- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] f16a48: Fix reports (supervisor runs on 9001)
by GitHub 17 Aug '16

17 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f16a4858e647e4040d45ff83afb681cd71e6320a https://github.com/galaxyproject/usegalaxy-playbook/commit/f16a4858e647e404… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-17 (Wed, 17 Aug 2016) Changed paths: M stage/inventory M templates/galaxy/common/config/reports.ini.j2 M templates/nginx/galaxy_test.j2 M templates/nginx/tacc_protected.j2 Log Message: ----------- Fix reports (supervisor runs on 9001)

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[galaxyproject/galaxy] dfccd9: Fix setting metadata in galaxy.json for working di...
by GitHub 17 Aug '16

17 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dfccd902b00426c79670e77ef11696f381f5e10d https://github.com/galaxyproject/galaxy/commit/dfccd902b00426c79670e77ef116… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Fix setting metadata in galaxy.json for working directory isolation change. This has been broken since 16.04 I guess? Maybe retry internally means it hasn't been an issue? Commit: af6bd40a57608464e3e70226c46490681d213446 https://github.com/galaxyproject/galaxy/commit/af6bd40a57608464e3e70226c464… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Fix setting dbkey in galaxy.json for discovered primary datasets. Based on the change - I guess this must have been broken a long time ago - so maybe it isn't used? A subsequent change will add a test though - so hopefully there will be no regressions of this again. Commit: e72201d2041a80db0042af9493b1f2f1512d68f7 https://github.com/galaxyproject/galaxy/commit/e72201d2041a80db0042af9493b1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M lib/galaxy/jobs/__init__.py M test/base/interactor.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_1.xml Log Message: ----------- Improvements for metadata specification w/galaxy.json of explicit outputs. I call explicit outputs galaxy.json entries of type="dataset" (as opposed to type="new_primary_dataset" - which I call discovered datasets). Previously galaxy.json could set the name and extension of these datasets. I've added a test case to verify this and a small tweak to the tool test framework to allow easy testing of such metadata setting. In order to bring explicit output metadata setting closer to parity with discovered dataset metadata setting, I've added the ability to define 'dbkey' and 'info' entries in galaxy.json for these outputs. Commit: 1fab4dfaff3ebbb0f1c80c7b51f44125272b6cb9 https://github.com/galaxyproject/galaxy/commit/1fab4dfaff3ebbb0f1c80c7b51f4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M test/base/interactor.py M test/functional/tools/tool_provided_metadata_1.xml Log Message: ----------- Add hack to test sleeping when verifying metadata. Seems like a race condition but I can't determine why there would be one here - this check should help determine if it is a race condition or something else. Commit: 76e84eb5e00e78e9e49667d39b2f3d91352f3d5a https://github.com/galaxyproject/galaxy/commit/76e84eb5e00e78e9e49667d39b2f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_2.xml Log Message: ----------- Add tool test for discovered dataset metadata from galaxy.json. Commit: 41701aa6fe696e2ef1b26dec261f416686d02e20 https://github.com/galaxyproject/galaxy/commit/41701aa6fe696e2ef1b26dec261f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M test/base/interactor.py Log Message: ----------- Improved error message when testing metadata in tool tests. Commit: 56bb42ad2536732c195c218c1b89cf174cd02b78 https://github.com/galaxyproject/galaxy/commit/56bb42ad2536732c195c218c1b89… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M lib/galaxy/tools/parser/xml.py M test/functional/tools/tool_provided_metadata_2.xml Log Message: ----------- Fix allow tool to just test discovered datasets. Previously some sort of test on the base file the primary datasets were keyed on was required. Commit: 9ae333987b2cd713526ae68800ade5e0a73b1e08 https://github.com/galaxyproject/galaxy/commit/9ae333987b2cd713526ae68800ad… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M test/base/interactor.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_3.xml Log Message: ----------- Test tool demo-ing discovered dataset datatype metadata w/galaxy.json. Also update the metadata test comparison to support non-textual values (e.g. floating point and integer metadata fields). Commit: 1e8dd73b6def69aa8533f087e22d99d3423f94b3 https://github.com/galaxyproject/galaxy/commit/1e8dd73b6def69aa8533f087e22d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Rework small for loop per @mvdbeek's suggestion... ... see https://github.com/galaxyproject/galaxy/pull/2697#discussion_r74939815 for context. Commit: 5cc3613ff55537df7dbcfe7d6ba7ef4a679be935 https://github.com/galaxyproject/galaxy/commit/5cc3613ff55537df7dbcfe7d6ba7… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-17 (Wed, 17 Aug 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/xml.py M lib/galaxy_ext/metadata/set_metadata.py M test/base/interactor.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_1.xml A test/functional/tools/tool_provided_metadata_2.xml A test/functional/tools/tool_provided_metadata_3.xml Log Message: ----------- Merge pull request #2697 from jmchilton/metadata_fixing Fixes and improvements for galaxy.json. Compare: https://github.com/galaxyproject/galaxy/compare/0210fb31b676...5cc3613ff555

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[galaxyproject/galaxy] 510290: Add example of regressed 16.04 behavior related to...
by GitHub 17 Aug '16

17 Aug '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 510290feea4bb328566770b636f9f093d00e93b0 https://github.com/galaxyproject/galaxy/commit/510290feea4bb328566770b636f9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: A test/functional/tools/dbkey_output_action.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add example of regressed 16.04 behavior related to dbkey output actions. Commit: 88d02dba6e851f0f60758a575920f6e7b130e261 https://github.com/galaxyproject/galaxy/commit/88d02dba6e851f0f60758a575920… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Don't fill in a cheetah default if unavailable. ... in metadata hack from #961. Commit: 0110d5a05a4b1b357a3f321471fce1b2d4960e67 https://github.com/galaxyproject/galaxy/commit/0110d5a05a4b1b357a3f321471fc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M test/functional/tools/dbkey_output_action.xml Log Message: ----------- Add a test case to dbkey_output_action.xml. Per @nsoranzo's template and suggestion. Commit: e06cf9a97802d4c6a2ab97d973a373675e68b751 https://github.com/galaxyproject/galaxy/commit/e06cf9a97802d4c6a2ab97d973a3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/util/template.py Log Message: ----------- Add None check to fill_template... ... as requested by @nsoranzo. Commit: d1c58f7ab039cc457d7e3fc97857cd2c314c5e5c https://github.com/galaxyproject/galaxy/commit/d1c58f7ab039cc457d7e3fc97857… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-17 (Wed, 17 Aug 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py M lib/galaxy/util/template.py A test/functional/tools/dbkey_output_action.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #2800 from jmchilton/dbkey_output_without_cond [16.04] Fix dbkey problem discovered by @hrhotz Compare: https://github.com/galaxyproject/galaxy/compare/752df7f82b12...d1c58f7ab039

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[galaxyproject/galaxy] 43320a: Conda explicitly checks for .sh in the command as ...
by GitHub 16 Aug '16

16 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 43320aa8d1443c3ca3b95185544ae27817ba71b6 https://github.com/galaxyproject/galaxy/commit/43320aa8d1443c3ca3b95185544a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Conda explicitly checks for .sh in the command as a part of it's logic to figure out that the shell is sh or bash compatible. Commit: 752df7f82b129d9a6f827f2421ffdb135ee111bc https://github.com/galaxyproject/galaxy/commit/752df7f82b129d9a6f827f2421ff… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #2788 from dannon/backport_condainstall [16.04] Conda explicitly checks for .sh in the command as a part of it's logi… Commit: 8d512c98e237b20235bddbd74424b3c0e09c0f1c https://github.com/galaxyproject/galaxy/commit/8d512c98e237b20235bddbd74424… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: 0210fb31b67635fe134b3c79e7abe3fb353c822e https://github.com/galaxyproject/galaxy/commit/0210fb31b67635fe134b3c79e7ab… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge branch 'release_16.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/3af38018a57c...0210fb31b676

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[galaxyproject/galaxy] 43320a: Conda explicitly checks for .sh in the command as ...
by GitHub 16 Aug '16

16 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 43320aa8d1443c3ca3b95185544ae27817ba71b6 https://github.com/galaxyproject/galaxy/commit/43320aa8d1443c3ca3b95185544a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Conda explicitly checks for .sh in the command as a part of it's logic to figure out that the shell is sh or bash compatible. Commit: 752df7f82b129d9a6f827f2421ffdb135ee111bc https://github.com/galaxyproject/galaxy/commit/752df7f82b129d9a6f827f2421ff… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #2788 from dannon/backport_condainstall [16.04] Conda explicitly checks for .sh in the command as a part of it's logi… Commit: 8d512c98e237b20235bddbd74424b3c0e09c0f1c https://github.com/galaxyproject/galaxy/commit/8d512c98e237b20235bddbd74424… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Compare: https://github.com/galaxyproject/galaxy/compare/a13117fdf570...8d512c98e237

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[galaxyproject/galaxy] 43320a: Conda explicitly checks for .sh in the command as ...
by GitHub 16 Aug '16

16 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 43320aa8d1443c3ca3b95185544ae27817ba71b6 https://github.com/galaxyproject/galaxy/commit/43320aa8d1443c3ca3b95185544a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Conda explicitly checks for .sh in the command as a part of it's logic to figure out that the shell is sh or bash compatible. Commit: 752df7f82b129d9a6f827f2421ffdb135ee111bc https://github.com/galaxyproject/galaxy/commit/752df7f82b129d9a6f827f2421ff… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #2788 from dannon/backport_condainstall [16.04] Conda explicitly checks for .sh in the command as a part of it's logi… Commit: bcfcd8184f297abc9f2e90fbf7504be08725600e https://github.com/galaxyproject/galaxy/commit/bcfcd8184f297abc9f2e90fbf750… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge branch 'release_16.04' Compare: https://github.com/galaxyproject/galaxy/compare/f8cf6f834bd9...bcfcd8184f29

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[galaxyproject/infrastructure-playbook] c79aa6: Missed one
by GitHub 16 Aug '16

16 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c79aa649300f70fec8462928c11d314b9603d31f https://github.com/galaxyproject/infrastructure-playbook/commit/c79aa649300… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M taccenv/group_vars/galaxyservers.yml Log Message: ----------- Missed one

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[galaxyproject/infrastructure-playbook] 58c9e2: Create Galaxy directories
by GitHub 16 Aug '16

16 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 58c9e218f4e1bfeefe7188bbe9a6b12b0111fd49 https://github.com/galaxyproject/infrastructure-playbook/commit/58c9e218f4e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M taccenv/group_vars/galaxyservers.yml A taccenv/group_vars/maingalaxyservers.yml A taccenv/group_vars/testgalaxyservers.yml Log Message: ----------- Create Galaxy directories

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[galaxyproject/galaxy] 43320a: Conda explicitly checks for .sh in the command as ...
by GitHub 16 Aug '16

16 Aug '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 43320aa8d1443c3ca3b95185544ae27817ba71b6 https://github.com/galaxyproject/galaxy/commit/43320aa8d1443c3ca3b95185544a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Conda explicitly checks for .sh in the command as a part of it's logic to figure out that the shell is sh or bash compatible. Commit: 752df7f82b129d9a6f827f2421ffdb135ee111bc https://github.com/galaxyproject/galaxy/commit/752df7f82b129d9a6f827f2421ff… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #2788 from dannon/backport_condainstall [16.04] Conda explicitly checks for .sh in the command as a part of it's logi… Compare: https://github.com/galaxyproject/galaxy/compare/ceeef39edb55...752df7f82b12

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[galaxyproject/usegalaxy-playbook] 2fd86c: Update Test
by GitHub 16 Aug '16

16 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2fd86c6db792153e0a26ac74abb46f08ab13dc88 https://github.com/galaxyproject/usegalaxy-playbook/commit/2fd86c6db792153e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M stage/galaxy_version.yml M stage/group_vars/galaxyservers.yml Log Message: ----------- Update Test Commit: dcfc8bcc28e3dd46d45c984c608c9371574e2bd0 https://github.com/galaxyproject/usegalaxy-playbook/commit/dcfc8bcc28e3dd46… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M production/galaxy_version.yml M production/group_vars/galaxyservers.yml Log Message: ----------- Update Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/c7c0a524a778...…

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