September 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/infrastructure-playbook] 80bb94: Update README.md
by GitHub 15 Sep '15

15 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 80bb94e97d6cb83b07e1f40b2575a933734c2a72 https://github.com/galaxyproject/infrastructure-playbook/commit/80bb94e97d6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M README.md Log Message: ----------- Update README.md

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[galaxyproject/galaxy] 3fafbb: Fix more MissingToolException when running "./run_...
by GitHub 15 Sep '15

15 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3fafbb5e34ed3f6f547bf1f184782b0f6967cf2f https://github.com/galaxyproject/galaxy/commit/3fafbb5e34ed3f6f547bf1f18478… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M test/api/test_workflow_extraction.py Log Message: ----------- Fix more MissingToolException when running "./run_tests.sh -api" without "-with_framework_test_tools". Commit: 63d1715679fb714f4c8f5ae426106edf6988e7ab https://github.com/galaxyproject/galaxy/commit/63d1715679fb714f4c8f5ae42610… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix API tests using collection_creates_pair tool. Commit: 89b42bf0603433b2b66a264c9a3a3d3fe4e12280 https://github.com/galaxyproject/galaxy/commit/89b42bf0603433b2b66a264c9a3a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M lib/galaxy/tools/__init__.py M test/api/test_workflow_extraction.py Log Message: ----------- Merge pull request #731 from nsoranzo/dev Fix more API tests. Compare: https://github.com/galaxyproject/galaxy/compare/4671ae8d4509...89b42bf06034

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[galaxyproject/infrastructure-playbook] fb8175: add virtualenv to n2
by GitHub 15 Sep '15

15 Sep '15

Branch: refs/heads/martenson-patch-2 Home: https://github.com/galaxyproject/infrastructure-playbook Commit: fb81757b634892f1b717b68a7ee3275a5e1ec2e1 https://github.com/galaxyproject/infrastructure-playbook/commit/fb81757b634… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M galaxyenv/host_vars/n2.galaxyproject.org.yml Log Message: ----------- add virtualenv to n2

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[galaxyproject/infrastructure-playbook] 41f8d6: install postgresql-9.4 on n2
by GitHub 15 Sep '15

15 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 41f8d6cc7e261b9f200ccc8e0efb57e41d8e846f https://github.com/galaxyproject/infrastructure-playbook/commit/41f8d6cc7e2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M galaxyenv/host_vars/n2.galaxyproject.org.yml Log Message: ----------- install postgresql-9.4 on n2 Commit: eafac90f95fb5e7674655ccc98419d9d4f3341fc https://github.com/galaxyproject/infrastructure-playbook/commit/eafac90f95f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M galaxyenv/host_vars/n2.galaxyproject.org.yml Log Message: ----------- Merge pull request #1 from galaxyproject/martenson-patch-1 install postgresql-9.4 on n2 Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/113caf158f…

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[galaxyproject/galaxy] 23051d: When rerunning a job w/ remap, reassociate PostJob...
by GitHub 15 Sep '15

15 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 23051da68c88f1173be8094c2597cc60cb054f27 https://github.com/galaxyproject/galaxy/commit/23051da68c88f1173be8094c2597… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- When rerunning a job w/ remap, reassociate PostJobActions when possible to the new job. Commit: 4671ae8d45092824db2f7b19b7d6896e6524c672 https://github.com/galaxyproject/galaxy/commit/4671ae8d45092824db2f7b19b7d6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #730 from dannon/pja_wf_rerun_fix When rerunning a job w/ remap, reassociate PostJobActions when possib… Compare: https://github.com/galaxyproject/galaxy/compare/1ea1da02291d...4671ae8d4509

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[galaxyproject/galaxy] 8dadfd: remove no-op __init__ methods
by GitHub 15 Sep '15

15 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8dadfdcaa0492bce485fb786aed0d29243356258 https://github.com/galaxyproject/galaxy/commit/8dadfdcaa0492bce485fb786aed0… Author: Michael R. Crusoe <crusoe(a)ucdavis.edu> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- remove no-op __init__ methods Commit: 1ea1da02291d3d9abbec32a09d63a16ddcef1084 https://github.com/galaxyproject/galaxy/commit/1ea1da02291d3d9abbec32a09d63… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #729 from mr-c/drop-noop-init remove no-op __init__ methods from lib/galaxy/datatypes/binary.py Compare: https://github.com/galaxyproject/galaxy/compare/34165913ba1e...1ea1da02291d

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[galaxyproject/galaxy] 471664: Merge "Issues" and "Galaxy Development" from READM...
by GitHub 14 Sep '15

14 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 471664c2692315b6699c586efccb6c7522fd6b56 https://github.com/galaxyproject/galaxy/commit/471664c2692315b6699c586efccb… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-07 (Mon, 07 Sep 2015) Changed paths: M CONTRIBUTING.md M README.rst Log Message: ----------- Merge "Issues" and "Galaxy Development" from README.rst in CONTRIBUTING.md . Commit: 3f40b7ca8f41403cc00e9fbbc88d8b48b6be6259 https://github.com/galaxyproject/galaxy/commit/3f40b7ca8f41403cc00e9fbbc88d… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-07 (Mon, 07 Sep 2015) Changed paths: M CONTRIBUTING.md M doc/source/project/organization.rst Log Message: ----------- Move "Handling Pull Requests" from CONTRIBUTING.md to organization.rst . Commit: 34165913ba1e70ee72db363aeea74cc1824301ec https://github.com/galaxyproject/galaxy/commit/34165913ba1e70ee72db363aeea7… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M CONTRIBUTING.md M README.rst M doc/source/project/organization.rst Log Message: ----------- Merge pull request #702 from nsoranzo/readme_contributing [PROCEDURES] Reorganize content Compare: https://github.com/galaxyproject/galaxy/compare/08668104e5aa...34165913ba1e

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[galaxyproject/infrastructure-playbook] 41f8d6: install postgresql-9.4 on n2
by GitHub 14 Sep '15

14 Sep '15

Branch: refs/heads/martenson-patch-1 Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 41f8d6cc7e261b9f200ccc8e0efb57e41d8e846f https://github.com/galaxyproject/infrastructure-playbook/commit/41f8d6cc7e2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M galaxyenv/host_vars/n2.galaxyproject.org.yml Log Message: ----------- install postgresql-9.4 on n2

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[galaxyproject/galaxy] 85480e: Fix Galaxy.user to be available when not using 1 r...
by GitHub 14 Sep '15

14 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 85480e72bfa62306d19ac03ff60b4406f01146e0 https://github.com/galaxyproject/galaxy/commit/85480e72bfa62306d19ac03ff60b… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Fix Galaxy.user to be available when not using 1 require Commit: 08668104e5aa9c564dba561bab403439a65cd0fd https://github.com/galaxyproject/galaxy/commit/08668104e5aa9c564dba561bab40… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Merge pull request #728 from carlfeberhard/fix.galaxy-user Fix Galaxy.user to be available when not using 1 require Compare: https://github.com/galaxyproject/galaxy/compare/ba2505792259...08668104e5aa

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[galaxyproject/galaxy] 8f1d3c: Dedupe one of the worse offenders
by GitHub 14 Sep '15

14 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8f1d3cac8d4506053d252687194962b7ee81538d https://github.com/galaxyproject/galaxy/commit/8f1d3cac8d4506053d2526871949… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py Log Message: ----------- Dedupe one of the worse offenders Commit: 5415e295ac4bf00e9ed9a903ae908c06f57ee0d4 https://github.com/galaxyproject/galaxy/commit/5415e295ac4bf00e9ed9a903ae90… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/transfer_manager.py Log Message: ----------- Refactor sleeper duplications Commit: 673c1cdbca1ce3bf9ce561c3041d5fa33a8275e8 https://github.com/galaxyproject/galaxy/commit/673c1cdbca1ce3bf9ce561c3041d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Refactor identical role queries into a single function Commit: a71ac4ee3144e1463064730a297627c9797382f6 https://github.com/galaxyproject/galaxy/commit/a71ac4ee3144e1463064730a2976… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py A lib/galaxy/webapps/util.py Log Message: ----------- Refactor copy-pasted function into separate module Commit: 7cd241f0d9dfb0d4b20bd1c3902a1405258f682d https://github.com/galaxyproject/galaxy/commit/7cd241f0d9dfb0d4b20bd1c3902a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py A lib/galaxy/webapps/util.py Log Message: ----------- Merge branch 'big-dedup' into deduplication Commit: 1a2413f8793dee35ae237003f743ac80df17ef74 https://github.com/galaxyproject/galaxy/commit/1a2413f8793dee35ae237003f743… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py Log Message: ----------- Refactor duplicate calculation code in reports Commit: 6dd4b2b11f14882e3d129261de950e6b61e5bbc0 https://github.com/galaxyproject/galaxy/commit/6dd4b2b11f14882e3d129261de95… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py Log Message: ----------- Correct copy-pasted typo Commit: 28143581d9270dc880433dd80687a47076d9ccd1 https://github.com/galaxyproject/galaxy/commit/28143581d9270dc880433dd80687… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Make flake8 happy Commit: 1aa7ef12ec88e469f5e635b9c28cd4f9055ceb33 https://github.com/galaxyproject/galaxy/commit/1aa7ef12ec88e469f5e635b9c28c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py Log Message: ----------- Refactor into a single method and flake Commit: a437083d429f605485745ce82b19c4825c57c161 https://github.com/galaxyproject/galaxy/commit/a437083d429f605485745ce82b19… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/util/topsort.py Log Message: ----------- refactor completely duplicated numpreds/successor processing Commit: 15edae24c8e3fae058aa7c7d017d47467febb5ff https://github.com/galaxyproject/galaxy/commit/15edae24c8e3fae058aa7c7d017d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/util/topsort.py Log Message: ----------- Fix formatting error Commit: 5fc366f7f7fa1231b2c1c643f2e3ff4bae2d26de https://github.com/galaxyproject/galaxy/commit/5fc366f7f7fa1231b2c1c643f2e3… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Correct typo'd _get_roles function Commit: 060fdffda8b2d4b0c7aad3e460248b3793fdb69d https://github.com/galaxyproject/galaxy/commit/060fdffda8b2d4b0c7aad3e46024… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M lib/galaxy/webapps/util.py Log Message: ----------- Correct import for @nsoranzo Commit: d3fa5066ca6e9ee23a25427050d3573f522bb1e0 https://github.com/galaxyproject/galaxy/commit/d3fa5066ca6e9ee23a25427050d3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-07 (Mon, 07 Sep 2015) Changed paths: M lib/galaxy/webapps/util.py Log Message: ----------- Fix wrong local import of galaxy. Commit: f2d7917cfca995ba6c8ea77e0475360b59496576 https://github.com/galaxyproject/galaxy/commit/f2d7917cfca995ba6c8ea77e0475… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-07 (Mon, 07 Sep 2015) Changed paths: M lib/galaxy/webapps/util.py Log Message: ----------- Merge pull request #8 from nsoranzo/fix_for_erasche Fix wrong local import of galaxy. Commit: 1f3486cb517a54c7dd9ae4a8c9020d07745774f6 https://github.com/galaxyproject/galaxy/commit/1f3486cb517a54c7dd9ae4a8c902… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-07 (Mon, 07 Sep 2015) Changed paths: M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py Log Message: ----------- Initialized variables Commit: d95b1cd37a564f6f72e6bfc453b09ed010c3e19a https://github.com/galaxyproject/galaxy/commit/d95b1cd37a564f6f72e6bfc453b0… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-07 (Mon, 07 Sep 2015) Changed paths: M lib/galaxy/webapps/util.py Log Message: ----------- Merge branch 'deduplication' of github.com:erasche/galaxy into deduplication Commit: 17d8e15e4ee696610799a46abdf3d0379e9d23d5 https://github.com/galaxyproject/galaxy/commit/17d8e15e4ee696610799a46abdf3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/security/__init__.py M lib/galaxy/util/topsort.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py A lib/galaxy/webapps/util.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py Log Message: ----------- Merge remote-tracking branch 'erasche/deduplication' into deduplication-merge Conflicts: lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py Commit: 57634f43ea4ed82bf2603df80545604d795e3896 https://github.com/galaxyproject/galaxy/commit/57634f43ea4ed82bf2603df80545… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py Log Message: ----------- Fix lint problems from merge. How did that happen, those pieces of code were largely unrelated. Ekkk... Commit: ba25057922594b1d2878ccf5e96dd83ffc0843a3 https://github.com/galaxyproject/galaxy/commit/ba25057922594b1d2878ccf5e96d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/security/__init__.py M lib/galaxy/util/topsort.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py A lib/galaxy/webapps/util.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py Log Message: ----------- Merge pull request #694 from erasche/deduplication Deduplication PR Compare: https://github.com/galaxyproject/galaxy/compare/1ba64709e668...ba2505792259

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