September 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 07cf96: Update Conda FAQ
by GitHub 02 Sep '16

02 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 07cf96c26053d8a0d0fe1a6365f6bf4272a3593d https://github.com/galaxyproject/galaxy/commit/07cf96c26053d8a0d0fe1a6365f6… Author: Enis Afgan <afgane(a)gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Update Conda FAQ Commit: ecdbf4d0b579f4dbae79a56aea1398224d9f2c93 https://github.com/galaxyproject/galaxy/commit/ecdbf4d0b579f4dbae79a56aea13… Author: Enis Afgan <afgane(a)gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Address PR #2891 comments Commit: 3cee333011bff6aed673429f361659132804f33c https://github.com/galaxyproject/galaxy/commit/3cee333011bff6aed673429f3616… Author: Enis Afgan <afgane(a)gmail.com> Date: 2016-09-02 (Fri, 02 Sep 2016) Changed paths: M lib/galaxy/tools/cwl/parser.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into dev Commit: 97b748c73a4eb169c5e1c6894ea2b30dbcc0343a https://github.com/galaxyproject/galaxy/commit/97b748c73a4eb169c5e1c6894ea2… Author: Enis Afgan <afgane(a)gmail.com> Date: 2016-09-02 (Fri, 02 Sep 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Shorten Conda environment naming as per https://github.com/galaxyproject/galaxy/commit/e9d81500caa3526200b204270aca… Thanks @lparsons. Commit: 2b6b5c82754a3ca9722e55d9828042e70d95d028 https://github.com/galaxyproject/galaxy/commit/2b6b5c82754a3ca9722e55d98280… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-02 (Fri, 02 Sep 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Merge pull request #2891 from afgane/dev Update Conda FAQ Compare: https://github.com/galaxyproject/galaxy/compare/a199590efa23...2b6b5c82754a

1 0

[galaxyproject/galaxy] 50c830: Small cwl fixes to sync with galaxy-lib.
by GitHub 01 Sep '16

01 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 50c8302b1525ebc2168bb0a9ab4439105d9317e7 https://github.com/galaxyproject/galaxy/commit/50c8302b1525ebc2168bb0a9ab44… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M lib/galaxy/tools/cwl/parser.py Log Message: ----------- Small cwl fixes to sync with galaxy-lib. description became doc in draft 1.0. Commit: a199590efa2378e2f1f865b8da68cc4fe12a33c1 https://github.com/galaxyproject/galaxy/commit/a199590efa2378e2f1f865b8da68… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M lib/galaxy/tools/cwl/parser.py Log Message: ----------- Merge pull request #2888 from jmchilton/cwl_fixes_from_lib Small cwl fixes to sync with galaxy-lib. Compare: https://github.com/galaxyproject/galaxy/compare/0d35f9435ad6...a199590efa23

1 0

[galaxyproject/galaxy] efac63: Restore database/info.txt.
by GitHub 01 Sep '16

01 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: efac63f7cd5a46a26eb9f27a78510f06e072b6b9 https://github.com/galaxyproject/galaxy/commit/efac63f7cd5a46a26eb9f27a7851… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: A database/info.txt Log Message: ----------- Restore database/info.txt. It was problematically removed with a recent PR and is causing Travis breakages - Galaxy assumes this directory exists. Commit: 0d35f9435ad6d9cd1636d7626dae97ad8d08027d https://github.com/galaxyproject/galaxy/commit/0d35f9435ad6d9cd1636d7626dae… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: A database/info.txt Log Message: ----------- Merge pull request #2887 from jmchilton/database_info_restore Restore database/info.txt. Compare: https://github.com/galaxyproject/galaxy/compare/55cd6d86333b...0d35f9435ad6

1 0

[galaxyproject/usegalaxy-playbook] d6dd8e: Update Main mutable configs
by GitHub 01 Sep '16

01 Sep '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d6dd8eec34ce9be4333bac5f6f1896489ab45e75 https://github.com/galaxyproject/usegalaxy-playbook/commit/d6dd8eec34ce9be4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Update Main mutable configs Commit: 186da5b95775c4d5023024a9f64c0f7f767d7c73 https://github.com/galaxyproject/usegalaxy-playbook/commit/186da5b95775c4d5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M common/secret_vars/ssl.yml M galaxy.yml M galaxy_infrastructure.yml M production/group_vars/galaxyjobservers.yml A production/group_vars/galaxystagingservers.yml M production/inventory M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 A templates/nginx/usegalaxy_staging.j2 Log Message: ----------- Stage Jetstream jobs through nginx/uWSGI on the job handler VM actually running the job. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/3cb0ebb01e16...…

1 0

[galaxyproject/galaxy] 75d2c0: Refactor - move filelock.py to galaxy.util.
by GitHub 01 Sep '16

01 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 75d2c0eac7a320a06ac1173045606fbd4bfbff72 https://github.com/galaxyproject/galaxy/commit/75d2c0eac7a320a06ac117304560… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-31 (Wed, 31 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py A lib/galaxy/util/filelock.py M lib/galaxy/web/proxy/__init__.py R lib/galaxy/web/proxy/filelock.py Log Message: ----------- Refactor - move filelock.py to galaxy.util. galaxy.tools.deps.resolvers.conda should not depend on galaxy.web.proxy - this is a smell that indicates filelock belongs in galaxy.util IMO. Commit: 55cd6d86333b63747c257911a16a68a42bb34828 https://github.com/galaxyproject/galaxy/commit/55cd6d86333b63747c257911a16a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py A lib/galaxy/util/filelock.py M lib/galaxy/web/proxy/__init__.py R lib/galaxy/web/proxy/filelock.py Log Message: ----------- Merge pull request #2879 from jmchilton/refactor_filelock Refactor - move filelock.py to galaxy.util. Compare: https://github.com/galaxyproject/galaxy/compare/3908a9a8361d...55cd6d86333b

1 0