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

[galaxyproject/infrastructure-playbook] f35e16: Fix Jetstream node mount points
by GitHub 08 Apr '16

08 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: f35e1659581e8fe4bc433accb393b2e862b0f73a https://github.com/galaxyproject/infrastructure-playbook/commit/f35e1659581… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M jetstreamiuenv/group_vars/galaxynodes.yml M jetstreamtaccenv/group_vars/galaxynodes.yml M roles/jetstream_nfs/tasks/main.yml Log Message: ----------- Fix Jetstream node mount points

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[galaxyproject/infrastructure-playbook] ed50d1: Add TACC Jetstream stuff
by GitHub 08 Apr '16

08 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: ed50d1a2f94f9874a30dd17fd9dea9c5235ef822 https://github.com/galaxyproject/infrastructure-playbook/commit/ed50d1a2f94… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: A galaxyenv/host_vars/cvmfs1-tacc0.galaxyproject.org.yml A jetstreamiuenv/group_vars/controllers.yml M jetstreamiuenv/group_vars/galaxynodes.yml A jetstreamtaccenv/group_vars/all.yml A jetstreamtaccenv/group_vars/controllers.yml A jetstreamtaccenv/group_vars/cvmfsclients.yml A jetstreamtaccenv/group_vars/galaxynodes.yml A jetstreamtaccenv/group_vars/slurmclients.yml A jetstreamtaccenv/instance_inventory A jetstreamtaccenv/inventory A jetstreamtaccenv/playbook.yml A jetstreamtaccenv/secret_group_vars/slurmclients.yml A jetstreamtaccenv/templates/slurm/slurm.conf.j2 R roles/jetstream_nfs/vars/main.yml Log Message: ----------- Add TACC Jetstream stuff

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[galaxyproject/galaxy]
by GitHub 08 Apr '16

08 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] 90b95d: Merge pull request #2043 from martenson/update_mer...
by GitHub 08 Apr '16

08 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 90b95dc665bd736a21bd16d2852caf5c23bb83c4 https://github.com/galaxyproject/galaxy/commit/90b95dc665bd736a21bd16d2852c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #2043 from martenson/update_mercurial_wheel [16.01] upgrade mercurial wheel to latest (fixing CVE issues) Commit: 20f61e6a2f36967e16a92cbcf8ad7f81ca76fb29 https://github.com/galaxyproject/galaxy/commit/20f61e6a2f36967e16a92cbcf8ad… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- workaround for error message in case original toolshed had been disabled Commit: 65a7ebee23364a89d72e528bfcde6b1f6b3c5cd9 https://github.com/galaxyproject/galaxy/commit/65a7ebee23364a89d72e528bfcde… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #2072 from mvdbeek/backport_1738 [16.01] backport #1738 Commit: 2a53be67ad4ac99b6e9fe5fb803bfa44442dbd3c https://github.com/galaxyproject/galaxy/commit/2a53be67ad4ac99b6e9fe5fb803b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Show sections in workflow run Commit: 3002e404ef17cd7db9b817085b2f3ed5a82bd109 https://github.com/galaxyproject/galaxy/commit/3002e404ef17cd7db9b817085b2f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Patch in visual separation of section parameters Commit: 040410b1d3f0ea01374f183ee0b9447e0fc3cefb https://github.com/galaxyproject/galaxy/commit/040410b1d3f0ea01374f183ee0b9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #2092 from erasche/workflow-section-backport [16.01] Workflow section fix backport Commit: 9ecf99c227466a586a6299e37555655f5ff79a25 https://github.com/galaxyproject/galaxy/commit/9ecf99c227466a586a6299e37555… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-06 (Wed, 06 Apr 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- make dependencies browsable again it would be denied previously as the dependency folder is outside of the repository (symlink protection) Commit: 0882b4d8fb31752f1fa8c963c3f260f975c918f7 https://github.com/galaxyproject/galaxy/commit/0882b4d8fb31752f1fa8c963c3f2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-06 (Wed, 06 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py Log Message: ----------- use proper method for detecting admin Commit: 50268cb8ca4a5f812346a71cc640141781f22a3d https://github.com/galaxyproject/galaxy/commit/50268cb8ca4a5f812346a71cc640… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-07 (Thu, 07 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- fix missing call; add docs and refactor a bit Commit: 455113d182236a0fec880db296b746a413a8edc4 https://github.com/galaxyproject/galaxy/commit/455113d182236a0fec880db296b7… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #2101 from martenson/fix-browsing-dependencies [16.01] make dependencies browsable again Commit: 094580909964c5fad91b1068917832bedaddf579 https://github.com/galaxyproject/galaxy/commit/094580909964c5fad91b10689178… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.01' into dev Commit: f377d069e2aa02434742b3061b2b300c50d6dd86 https://github.com/galaxyproject/galaxy/commit/f377d069e2aa02434742b3061b2b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #2115 from jmchilton/dev-merge Merge release into latest dev. Compare: https://github.com/galaxyproject/galaxy/compare/ce278630860e...f377d069e2aa

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[galaxyproject/galaxy] 4df7e4: Consolidate duplicated method.
by GitHub 08 Apr '16

08 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4df7e45f61f505d94b854c312d970a4a363bc50f https://github.com/galaxyproject/galaxy/commit/4df7e45f61f505d94b854c312d97… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-06 (Wed, 06 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/model/__init__.py Log Message: ----------- Consolidate duplicated method. Commit: 4b8b7b46476d0ec9d56b2710759e963938e53bd0 https://github.com/galaxyproject/galaxy/commit/4b8b7b46476d0ec9d56b2710759e… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-07 (Thu, 07 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Update which method is used in API. Commit: ce278630860e38e0e103c71fdae7674e2e40f56b https://github.com/galaxyproject/galaxy/commit/ce278630860e38e0e103c71fdae7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/model/__init__.py Log Message: ----------- Merge pull request #2099 from davebx/shed_model_trim Consolidate duplicated method in tool_shed/model. Compare: https://github.com/galaxyproject/galaxy/compare/0d616af28a17...ce278630860e

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[galaxyproject/galaxy] b4e768: Workaround for the toolshed's hgweb.
by GitHub 08 Apr '16

08 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b4e768b82804c54d107c8cf866e3814135867211 https://github.com/galaxyproject/galaxy/commit/b4e768b82804c54d107c8cf866e3… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-07 (Thu, 07 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/hg.py Log Message: ----------- Workaround for the toolshed's hgweb. Commit: 2a76eb19c1d8d442859ea33b19100689ca6bf1fb https://github.com/galaxyproject/galaxy/commit/2a76eb19c1d8d442859ea33b1910… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-07 (Thu, 07 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/hg.py Log Message: ----------- Remove unused import, restore used import. Commit: 5ead1c089f2f2a3f06ee55ac77be1d9f89a377ae https://github.com/galaxyproject/galaxy/commit/5ead1c089f2f2a3f06ee55ac77be… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/hg.py Log Message: ----------- Remove refactoring that belongs in a different PR. Commit: 0d616af28a175bae8e193f429a18f97cd8b274ec https://github.com/galaxyproject/galaxy/commit/0d616af28a175bae8e193f429a18… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Merge pull request #2106 from davebx/hg_middleware Workaround for the toolshed's hgweb. Compare: https://github.com/galaxyproject/galaxy/compare/6f6554ea8c7e...0d616af28a17

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[galaxyproject/galaxy] c720c0: Updated to Dependency change in b167a741a444c39884...
by GitHub 08 Apr '16

08 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c720c0fde89174445a6bbb96436d781bbbdc0941 https://github.com/galaxyproject/galaxy/commit/c720c0fde89174445a6bbb96436d… Author: Christian-B <github(a)brenn.co.uk> Date: 2016-04-07 (Thu, 07 Apr 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py Log Message: ----------- Updated to Dependency change in b167a741a444c3988447b0d63a1ba3dc5e4e62f5 Commit: 6f6554ea8c7e8f6511db0899ce5c8050056d802c https://github.com/galaxyproject/galaxy/commit/6f6554ea8c7e8f6511db0899ce5c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py Log Message: ----------- Merge pull request #2104 from Christian-B/unlinked_depenency_resolver_update_to_new_dependency Updated to Dependency change in b167a741a444c3988447b0d63a1ba3dc5e4e62f5 Compare: https://github.com/galaxyproject/galaxy/compare/f0272e02f7eb...6f6554ea8c7e

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[galaxyproject/galaxy] d6a7ac: Update debian init script
by GitHub 08 Apr '16

08 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d6a7acab996b7a157ce7de07117b523ae4e0fa46 https://github.com/galaxyproject/galaxy/commit/d6a7acab996b7a157ce7de07117b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M contrib/galaxy.debian-init Log Message: ----------- Update debian init script to include instructions for starting galaxy >= 16.01. Commit: f0272e02f7eb9b433c31eecaa5ce2986b2e728dd https://github.com/galaxyproject/galaxy/commit/f0272e02f7eb9b433c31eecaa5ce… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M contrib/galaxy.debian-init Log Message: ----------- Merge pull request #2109 from mvdbeek/fix_debian_init_script Update debian init script Compare: https://github.com/galaxyproject/galaxy/compare/4c7f187b353d...f0272e02f7eb

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[galaxyproject/galaxy] be1025: Remove stray print statements.
by GitHub 08 Apr '16

08 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: be10253b6947c8badfc71463d8331a1b53f5db9a https://github.com/galaxyproject/galaxy/commit/be10253b6947c8badfc71463d833… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/runtime_actions.py Log Message: ----------- Remove stray print statements. Not Python 3 compat. Commit: 0414c2628aa08d2303f6a50eb2cd556802ed416b https://github.com/galaxyproject/galaxy/commit/0414c2628aa08d2303f6a50eb2cd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M .ci/py3_sources.txt Log Message: ----------- Expand PY3 linting to include another galaxy-lib module. Commit: 4c7f187b353d0a476e8c482b090538c7f8970606 https://github.com/galaxyproject/galaxy/commit/4c7f187b353d0a476e8c482b0905… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M .ci/py3_sources.txt M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/runtime_actions.py Log Message: ----------- Merge pull request #2110 from jmchilton/remove_stray_prints galaxy-lib tweaks Compare: https://github.com/galaxyproject/galaxy/compare/2744d5541f7c...4c7f187b353d

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[galaxyproject/infrastructure-playbook] f2ae9a: Additional Jetstream fixes, launched what will hop...
by GitHub 08 Apr '16

08 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: f2ae9af45bf403d15bc91af6bcf54f7fb13cc102 https://github.com/galaxyproject/infrastructure-playbook/commit/f2ae9af45bf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M jetstreamiuenv/group_vars/galaxynodes.yml M jetstreamiuenv/group_vars/slurmclients.yml M jetstreamiuenv/inventory A roles/cvmfs/defaults/main.yml R roles/cvmfs/vars/main.yml M roles/jetstream_nfs/vars/main.yml M roles/slurm/handlers/main.yml M roles/slurm/tasks/main.yml Log Message: ----------- Additional Jetstream fixes, launched what will hopefully be the first "real" node

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