October 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 18977d: Don't load hidden tools into the tool panel at all...
by GitHub 02 Oct '17

02 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 18977d4132556a0c2bd0348db510cf765d434e6a https://github.com/galaxyproject/galaxy/commit/18977d4132556a0c2bd0348db510… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-29 (Fri, 29 Sep 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Don't load hidden tools into the tool panel at all. Commit: 2eed478545857ab2c3b4c958bc3e2c360656af42 https://github.com/galaxyproject/galaxy/commit/2eed478545857ab2c3b4c958bc3e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Update conda channel order to sync with Bioconda Commit: a5b7dce09fb690f09d25f1b806d3339bdf2171c9 https://github.com/galaxyproject/galaxy/commit/a5b7dce09fb690f09d25f1b806d3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Remove _ensure_conda_context() function and make conda_context argument mandatory in functions/methods. This should help making sure the correct context (e.g. channels) is used for all Conda operations. Also remove unused is_target_available() function. Conflicts: lib/galaxy/tools/deps/conda_util.py Commit: 3551386a1ac667e0d2f7c6e82256d180aa5100f7 https://github.com/galaxyproject/galaxy/commit/3551386a1ac667e0d2f7c6e82256… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Override channel list on the command line instead of modifying condarc The way we were modifying condarc in the ensure_channels_configured() method was broken because we were appending the missing channels at the end, so the final order may not be the one specified in conda_ensure_channels . Also: - not modifying the user condarc is a much better approach - overriding the channel list on the command line will make debugging easier Commit: 04a572e509e875414b07e73c295f1c4bb37c1e0c https://github.com/galaxyproject/galaxy/commit/04a572e509e875414b07e73c295f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #4726 from natefoo/panel-hidden-fix [17.09] If the newest version of a tool is hidden, load the newest older version, if any, into the tool panel Commit: 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071 https://github.com/galaxyproject/galaxy/commit/81ece2551cea27cbd0e718ef5b7a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #4731 from nsoranzo/release_17.05_backport_4409 [17.05] Backport #4409 Commit: 280dc48c386f41c850ae3bbf9971979296b5abbc https://github.com/galaxyproject/galaxy/commit/280dc48c386f41c850ae3bbf9971… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-02 (Mon, 02 Oct 2017) Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Commit: 3d87afbb4174be1068aa701ca4d36d3b3f89591c https://github.com/galaxyproject/galaxy/commit/3d87afbb4174be1068aa701ca4d3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge branch 'release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/068c61a310e6...3d87afbb4174

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[galaxyproject/galaxy] 2eed47: Update conda channel order to sync with Bioconda
by GitHub 02 Oct '17

02 Oct '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 2eed478545857ab2c3b4c958bc3e2c360656af42 https://github.com/galaxyproject/galaxy/commit/2eed478545857ab2c3b4c958bc3e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Update conda channel order to sync with Bioconda Commit: a5b7dce09fb690f09d25f1b806d3339bdf2171c9 https://github.com/galaxyproject/galaxy/commit/a5b7dce09fb690f09d25f1b806d3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Remove _ensure_conda_context() function and make conda_context argument mandatory in functions/methods. This should help making sure the correct context (e.g. channels) is used for all Conda operations. Also remove unused is_target_available() function. Conflicts: lib/galaxy/tools/deps/conda_util.py Commit: 3551386a1ac667e0d2f7c6e82256d180aa5100f7 https://github.com/galaxyproject/galaxy/commit/3551386a1ac667e0d2f7c6e82256… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Override channel list on the command line instead of modifying condarc The way we were modifying condarc in the ensure_channels_configured() method was broken because we were appending the missing channels at the end, so the final order may not be the one specified in conda_ensure_channels . Also: - not modifying the user condarc is a much better approach - overriding the channel list on the command line will make debugging easier Commit: 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071 https://github.com/galaxyproject/galaxy/commit/81ece2551cea27cbd0e718ef5b7a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #4731 from nsoranzo/release_17.05_backport_4409 [17.05] Backport #4409 Commit: 280dc48c386f41c850ae3bbf9971979296b5abbc https://github.com/galaxyproject/galaxy/commit/280dc48c386f41c850ae3bbf9971… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-02 (Mon, 02 Oct 2017) Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Compare: https://github.com/galaxyproject/galaxy/compare/04a572e509e8...280dc48c386f

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[galaxyproject/galaxy] 2eed47: Update conda channel order to sync with Bioconda
by GitHub 02 Oct '17

02 Oct '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 2eed478545857ab2c3b4c958bc3e2c360656af42 https://github.com/galaxyproject/galaxy/commit/2eed478545857ab2c3b4c958bc3e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Update conda channel order to sync with Bioconda Commit: a5b7dce09fb690f09d25f1b806d3339bdf2171c9 https://github.com/galaxyproject/galaxy/commit/a5b7dce09fb690f09d25f1b806d3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Remove _ensure_conda_context() function and make conda_context argument mandatory in functions/methods. This should help making sure the correct context (e.g. channels) is used for all Conda operations. Also remove unused is_target_available() function. Conflicts: lib/galaxy/tools/deps/conda_util.py Commit: 3551386a1ac667e0d2f7c6e82256d180aa5100f7 https://github.com/galaxyproject/galaxy/commit/3551386a1ac667e0d2f7c6e82256… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Override channel list on the command line instead of modifying condarc The way we were modifying condarc in the ensure_channels_configured() method was broken because we were appending the missing channels at the end, so the final order may not be the one specified in conda_ensure_channels . Also: - not modifying the user condarc is a much better approach - overriding the channel list on the command line will make debugging easier Commit: 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071 https://github.com/galaxyproject/galaxy/commit/81ece2551cea27cbd0e718ef5b7a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #4731 from nsoranzo/release_17.05_backport_4409 [17.05] Backport #4409 Compare: https://github.com/galaxyproject/galaxy/compare/cfabe37d6954...81ece2551cea

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[galaxyproject/galaxy] 18977d: Don't load hidden tools into the tool panel at all...
by GitHub 02 Oct '17

02 Oct '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 18977d4132556a0c2bd0348db510cf765d434e6a https://github.com/galaxyproject/galaxy/commit/18977d4132556a0c2bd0348db510… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-29 (Fri, 29 Sep 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Don't load hidden tools into the tool panel at all. Commit: 04a572e509e875414b07e73c295f1c4bb37c1e0c https://github.com/galaxyproject/galaxy/commit/04a572e509e875414b07e73c295f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #4726 from natefoo/panel-hidden-fix [17.09] If the newest version of a tool is hidden, load the newest older version, if any, into the tool panel Compare: https://github.com/galaxyproject/galaxy/compare/38b19d4c47d2...04a572e509e8

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[galaxyproject/galaxy] 10b9ac: Stricter checks for SDF sniffing
by GitHub 01 Oct '17

01 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 10b9ac8c7de9e7f2c04d6a25777209abb350a0cc https://github.com/galaxyproject/galaxy/commit/10b9ac8c7de9e7f2c04d6a257772… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-29 (Fri, 29 Sep 2017) Changed paths: M lib/galaxy/datatypes/molecules.py Log Message: ----------- Stricter checks for SDF sniffing I had a bunch of protein FASTA files being sniffed as 'sdf'. Also fix https://github.com/galaxyproject/galaxy/issues/4558 . Commit: e3307c5be96d479dc7731fbfefefbb1bc6854fa5 https://github.com/galaxyproject/galaxy/commit/e3307c5be96d479dc7731fbfefef… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2017-10-01 (Sun, 01 Oct 2017) Changed paths: M lib/galaxy/datatypes/molecules.py A lib/galaxy/datatypes/test/chebi_57262.v3k.mol A lib/galaxy/datatypes/test/github88.v3k.sdf Log Message: ----------- More precise SDF sniffer First check 4th line: if this is conforming, scan up to 10000 lines. Add 2 test files downloaded from: https://github.com/rdkit/rdkit/tree/master/Code/GraphMol/FileParsers/test_d… Commit: 068c61a310e65055a5a7b6747696f71d0fdb0e7f https://github.com/galaxyproject/galaxy/commit/068c61a310e65055a5a7b6747696… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-01 (Sun, 01 Oct 2017) Changed paths: M lib/galaxy/datatypes/molecules.py A lib/galaxy/datatypes/test/chebi_57262.v3k.mol A lib/galaxy/datatypes/test/github88.v3k.sdf Log Message: ----------- Merge pull request #4729 from nsoranzo/fix_molecule_datatypes Stricter checks for SDF sniffing Compare: https://github.com/galaxyproject/galaxy/compare/73bb4ba8c2e5...068c61a310e6

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[galaxyproject/infrastructure-playbook] 3755a8: Make mjolnir0 a jenkins builder.
by GitHub 01 Oct '17

01 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 3755a8de3d7ee468278dbc9240591083117cb819 https://github.com/galaxyproject/infrastructure-playbook/commit/3755a8de3d7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-30 (Sat, 30 Sep 2017) Changed paths: M common_roles M galaxyenv/files/jenkins/jenkins_server_user_ssh_config M galaxyenv/group_vars/jenkinsslaves.yml M galaxyenv/group_vars/starforgebuilders.yml M galaxyenv/inventory Log Message: ----------- Make mjolnir0 a jenkins builder. Commit: 46d7c1bd9c5fc74d5042071080b1cf36095f1804 https://github.com/galaxyproject/infrastructure-playbook/commit/46d7c1bd9c5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-01 (Sun, 01 Oct 2017) Changed paths: M galaxyenv/templates/nginx/galaxydomains.j2 Log Message: ----------- Fix gdc2010/gcc2011 redirects from galaxy.psu.edu. Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/fd16374d80…

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