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

[galaxyproject/galaxy] d8196a: Add sam_to_bam to list of tools requiring Galaxy's...
by GitHub 27 Jan '17

27 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d8196a5808f13c499afba791ea0677f949a943cd https://github.com/galaxyproject/galaxy/commit/d8196a5808f13c499afba791ea06… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Add sam_to_bam to list of tools requiring Galaxy's environment. Only a very old version of sam_to_bam required this - but I guess it is actively used on usegalaxy.org since there was a bug report from @jennaj. Commit: 457083a7b7678948a48fbf6b8fed562ab988cf17 https://github.com/galaxyproject/galaxy/commit/457083a7b7678948a48fbf6b8fed… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3502 from jmchilton/galaxy_lib_tool_fixes [17.01] Add sam_to_bam to list of tools requiring Galaxy's environment. Compare: https://github.com/galaxyproject/galaxy/compare/3a44c793e3fb...457083a7b767

1 0

[galaxyproject/galaxy] ebfd74: Fix selenium workflow tests broken with #3181.
by GitHub 27 Jan '17

27 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ebfd740025893269940e67d4df8b446632bd9e76 https://github.com/galaxyproject/galaxy/commit/ebfd740025893269940e67d4df8b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Fix selenium workflow tests broken with #3181. Commit: 3a44c793e3fb9a27b47820b5c956b15b63043548 https://github.com/galaxyproject/galaxy/commit/3a44c793e3fb9a27b47820b5c956… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Merge pull request #3504 from jmchilton/selenium_fixes_4 Fix selenium workflow tests broken with #3181. Compare: https://github.com/galaxyproject/galaxy/compare/9de375fd01ca...3a44c793e3fb

1 0

[galaxyproject/galaxy] 9a8a0a: include example of deps pinning
by GitHub 27 Jan '17

27 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9a8a0a9efec63cefbc17dcede4b8046116ed9aaa https://github.com/galaxyproject/galaxy/commit/9a8a0a9efec63cefbc17dcede4b8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-26 (Thu, 26 Jan 2017) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- include example of deps pinning Commit: 9de375fd01caef39454dd18c0b5962e266291479 https://github.com/galaxyproject/galaxy/commit/9de375fd01caef39454dd18c0b59… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #3496 from martenson/enhance-release-doc improve release issue docs Compare: https://github.com/galaxyproject/galaxy/compare/f8ef6e33a802...9de375fd01ca

1 0

[galaxyproject/usegalaxy-playbook] 8d4d5c: Add public galaxy servers redirect to 'new' for an...
by GitHub 26 Jan '17

26 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8d4d5c3d2b633eebd774d054aa7db5106c81aaa6 https://github.com/galaxyproject/usegalaxy-playbook/commit/8d4d5c3d2b633eeb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-26 (Thu, 26 Jan 2017) Changed paths: M templates/nginx/galaxyproject.j2 Log Message: ----------- Add public galaxy servers redirect to 'new' for an interim URL.

1 0

[galaxyproject/infrastructure-playbook] 05d240: Update getgalaxy redirect.
by GitHub 26 Jan '17

26 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 05d2406ed67f480e856670039653a7d229fecf3d https://github.com/galaxyproject/infrastructure-playbook/commit/05d2406ed67… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-26 (Thu, 26 Jan 2017) Changed paths: M galaxyenv/templates/nginx/galaxydomains.j2 Log Message: ----------- Update getgalaxy redirect.

1 0

[galaxyproject/galaxy] 780119: Python3: use @six.add_metaclass() decorator
by GitHub 25 Jan '17

25 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 78011993a1c57485e0711e7ae7ec93aadb8452fc https://github.com/galaxyproject/galaxy/commit/78011993a1c57485e0711e7ae7ec… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/auth/providers/__init__.py M lib/galaxy/dataset_collections/types/__init__.py M lib/galaxy/jobs/datasets.py M lib/galaxy/jobs/metrics/instrumenters/__init__.py M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/job/__init__.py M lib/galaxy/jobs/runners/util/cli/job/slurm.py M lib/galaxy/jobs/runners/util/cli/shell/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/jobs/runners/util/condor/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/runners/util/retry.py M lib/galaxy/jobs/runners/util/sudo.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/installable.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/tools/toolbox/tags.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/workflow/schedulers/__init__.py M lib/galaxy_utils/sequence/sequence.py Log Message: ----------- Python3: use @six.add_metaclass() decorator Also fix import order. Commit: f8ef6e33a802aeb9eab06f7ca6ff039ed40e8df5 https://github.com/galaxyproject/galaxy/commit/f8ef6e33a802aeb9eab06f7ca6ff… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/auth/providers/__init__.py M lib/galaxy/dataset_collections/types/__init__.py M lib/galaxy/jobs/datasets.py M lib/galaxy/jobs/metrics/instrumenters/__init__.py M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/job/__init__.py M lib/galaxy/jobs/runners/util/cli/job/slurm.py M lib/galaxy/jobs/runners/util/cli/shell/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/jobs/runners/util/condor/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/runners/util/retry.py M lib/galaxy/jobs/runners/util/sudo.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/installable.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/tools/toolbox/tags.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/workflow/schedulers/__init__.py M lib/galaxy_utils/sequence/sequence.py Log Message: ----------- Merge pull request #3491 from nsoranzo/python3 Python3: use @six.add_metaclass() decorator Compare: https://github.com/galaxyproject/galaxy/compare/c163b70af23e...f8ef6e33a802

1 0

[galaxyproject/usegalaxy-playbook] 372e04: update MTS to 17.01
by GitHub 25 Jan '17

25 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 372e044baebdbc6b604138004ffc270ebd06d541 https://github.com/galaxyproject/usegalaxy-playbook/commit/372e044baebdbc6b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M production/group_vars/toolshedservers.yml Log Message: ----------- update MTS to 17.01

1 0

[galaxyproject/usegalaxy-playbook] cc08c4: Run update docker commands as the galaxy user
by GitHub 25 Jan '17

25 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: cc08c4faf5b51e05158368b87dfb4c68830d7f37 https://github.com/galaxyproject/usegalaxy-playbook/commit/cc08c4faf5b51e05… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M galaxy.yml Log Message: ----------- Run update docker commands as the galaxy user

1 0

[galaxyproject/usegalaxy-playbook] cfd8d1: switch Main to release_17.01
by GitHub 25 Jan '17

25 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: cfd8d165cc8011898461131de74255f801491fab https://github.com/galaxyproject/usegalaxy-playbook/commit/cfd8d165cc801189… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M production/galaxy_version.yml Log Message: ----------- switch Main to release_17.01

1 0

[galaxyproject/galaxy] a43d70: Dependency resolver documentation fixes
by GitHub 25 Jan '17

25 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a43d70e9bc694d50ebd091a8e2fed372c5a17e77 https://github.com/galaxyproject/galaxy/commit/a43d70e9bc694d50ebd091a8e2fe… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst Log Message: ----------- Dependency resolver documentation fixes Commit: c163b70af23effdd3a370c16b13120af586d6eb6 https://github.com/galaxyproject/galaxy/commit/c163b70af23effdd3a370c16b131… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst Log Message: ----------- Merge pull request #3490 from nsoranzo/followup_on_3483 Dependency resolver documentation fixes Compare: https://github.com/galaxyproject/galaxy/compare/27ec016cdf06...c163b70af23e

1 0