4eb4… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-05 (Wed, 05 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Populate env.sh files with X_ROOT_DIR. Where X is tool_dependency.name.upper() Commit: 495e3db97fdc16ed3b8df3f64ab2f6d698d1b421 https://github.com/galaxyproject/galaxy/commit/495e3db97fdc16ed3b8df3f64ab2… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #564 from davebx/root_dir_env Populate env.sh files with X_ROOT_DIR. Compare: https://github.com/galaxyproject/galaxy/compare/c98ad3e32ddd...495e3db97fdc

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[galaxyproject/galaxy] abf169: Reduce handle inputs and remove update state from ...
by GitHub 07 Oct '15

07 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: abf16905d600a75dbc80c1b011c16bc05ad894f1 https://github.com/galaxyproject/galaxy/commit/abf16905d600a75dbc80c1b011c1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M templates/base/base_panels.mako M templates/webapps/galaxy/tool_executed.mako Log Message: ----------- Reduce handle inputs and remove update state from tools Fix lint Strip default makos from tools, handle input returns a dictionary now Commit: 862a1d11939a9e2d2807decf991e5fd61be72ad0 https://github.com/galaxyproject/galaxy/commit/862a1d11939a9e2d2807decf991e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py A templates/webapps/galaxy/root/tool_runner.mako R templates/webapps/galaxy/tool_executed.mako Log Message: ----------- Move remaining mako code to root/tool_runner Fix async controller (deprecated?) Fix lint Fix lint Commit: 59885c3afdce3c9f08f6fb94f78df636a974161b https://github.com/galaxyproject/galaxy/commit/59885c3afdce3c9f08f6fb94f78d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-jobs.js Log Message: ----------- Fix error message handling Use common exception handlers Fix error message Fix error message More fixes Commit: ee1136d5bf9d5e8e0a7cf0a58130216c5dc217ee https://github.com/galaxyproject/galaxy/commit/ee1136d5bf9d5e8e0a7cf0a58130… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M static/maps/mvc/tools/tools-form-base.js.map M test/base/interactor.py M test/unit/tools/test_execution.py Log Message: ----------- Fix test cases Fix lint Fix lint Fix test messages Remove unnecessary variable Remove unused test helper functions Fix lint Fix error message in tests Fix spaces Commit: c98ad3e32ddda29e0ef175eeb7ecebdd25d4e758 https://github.com/galaxyproject/galaxy/commit/c98ad3e32ddda29e0ef175eeb7ec… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-jobs.js M templates/base/base_panels.mako A templates/webapps/galaxy/root/tool_runner.mako R templates/webapps/galaxy/tool_executed.mako M test/base/interactor.py M test/unit/tools/test_execution.py Log Message: ----------- Merge pull request #829 from guerler/tool_execution_000 Reduce handle inputs and remove update state from tools Compare: https://github.com/galaxyproject/galaxy/compare/8b2b55c989bb...c98ad3e32ddd

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[galaxyproject/galaxy] f8268f: Tighten up GG sniffing.
by GitHub 07 Oct '15

07 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f8268f576aebcc4b1bf22eb9b5fe5a1f68871db5 https://github.com/galaxyproject/galaxy/commit/f8268f576aebcc4b1bf22eb9b5fe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M lib/galaxy/datatypes/genetics.py A lib/galaxy/datatypes/test/1.gg Log Message: ----------- Tighten up GG sniffing. Commit: 06da566d46b3cb74973796637fc12b93ab6f3bc1 https://github.com/galaxyproject/galaxy/commit/06da566d46b3cb74973796637fc1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M lib/galaxy/datatypes/genetics.py Log Message: ----------- Allow simple gg files with only one data column. Commit: 8b2b55c989bbf6645f3c2220dcbcce4e890c38bc https://github.com/galaxyproject/galaxy/commit/8b2b55c989bbf6645f3c2220dcbc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M lib/galaxy/datatypes/genetics.py A lib/galaxy/datatypes/test/1.gg Log Message: ----------- Merge pull request #864 from dannon/gg_fix Tighten up GG sniffing Compare: https://github.com/galaxyproject/galaxy/compare/57a88a167dcc...8b2b55c989bb

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[galaxyproject/galaxy] 996497: Test if parameter value is present to avoid index ...
by GitHub 07 Oct '15

07 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 99649713c3105adc1137541a0d307c642df4e66a https://github.com/galaxyproject/galaxy/commit/99649713c3105adc1137541a0d30… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Test if parameter value is present to avoid index error. Commit: 77b96a6ca63c4c344c3ba61d7a48948ddc894e4b https://github.com/galaxyproject/galaxy/commit/77b96a6ca63c4c344c3ba61d7a48… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Change parameter value to None instead of leaving the parameter out entirely. Commit: 61a2b4ba10a36f987f21fd6775ccafb5829a6383 https://github.com/galaxyproject/galaxy/commit/61a2b4ba10a36f987f21fd6775cc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Revert "Change parameter value to None instead of leaving the parameter out entirely." This reverts commit 77b96a6ca63c4c344c3ba61d7a48948ddc894e4b. Commit: 57a88a167dccb09aa6d1c9d129f0f31e870901c7 https://github.com/galaxyproject/galaxy/commit/57a88a167dccb09aa6d1c9d129f0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Merge pull request #863 from mvdbeek/fix_workflow_import Test if parameter present in value to avoid index error. Compare: https://github.com/galaxyproject/galaxy/compare/6dbdaa9bfa79...57a88a167dcc

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[galaxyproject/galaxy] d45d66: Avoid confusing error message and double evaluatio...
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d45d6676b00a3ef6c14742066bd68f520dacbffa https://github.com/galaxyproject/galaxy/commit/d45d6676b00a3ef6c14742066bd6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Avoid confusing error message and double evaluation of to_dict in parameter handling Commit: 6dbdaa9bfa7918e19874419dcca6d4b793b03fdc https://github.com/galaxyproject/galaxy/commit/6dbdaa9bfa7918e19874419dcca6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #815 from guerler/tool_parameters_000 Avoid confusing error message and double evaluation of to_dict in par… Compare: https://github.com/galaxyproject/galaxy/compare/2b966ca4fae9...6dbdaa9bfa79

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[galaxyproject/galaxy] e9d77a: Attempt to fix transiently failing API tests.
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e9d77ac763239ccbae43ed553a1ce9541a5b8af3 https://github.com/galaxyproject/galaxy/commit/e9d77ac763239ccbae43ed553a1c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M test/api/helpers.py M test/api/test_jobs.py Log Message: ----------- Attempt to fix transiently failing API tests. - Fix default timeout of wait_on_state api helper. Had the wrong default specified and might fix this failure: https://jenkins.galaxyproject.org/job/docker-api/229/testReport/junit/api.t… - Modify job search test case to allow a little more time between the history being "ok" and the job, in case there is a timing condition if the HDA is committed first and then job. Also improve the test output in case this isn't the problem. Commit: 2b966ca4fae9e7348ac3a17de8d1567ebdacd21d https://github.com/galaxyproject/galaxy/commit/2b966ca4fae9e7348ac3a17de8d1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M test/api/helpers.py M test/api/test_jobs.py Log Message: ----------- Merge pull request #859 from jmchilton/test_fix_2 Attempt to fix more transiently failing API tests. Compare: https://github.com/galaxyproject/galaxy/compare/a2a4ce43ec3f...2b966ca4fae9

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[galaxyproject/galaxy] 84b572: Extend tool API to allow cross product mapping ove...
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 84b5726ca99bb681b6883bd42093c3a58e036d24 https://github.com/galaxyproject/galaxy/commit/84b5726ca99bb681b6883bd42093… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/tools/parameters/meta.py M test/api/test_tools.py Log Message: ----------- Extend tool API to allow cross product mapping over collections. By default if single data parameters are mapped over by collections, the collections are matched up (e.g. for two collections the items are paired off and two collections of dimension (N) will result in running N jobs and producing an (N) dimensional output for each define output). In the parameter meta value wrapper (where batch mode can be set with the ``batch`` flag), the linked flag is now respected for collection operations. If ``linked`` is ``False``, then the cross product of the inputs will be used to map over the tool. In the above simplest case, this would cause an NxN (``list:list``) collection to be created for each tool output. This operation was previously available for individual datasets, but when supplied a collection it would not create an implicit collection pulling together all the relevant datasets with the correct structure - it would just run the jobs and leave the datasets uncollected. Now a collection with the correct structure and identifiers is created. Limitations: ----------------- This does not enable tool form support but the API for collections matches that for doing cross product operations over sets of individual datasets, so once support is added to the tool form for that collection support should be trivial. Testing: ----------------- The following test case has been extended to now ensure that an implicit collection is created and that it has the right dimensionality/structure and contents. ./run_tests.sh -with_framework_test_tools -api test/api/test_tools.py:ToolsTestCase.test_map_over_two_collections_unlinked Commit: a2a4ce43ec3f7571be12e08a801ea9f21d41f992 https://github.com/galaxyproject/galaxy/commit/a2a4ce43ec3f7571be12e08a801e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/tools/parameters/meta.py M test/api/test_tools.py Log Message: ----------- Merge pull request #743 from jmchilton/cross_product_collection_mapping Extend tool API to allow cross product mapping over collections. Compare: https://github.com/galaxyproject/galaxy/compare/d309535f6871...a2a4ce43ec3f

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[galaxyproject/galaxy] b396b6: concatenate in one VCF some splitted vcfs whith bc...
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b396b6383bc89a56e6d37b291cc47a2622d02620 https://github.com/galaxyproject/galaxy/commit/b396b6383bc89a56e6d37b291cc4… Author: roalva1 <roalva1(a)gmail.com> Date: 2015-05-04 (Mon, 04 May 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- concatenate in one VCF some splitted vcfs whith bcftools Commit: 9599ab6c3851f72261327d5edf2fa2c6d831254e https://github.com/galaxyproject/galaxy/commit/9599ab6c3851f72261327d5edf2f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Cleanup b396b6383bc89a56e6d37b291cc47a2622d02620 a bit. Use logs instead of print statements, PEP-8 improvements. Commit: 62c7f3ea9a92ab777fc4f7e0995a2db126177e12 https://github.com/galaxyproject/galaxy/commit/62c7f3ea9a92ab777fc4f7e0995a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge branch dev into merge-vcf. Conflicts: lib/galaxy/datatypes/tabular.py Commit: 26be140f28483c7de544fb6aeaf342e834664e29 https://github.com/galaxyproject/galaxy/commit/26be140f28483c7de544fb6aeaf3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Cleanup vcf.merge some more based on PR comments. Commit: ef84888863ebf27529c892917191dc232e7e931a https://github.com/galaxyproject/galaxy/commit/ef84888863ebf27529c892917191… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Another vcf.merge fix thanks to @nsoranzo. Commit: 5bb2fcabf4ec493cce5d63601d86c02f01b66e0c https://github.com/galaxyproject/galaxy/commit/5bb2fcabf4ec493cce5d63601d86… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Remove unused commit. Commit: d309535f687125b81f2cf594889d5bdbb803f964 https://github.com/galaxyproject/galaxy/commit/d309535f687125b81f2cf594889d… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #845 from jmchilton/merge-vcf-new Update and cleanup of #209. Compare: https://github.com/galaxyproject/galaxy/compare/903823f2986f...d309535f6871

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[galaxyproject/galaxy] c3ef54: Eliminate LWR from Galaxy.
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c3ef5467c71e69aa4570613e27bb8bd46d7de4f4 https://github.com/galaxyproject/galaxy/commit/c3ef5467c71e69aa4570613e27bb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: R doc/source/lib/galaxy.jobs.runners.lwr_client.rst R doc/source/lib/galaxy.jobs.runners.lwr_client.staging.rst R doc/source/lib/galaxy.jobs.runners.lwr_client.transport.rst M doc/source/lib/galaxy.jobs.runners.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py R lib/galaxy/jobs/runners/lwr.py R lib/galaxy/jobs/runners/lwr_client/__init__.py R lib/galaxy/jobs/runners/lwr_client/action_mapper.py R lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py R lib/galaxy/jobs/runners/lwr_client/amqp_exchange_factory.py R lib/galaxy/jobs/runners/lwr_client/client.py R lib/galaxy/jobs/runners/lwr_client/config_util.py R lib/galaxy/jobs/runners/lwr_client/decorators.py R lib/galaxy/jobs/runners/lwr_client/destination.py R lib/galaxy/jobs/runners/lwr_client/interface.py R lib/galaxy/jobs/runners/lwr_client/job_directory.py R lib/galaxy/jobs/runners/lwr_client/manager.py R lib/galaxy/jobs/runners/lwr_client/object_client.py R lib/galaxy/jobs/runners/lwr_client/path_mapper.py R lib/galaxy/jobs/runners/lwr_client/setup_handler.py R lib/galaxy/jobs/runners/lwr_client/staging/__init__.py R lib/galaxy/jobs/runners/lwr_client/staging/down.py R lib/galaxy/jobs/runners/lwr_client/staging/up.py R lib/galaxy/jobs/runners/lwr_client/transport/__init__.py R lib/galaxy/jobs/runners/lwr_client/transport/curl.py R lib/galaxy/jobs/runners/lwr_client/transport/standard.py R lib/galaxy/jobs/runners/lwr_client/util.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/wrappers.py Log Message: ----------- Eliminate LWR from Galaxy. Commit: 903823f2986fad624770166a7d31f7936ce1a9f1 https://github.com/galaxyproject/galaxy/commit/903823f2986fad624770166a7d31… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: R doc/source/lib/galaxy.jobs.runners.lwr_client.rst R doc/source/lib/galaxy.jobs.runners.lwr_client.staging.rst R doc/source/lib/galaxy.jobs.runners.lwr_client.transport.rst M doc/source/lib/galaxy.jobs.runners.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py R lib/galaxy/jobs/runners/lwr.py R lib/galaxy/jobs/runners/lwr_client/__init__.py R lib/galaxy/jobs/runners/lwr_client/action_mapper.py R lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py R lib/galaxy/jobs/runners/lwr_client/amqp_exchange_factory.py R lib/galaxy/jobs/runners/lwr_client/client.py R lib/galaxy/jobs/runners/lwr_client/config_util.py R lib/galaxy/jobs/runners/lwr_client/decorators.py R lib/galaxy/jobs/runners/lwr_client/destination.py R lib/galaxy/jobs/runners/lwr_client/interface.py R lib/galaxy/jobs/runners/lwr_client/job_directory.py R lib/galaxy/jobs/runners/lwr_client/manager.py R lib/galaxy/jobs/runners/lwr_client/object_client.py R lib/galaxy/jobs/runners/lwr_client/path_mapper.py R lib/galaxy/jobs/runners/lwr_client/setup_handler.py R lib/galaxy/jobs/runners/lwr_client/staging/__init__.py R lib/galaxy/jobs/runners/lwr_client/staging/down.py R lib/galaxy/jobs/runners/lwr_client/staging/up.py R lib/galaxy/jobs/runners/lwr_client/transport/__init__.py R lib/galaxy/jobs/runners/lwr_client/transport/curl.py R lib/galaxy/jobs/runners/lwr_client/transport/standard.py R lib/galaxy/jobs/runners/lwr_client/util.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/wrappers.py Log Message: ----------- Merge pull request #857 from jmchilton/lwr_remove Eliminate LWR from Galaxy. Compare: https://github.com/galaxyproject/galaxy/compare/920f7950fdb1...903823f2986f

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[galaxyproject/galaxy] 31c89e: UI, Collections: allow expansion to fetch details ...
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 31c89ea29c2c504878f336d90dfcf320b873b2ee https://github.com/galaxyproject/galaxy/commit/31c89ea29c2c504878f336d90dfc… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M static/maps/mvc/collection/collection-li-edit.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/history/hda-li-edit.js Log Message: ----------- UI, Collections: allow expansion to fetch details for DatasetDCEs (assuming they're HDAs); move rerunnable and creating_job fetch to HDAs Commit: 69cd5a98dcda30771ce78118ebd3a934dfb09c65 https://github.com/galaxyproject/galaxy/commit/69cd5a98dcda30771ce78118ebd3… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M static/maps/mvc/collection/collection-li-edit.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/history/hda-li-edit.js Log Message: ----------- Merge pull request #854 from carlfeberhard/release_15.10 [15.10] UI, Collections: allow expansion to fetch details for DatasetDCEs (as… Compare: https://github.com/galaxyproject/galaxy/compare/cc23adb0a962...69cd5a98dcda

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[galaxyproject/galaxy] fd1fd5: flake8 lib/galaxy/model/migrate/versions/ .
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fd1fd5e73c1828f79526ac712e3a4d9d5e9afa1c https://github.com/galaxyproject/galaxy/commit/fd1fd5e73c1828f79526ac712e3a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-10-02 (Fri, 02 Oct 2015) Changed paths: M .ci/flake8_blacklist.txt M lib/galaxy/model/migrate/versions/0001_initial_tables.py M lib/galaxy/model/migrate/versions/0002_metadata_file_table.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/0022_visualization_tables.py M lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0025_user_info.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.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/0032_stored_workflow_slug_column.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/0039_add_synopsis_column_to_library_table.py M lib/galaxy/model/migrate/versions/0040_page_annotations.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py M lib/galaxy/model/migrate/versions/0046_post_job_actions.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/0054_visualization_dbkey.py M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py M lib/galaxy/model/migrate/versions/0056_workflow_outputs.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/0061_tasks.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/0069_rename_sequencer_form_type.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/0076_fix_form_values_data_corruption.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/0104_update_genome_downloader_job_parameters.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/0115_longer_user_password_field.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/0119_job_metrics.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.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/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py M lib/galaxy/model/migrate/versions/0128_session_timeout.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py Log Message: ----------- flake8 lib/galaxy/model/migrate/versions/ . Fix 1429 linting errors. Commit: 920f7950fdb10a4df4a237406c680f65e721942b https://github.com/galaxyproject/galaxy/commit/920f7950fdb10a4df4a237406c68… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M .ci/flake8_blacklist.txt M lib/galaxy/model/migrate/versions/0001_initial_tables.py M lib/galaxy/model/migrate/versions/0002_metadata_file_table.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/0022_visualization_tables.py M lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0025_user_info.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.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/0032_stored_workflow_slug_column.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/0039_add_synopsis_column_to_library_table.py M lib/galaxy/model/migrate/versions/0040_page_annotations.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py M lib/galaxy/model/migrate/versions/0046_post_job_actions.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/0054_visualization_dbkey.py M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py M lib/galaxy/model/migrate/versions/0056_workflow_outputs.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/0061_tasks.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/0069_rename_sequencer_form_type.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/0076_fix_form_values_data_corruption.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/0104_update_genome_downloader_job_parameters.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/0115_longer_user_password_field.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/0119_job_metrics.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.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/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py M lib/galaxy/model/migrate/versions/0128_session_timeout.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py Log Message: ----------- Merge pull request #832 from nsoranzo/flake8_fixes Flake8 lib/galaxy/model/migrate/versions/ . Compare: https://github.com/galaxyproject/galaxy/compare/c8533f6e3a86...920f7950fdb1

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[galaxyproject/galaxy] 6d3c8a: Do not split parameter of type "text" during funct...
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6d3c8a8b08367a6063c06b75778b006df596d4e8 https://github.com/galaxyproject/galaxy/commit/6d3c8a8b08367a6063c06b75778b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-10-04 (Sun, 04 Oct 2015) Changed paths: M lib/galaxy/tools/test.py Log Message: ----------- Do not split parameter of type "text" during functional tests. Commit: 35dcbc5afb697a663866033372aaefed6912aaa6 https://github.com/galaxyproject/galaxy/commit/35dcbc5afb697a663866033372aa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M lib/galaxy/tools/test.py Log Message: ----------- Unindent value.type check Commit: c8533f6e3a8602531c438b379c559a8bd9102e25 https://github.com/galaxyproject/galaxy/commit/c8533f6e3a8602531c438b379c55… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M lib/galaxy/tools/test.py Log Message: ----------- Merge pull request #837 from mvdbeek/No_split_text_functional_tests Do not split parameter of type text during functional tests. Compare: https://github.com/galaxyproject/galaxy/compare/fd3cadc371d7...c8533f6e3a86

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[galaxyproject/galaxy] d4fba9: graph visualization added
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d4fba962310ea8357516526a941df05572fa2a9e https://github.com/galaxyproject/galaxy/commit/d4fba962310ea8357516526a941d… Author: Eteri <eteri(a)eteri-HP-ENVY-Sleekbook-4-PC.(none)> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: A config/plugins/visualizations/graphviz/README.md A config/plugins/visualizations/graphviz/config/graphviz.xml A config/plugins/visualizations/graphviz/static/css/style.css A config/plugins/visualizations/graphviz/static/img/15xvbd5.png A config/plugins/visualizations/graphviz/static/img/lite-blue-check.png A config/plugins/visualizations/graphviz/static/js/collapse.js A config/plugins/visualizations/graphviz/static/js/cytoscape.min.js A config/plugins/visualizations/graphviz/static/js/graphVis.js A config/plugins/visualizations/graphviz/static/js/jquery.qtip.js A config/plugins/visualizations/graphviz/static/js/tip_centerwindow.js A config/plugins/visualizations/graphviz/static/js/tip_followscroll.js A config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js A config/plugins/visualizations/graphviz/static/js/wz_tooltip.js A config/plugins/visualizations/graphviz/templates/graphviz.mako Log Message: ----------- graph visualization added Commit: fd3cadc371d738ae9dfad68988f08c2508790bfd https://github.com/galaxyproject/galaxy/commit/fd3cadc371d738ae9dfad68988f0… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: A config/plugins/visualizations/graphviz/README.md A config/plugins/visualizations/graphviz/config/graphviz.xml A config/plugins/visualizations/graphviz/static/css/style.css A config/plugins/visualizations/graphviz/static/img/15xvbd5.png A config/plugins/visualizations/graphviz/static/img/lite-blue-check.png A config/plugins/visualizations/graphviz/static/js/collapse.js A config/plugins/visualizations/graphviz/static/js/cytoscape.min.js A config/plugins/visualizations/graphviz/static/js/graphVis.js A config/plugins/visualizations/graphviz/static/js/jquery.qtip.js A config/plugins/visualizations/graphviz/static/js/tip_centerwindow.js A config/plugins/visualizations/graphviz/static/js/tip_followscroll.js A config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js A config/plugins/visualizations/graphviz/static/js/wz_tooltip.js A config/plugins/visualizations/graphviz/templates/graphviz.mako Log Message: ----------- Merge pull request #378 from eteriSokhoyan/dev graph visualization added Compare: https://github.com/galaxyproject/galaxy/compare/cc23adb0a962...fd3cadc371d7

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[galaxyproject/galaxy]
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] ea2828: Add new run_tests.sh command to mount the external...
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ea28282b59e286570d6a4fb2c93259f99db0d1df https://github.com/galaxyproject/galaxy/commit/ea28282b59e286570d6a4fb2c932… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M run_tests.sh Log Message: ----------- Add new run_tests.sh command to mount the external tmp directory. This is an attempt to potentially end these "Text file busy" problems on test: https://jenkins.galaxyproject.org/job/docker-api/170/testReport/junit/api.t…. Commit: cc23adb0a962f1c9780b838604718319a0a71888 https://github.com/galaxyproject/galaxy/commit/cc23adb0a962f1c9780b83860471… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #843 from jmchilton/text_file_busy_2 Allow reuse of parent /tmp directory in dockerized testing. Compare: https://github.com/galaxyproject/galaxy/compare/b5b36c0ab184...cc23adb0a962

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[galaxyproject/galaxy] 47113b: Merge branch 'dev' of github.com:galaxyproject/gal...
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 47113bedcabe3c82ad99ea1ef16307f8c3c5512f https://github.com/galaxyproject/galaxy/commit/47113bedcabe3c82ad99ea1ef163… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M .ci/flake8_blacklist.txt 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-model.js M client/galaxy/scripts/mvc/tools/tools-form.js M lib/galaxy/datatypes/registry.py A lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/imp_exp/__init__.py A lib/galaxy/tools/imp_exp/exp_history_to_archive.xml M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/user.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/0021_change_repository_type_value.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/model/migrate/versions/0024_password_reset.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py M lib/pulsar/client/amqp_exchange.py 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-model.js.map M static/maps/mvc/tools/tools-form.js.map 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-model.js M static/scripts/mvc/tools/tools-form.js M test/unit/tools/test_parsing.py Log Message: ----------- Merge branch 'dev' of github.com:galaxyproject/galaxy into dev Commit: 5f4502b6500ca0aae57d6d76da12804d5d2fb9d1 https://github.com/galaxyproject/galaxy/commit/5f4502b6500ca0aae57d6d76da12… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Log Message: ----------- Pin images for next release of Galaxy Commit: e9a3ec95b9485ea3b5b15bce4f8a96751f225b53 https://github.com/galaxyproject/galaxy/commit/e9a3ec95b9485ea3b5b15bce4f8a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M doc/source/dev/faq.rst Log Message: ----------- Update faq.rst Commit: b5b36c0ab184d38b611fe0b293424bedd687cb28 https://github.com/galaxyproject/galaxy/commit/b5b36c0ab184d38b611fe0b29342… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Log Message: ----------- Merge pull request #849 from erasche/gie-pinning-15.10 GIE pinning 15.10 Compare: https://github.com/galaxyproject/galaxy/compare/092fc17ec008...b5b36c0ab184

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[galaxyproject/galaxy] 1aebbc: Remove likely broken UCSC proxy and associated too...
by GitHub 05 Oct '15

05 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1aebbc3f68ad5a82834edb82ef52e3840fec697b https://github.com/galaxyproject/galaxy/commit/1aebbc3f68ad5a82834edb82ef52… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: R lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py R tools/data_source/ucsc_archaea.xml R tools/data_source/ucsc_filter.py R tools/data_source/ucsc_proxy.py R tools/data_source/ucsc_proxy.xml R tools/data_source/ucsc_testproxy.xml Log Message: ----------- Remove likely broken UCSC proxy and associated tools. Unused for many, many years and likely no longer works. Commit: a6f9e62c1a4048d3f7669d5783a836d38d6f8f96 https://github.com/galaxyproject/galaxy/commit/a6f9e62c1a4048d3f7669d5783a8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M tools/data_source/ucsc_tablebrowser.xml M tools/data_source/ucsc_tablebrowser_archaea.xml M tools/data_source/ucsc_tablebrowser_test.xml Log Message: ----------- Add citations to ucsc browser tools. Commit: 092fc17ec008f092f016014f30317bdf68b9c567 https://github.com/galaxyproject/galaxy/commit/092fc17ec008f092f016014f3031… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: R lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py R tools/data_source/ucsc_archaea.xml R tools/data_source/ucsc_filter.py R tools/data_source/ucsc_proxy.py R tools/data_source/ucsc_proxy.xml M tools/data_source/ucsc_tablebrowser.xml M tools/data_source/ucsc_tablebrowser_archaea.xml M tools/data_source/ucsc_tablebrowser_test.xml R tools/data_source/ucsc_testproxy.xml Log Message: ----------- Merge pull request #846 from jmchilton/ucsc_cleanup UCSC Tool Cleanup Compare: https://github.com/galaxyproject/galaxy/compare/f90c49e2705e...092fc17ec008

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[galaxyproject/galaxy] 591519: Add citations to a few more tools.
by GitHub 05 Oct '15

05 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 591519009b0ead989ddf5a87fee9d5c69216b97c https://github.com/galaxyproject/galaxy/commit/591519009b0ead989ddf5a87fee9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M tools/sr_mapping/srma_wrapper.xml M tools/visualization/LAJ.xml Log Message: ----------- Add citations to a few more tools. Commit: 88239abf5c2473af841eea139edc0164b3a4856c https://github.com/galaxyproject/galaxy/commit/88239abf5c2473af841eea139edc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M tools/data_source/biomart.xml M tools/data_source/biomart_test.xml M tools/sr_mapping/bfast_wrapper.xml M tools/sr_mapping/fastq_statistics.xml M tools/sr_mapping/mosaik.xml Log Message: ----------- Add more distribution tool citations. xref #361. Commit: f90c49e2705ed66bfa668de96568ea53126edc94 https://github.com/galaxyproject/galaxy/commit/f90c49e2705ed66bfa668de96568… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M tools/data_source/biomart.xml M tools/data_source/biomart_test.xml M tools/sr_mapping/bfast_wrapper.xml M tools/sr_mapping/fastq_statistics.xml M tools/sr_mapping/mosaik.xml M tools/sr_mapping/srma_wrapper.xml M tools/visualization/LAJ.xml Log Message: ----------- Merge pull request #847 from jmchilton/citations_5 Add more distribution tool citations. Compare: https://github.com/galaxyproject/galaxy/compare/3201005739ab...f90c49e2705e

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[galaxyproject/galaxy] 053f51: forgoten minification and map
by GitHub 05 Oct '15

05 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 053f51eb537a4624bc0751c0ae39efb59eb996ea https://github.com/galaxyproject/galaxy/commit/053f51eb537a4624bc0751c0ae39… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M static/maps/mvc/form/form-view.js.map M static/scripts/mvc/form/form-view.js Log Message: ----------- forgoten minification and map Commit: 3201005739ab5071399a55b0aa99682ffb539c26 https://github.com/galaxyproject/galaxy/commit/3201005739ab5071399a55b0aa99… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M static/maps/mvc/form/form-view.js.map M static/scripts/mvc/form/form-view.js Log Message: ----------- Merge pull request #850 from martenson/forgotten-minification forgoten minification and map Compare: https://github.com/galaxyproject/galaxy/compare/4cd4dac0a088...3201005739ab

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[galaxyproject/galaxy] f50702: Remove unused echo tool
by GitHub 05 Oct '15

05 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f50702f96253d1d4a6ad1dbe088b1d04c6e1506a https://github.com/galaxyproject/galaxy/commit/f50702f96253d1d4a6ad1dbe088b… Author: Eric Rasche <rasche.eric(a)yandex.ru> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: R tools/data_source/echo.py R tools/data_source/echo.xml Log Message: ----------- Remove unused echo tool Commit: 4cd4dac0a088b3d040766853fee8b179d94f144a https://github.com/galaxyproject/galaxy/commit/4cd4dac0a088b3d040766853fee8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: R tools/data_source/echo.py R tools/data_source/echo.xml Log Message: ----------- Merge pull request #848 from jmchilton/echo_remove Remove unused echo tool Compare: https://github.com/galaxyproject/galaxy/compare/753bb9de0fa0...4cd4dac0a088

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[galaxyproject/galaxy] 4e35ff: More improved file handling for job code.
by GitHub 05 Oct '15

05 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4e35ff04a116a4a9ca1d96e9b3c5842be9fa9f7f https://github.com/galaxyproject/galaxy/commit/4e35ff04a116a4a9ca1d96e9b3c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- More improved file handling for job code. Another stab in the dark that won't actually fix the testing issues with Docker. Commit: b75175f18d15000a2dc5826f49424eba6dc7d489 https://github.com/galaxyproject/galaxy/commit/b75175f18d15000a2dc5826f4942… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py Log Message: ----------- Centralize logic for writing job scripts. Runners were using various permissions, some didn't close file handles, etc.... In addition, run sync after script is written to avoid "Text file busy" problems in all job script scenerios. Commit: 753bb9de0fa031720b8c7881ff1d52cbf6a522d3 https://github.com/galaxyproject/galaxy/commit/753bb9de0fa031720b8c7881ff1d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py Log Message: ----------- Merge pull request #839 from jmchilton/text_file_busy Attempt to fix "Text file busy" errors (testing and production) Compare: https://github.com/galaxyproject/galaxy/compare/bb43ace50927...753bb9de0fa0

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[galaxyproject/galaxy] 6430b9: Update documentation for the gff_filter_by_attribu...
by GitHub 05 Oct '15

05 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6430b9c4e834161910c23438f9fd779b78846de7 https://github.com/galaxyproject/galaxy/commit/6430b9c4e834161910c23438f9fd… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M tools/filters/gff/gff_filter_by_attribute.xml Log Message: ----------- Update documentation for the gff_filter_by_attribute tool Commit: bb43ace5092799e49875589f6da7404806e27137 https://github.com/galaxyproject/galaxy/commit/bb43ace5092799e49875589f6da7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M tools/filters/gff/gff_filter_by_attribute.xml Log Message: ----------- Merge pull request #842 from bgruening/filter_by_attribute Update documentation for the gff_filter_by_attribute tool Compare: https://github.com/galaxyproject/galaxy/compare/3687d45a0371...bb43ace50927

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[galaxyproject/galaxy] 54410d: Use eggs.require() instead of pkg_resources in lib...
by GitHub 05 Oct '15

05 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 54410d7d70c13c76ac370e83c12db7810192fc71 https://github.com/galaxyproject/galaxy/commit/54410d7d70c13c76ac370e83c12d… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/display_applications/util.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- Use eggs.require() instead of pkg_resources in lib/galaxy/datatypes/ . Fix https://github.com/galaxyproject/galaxy/issues/809#issuecomment-145107037 . Commit: 3687d45a037166e2fffcdfe7fda4cfd6d2b08346 https://github.com/galaxyproject/galaxy/commit/3687d45a037166e2fffcdfe7fda4… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/display_applications/util.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- Merge pull request #838 from nsoranzo/pkg_resources Use eggs.require() instead of pkg_resources in lib/galaxy/datatypes/ . Compare: https://github.com/galaxyproject/galaxy/compare/0a83a244f170...3687d45a0371

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