- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] c260e0: Sort tags for display (note, this is stupid to hav...
by GitHub 02 Jun '17

02 Jun '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: c260e0b0c8ec1b8c479ab2aa2f60b7dfd533b324 https://github.com/galaxyproject/galaxy/commit/c260e0b0c8ec1b8c479ab2aa2f60… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js Log Message: ----------- Sort tags for display (note, this is stupid to have in 3 places -- refactor) Commit: 967c363786f36a4d4aab020a073b7c5e7eefbce6 https://github.com/galaxyproject/galaxy/commit/967c363786f36a4d4aab020a073b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Filter tags for empties (fixes #4127) Commit: 0c43954e8d09f9f6dc7ac3af02b14821e8fc53ae https://github.com/galaxyproject/galaxy/commit/0c43954e8d09f9f6dc7ac3af02b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Slight tweak of logic in tag filtering PJA Commit: 12905321ca8083e4b41eb0fe03193463b8efb019 https://github.com/galaxyproject/galaxy/commit/12905321ca8083e4b41eb0fe0319… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Allow hashtag usage in workflow PJA tag addition mechanism Commit: 0954290e5dfe74ab4d7a658dca9e2896e7aa020e https://github.com/galaxyproject/galaxy/commit/0954290e5dfe74ab4d7a658dca9e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Combine list comprehensions, slightly tweak logic. Commit: 0272e188a81b89d743c22956c88e6cdac433b8db https://github.com/galaxyproject/galaxy/commit/0272e188a81b89d743c22956c88e… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-06-02 (Fri, 02 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M lib/galaxy/jobs/actions/post.py M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js Log Message: ----------- Merge pull request #4139 from dannon/tag_sorting [17.05] Tag fixes Compare: https://github.com/galaxyproject/galaxy/compare/b0c46cc4d0ec...0272e188a81b

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[galaxyproject/infrastructure-playbook] 34639f: Updates for CVMFS 2.3(.5), disable auto garbage co...
by GitHub 01 Jun '17

01 Jun '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 34639fc49f019f88483a8a2a4f18d5bfc226be15 https://github.com/galaxyproject/infrastructure-playbook/commit/34639fc49f0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M galaxyenv/host_vars/cvmfs0-psu0.galaxyproject.org.yml M galaxyenv/host_vars/cvmfs0-tacc0.galaxyproject.org.yml M galaxyenv/playbook.yml M galaxyenv/secret_host_vars/cvmfs0-psu0.galaxyproject.org.yml M roles/cvmfs/defaults/main.yml M roles/cvmfs/tasks/stratum0.yml M roles/cvmfs/tasks/stratum1.yml Log Message: ----------- Updates for CVMFS 2.3(.5), disable auto garbage collection on publish/snapshot and schedule weekly collection (makes publishing/snapshotting, and therefore updating Galaxy, much quicker).

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[galaxyproject/usegalaxy-playbook] ce7d00: Update Main
by GitHub 01 Jun '17

01 Jun '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ce7d009db5b56e7a31c37b6858418a34d9a0e8c2 https://github.com/galaxyproject/usegalaxy-playbook/commit/ce7d009db5b56e7a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main

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[galaxyproject/usegalaxy-playbook] 2fd3b1: Update Main
by GitHub 01 Jun '17

01 Jun '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2fd3b1fc1cb22a423496f2ddf34b95911eed5a6f https://github.com/galaxyproject/usegalaxy-playbook/commit/2fd3b1fc1cb22a42… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M production/files/interactive_environments/plugins/.ansible_ie_role_current_version M production/files/interactive_environments/proxy/.ansible_ie_role_current_version M production/galaxy_version.yml Log Message: ----------- Update Main

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[galaxyproject/galaxy] c40957: Handle potential regex expression in workflow para...
by GitHub 01 Jun '17

01 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c409572ef8510e0c4322d835c5ba90f32bc9c653 https://github.com/galaxyproject/galaxy/commit/c409572ef8510e0c4322d835c5ba… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-31 (Wed, 31 May 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Handle potential regex expression in workflow parameter names Commit: a9d0d3671afc2be90509517b53b96af694ff22e5 https://github.com/galaxyproject/galaxy/commit/a9d0d3671afc2be90509517b53b9… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-05-31 (Wed, 31 May 2017) Changed paths: M lib/galaxy/util/compression_utils.py Log Message: ----------- Fix for returning a fileobject in compression_utils.py when handling a zipfile. Will return the first named object in the archive. zipfile.os_zipfile does not exist... Commit: f6ced00ef0de0fa67e2ecd06fa2db204e73f25ad https://github.com/galaxyproject/galaxy/commit/f6ced00ef0de0fa67e2ecd06fa2d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-31 (Wed, 31 May 2017) Changed paths: M lib/galaxy/util/compression_utils.py Log Message: ----------- Merge pull request #4135 from blankenberg/17.05_zipfile [17.05] Fix for returning a fileobject in compression_utils.py when handling a zipfile. Commit: 75028ac1eec7de53a197217921ebd5b7dac4daac https://github.com/galaxyproject/galaxy/commit/75028ac1eec7de53a197217921eb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-31 (Wed, 31 May 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge pull request #4133 from guerler/escape_regex [17.05] Properly escape potential regex expression in workflow parameters Commit: c2348340cfa865ac33ed38311f22c0e8043c89ae https://github.com/galaxyproject/galaxy/commit/c2348340cfa865ac33ed38311f22… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Fix for Data Tables loaded from a URL. Commit: b0c46cc4d0ec554d10186050c91a5c8a4880a8ff https://github.com/galaxyproject/galaxy/commit/b0c46cc4d0ec554d10186050c91a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge pull request #4140 from blankenberg/17.05_data_tables_URL_fix [17.05] Fix for Data Tables loaded from a URL. Commit: 20d2303d34636b77d631eb3d1a99e3df8690d865 https://github.com/galaxyproject/galaxy/commit/20d2303d34636b77d631eb3d1a99… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/tools/data/__init__.py M lib/galaxy/util/compression_utils.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c1d822d96de0...20d2303d3463

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[galaxyproject/galaxy] c23483: Fix for Data Tables loaded from a URL.
by GitHub 01 Jun '17

01 Jun '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: c2348340cfa865ac33ed38311f22c0e8043c89ae https://github.com/galaxyproject/galaxy/commit/c2348340cfa865ac33ed38311f22… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Fix for Data Tables loaded from a URL. Commit: b0c46cc4d0ec554d10186050c91a5c8a4880a8ff https://github.com/galaxyproject/galaxy/commit/b0c46cc4d0ec554d10186050c91a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge pull request #4140 from blankenberg/17.05_data_tables_URL_fix [17.05] Fix for Data Tables loaded from a URL. Compare: https://github.com/galaxyproject/galaxy/compare/75028ac1eec7...b0c46cc4d0ec

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[galaxyproject/galaxy] 2f992d: Rebase
by GitHub 01 Jun '17

01 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2f992d90ae8e0a4efec313fa0064b1576a26c2ba https://github.com/galaxyproject/galaxy/commit/2f992d90ae8e0a4efec313fa0064… Author: E Rasche <hxr(a)hx42.org> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M README.rst M contrib/galaxy.debian-init M contrib/galaxy_supervisor.conf M doc/source/admin/authentication.md M doc/source/admin/special_topics/mulled_containers.rst M doc/source/dev/build_a_job_runner.rst M doc/source/releases/13.01_announce.rst M doc/source/releases/13.02_announce.rst M doc/source/releases/13.04_announce.rst M doc/source/releases/13.06_announce.rst M doc/source/releases/13.08_announce.rst M doc/source/releases/13.11_announce.rst M doc/source/releases/14.02_announce.rst M doc/source/releases/14.04_announce.rst M doc/source/releases/14.06_announce.rst M doc/source/releases/14.08_announce.rst M doc/source/releases/14.10_announce.rst M doc/source/releases/15.01_announce.rst M doc/source/releases/15.03_announce.rst M doc/source/releases/15.05.rst M doc/source/releases/15.05_announce.rst M doc/source/releases/15.07_announce.rst M doc/source/releases/15.10_announce.rst M doc/source/releases/16.01_announce.rst M doc/source/releases/16.04_announce.rst M doc/source/releases/16.07_announce.rst M doc/source/releases/16.10_announce.rst M doc/source/releases/17.01_announce.rst M doc/source/slideshow/architecture/galaxy_architecture.md M lib/galaxy/tools/xsd/README.md M lib/galaxy/tools/xsd/galaxy.xsd M scripts/bootstrap_history.py M static/welcome.html.sample M test/functional/tools/sample_datatypes_conf.xml M test/qunit/test-data/bootstrapped.js M test/qunit/tests/galaxy-app-base.js Log Message: ----------- Rebase Commit: c1d822d96de0e97b39d5da4d51577d3823fdd8b1 https://github.com/galaxyproject/galaxy/commit/c1d822d96de0e97b39d5da4d5157… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M README.rst M contrib/galaxy.debian-init M contrib/galaxy_supervisor.conf M doc/source/admin/authentication.md M doc/source/admin/special_topics/mulled_containers.rst M doc/source/dev/build_a_job_runner.rst M doc/source/releases/13.01_announce.rst M doc/source/releases/13.02_announce.rst M doc/source/releases/13.04_announce.rst M doc/source/releases/13.06_announce.rst M doc/source/releases/13.08_announce.rst M doc/source/releases/13.11_announce.rst M doc/source/releases/14.02_announce.rst M doc/source/releases/14.04_announce.rst M doc/source/releases/14.06_announce.rst M doc/source/releases/14.08_announce.rst M doc/source/releases/14.10_announce.rst M doc/source/releases/15.01_announce.rst M doc/source/releases/15.03_announce.rst M doc/source/releases/15.05.rst M doc/source/releases/15.05_announce.rst M doc/source/releases/15.07_announce.rst M doc/source/releases/15.10_announce.rst M doc/source/releases/16.01_announce.rst M doc/source/releases/16.04_announce.rst M doc/source/releases/16.07_announce.rst M doc/source/releases/16.10_announce.rst M doc/source/releases/17.01_announce.rst M doc/source/slideshow/architecture/galaxy_architecture.md M lib/galaxy/tools/xsd/README.md M lib/galaxy/tools/xsd/galaxy.xsd M scripts/bootstrap_history.py M static/welcome.html.sample M test/functional/tools/sample_datatypes_conf.xml M test/qunit/test-data/bootstrapped.js M test/qunit/tests/galaxy-app-base.js Log Message: ----------- Merge pull request #4141 from erasche/wiki-links Swap over all URLs to new wiki location Compare: https://github.com/galaxyproject/galaxy/compare/e43ef79576bd...c1d822d96de0

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[galaxyproject/usegalaxy-playbook] b19102: Prevent accidental attempts to run the playbook on...
by GitHub 01 Jun '17

01 Jun '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b19102b88cc335eacb6d45368d605c9af614334c https://github.com/galaxyproject/usegalaxy-playbook/commit/b19102b88cc335ea… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M stage/inventory Log Message: ----------- Prevent accidental attempts to run the playbook on Test/TTS

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[galaxyproject/infrastructure-playbook] 86239e: Slurm DBD/Slurm controller improvements and reloca...
by GitHub 01 Jun '17

01 Jun '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 86239ef77522e797bfdc0b66737976e96f1d87de https://github.com/galaxyproject/infrastructure-playbook/commit/86239ef7752… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M common_roles A roles/mariadb/handlers/main.yml A roles/mariadb/tasks/install_redhat.yml A roles/mariadb/tasks/main.yml A roles/slurm/meta/main.yml R roles/slurm/tasks/elastic.yml M roles/slurm/tasks/main.yml A roles/slurm/tasks/slurmctld.yml A roles/slurm/tasks/slurmd.yml A roles/slurm/tasks/slurmdbd.yml M roles/slurm/templates/slurmdbd.conf.j2 M taccenv/group_vars/all.yml M taccenv/group_vars/galaxyservers.yml M taccenv/group_vars/slurmclients.yml A taccenv/group_vars/slurmdbdservers/vars.yml A taccenv/group_vars/slurmdbdservers/vault.yml M taccenv/inventory M taccenv/templates/slurm/slurm.conf.j2 Log Message: ----------- Slurm DBD/Slurm controller improvements and relocation to galaxy08

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[galaxyproject/usegalaxy-playbook] 622272: move rna_star to different destination
by GitHub 01 Jun '17

01 Jun '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 622272d426088faad13f230d765b6cb42d2aa2dd https://github.com/galaxyproject/usegalaxy-playbook/commit/622272d426088faa… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- move rna_star to different destination to dynamic_local_stampede_select_dynamic_walltime

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