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

[galaxyproject/galaxy] 97415d: Move idpDB and MzSQlite formats from proteomics.py...
by GitHub 03 Dec '15

03 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 97415de3ce2bda54fb0730a41b4e0c7d8e93778a https://github.com/galaxyproject/galaxy/commit/97415de3ce2bda54fb0730a41b4e… Author: chambm <matt.chambers42(a)gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/test.idpDB A lib/galaxy/datatypes/test/test.mz5 Log Message: ----------- Move idpDB and MzSQlite formats from proteomics.py to binary.py, because the SQLite sniffer lives there, and more specialized formats must be registered for sniffing before the generic format Add proper idpDB sniffing logic (akin to MzSQlite) and test case Add H5 sniffing based on magic number and test case Add SQLite/IdpDB/MzSQlite/GeminiSQLite and H5 to default datatypes in registry.py Commit: 65e6a1c3b6ca26e9f0d760cb39be7ec177d6c40f https://github.com/galaxyproject/galaxy/commit/65e6a1c3b6ca26e9f0d760cb39be… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/test.idpDB A lib/galaxy/datatypes/test/test.mz5 Log Message: ----------- Merge pull request #1209 from chambm/feature/idpdb_hdf5_sniffers Add idpDB and HDF5 sniffers and fix MzSQlite sniffer Compare: https://github.com/galaxyproject/galaxy/compare/c034dc3e33a4...65e6a1c3b6ca

1 0

[galaxyproject/galaxy] ee5a87: Fix for updating tool parameter dicts when a new p...
by GitHub 03 Dec '15

03 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: ee5a87af2e3d0a76da5df398826478bc4854c599 https://github.com/galaxyproject/galaxy/commit/ee5a87af2e3d0a76da5df3988264… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix for updating tool parameter dicts when a new parameter has been added to a section. Fixes issues seen during rerun under mentioned condition. Commit: d83e8d358f1b04683fa20245a66f12a8d881be4e https://github.com/galaxyproject/galaxy/commit/d83e8d358f1b04683fa20245a66f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1215 from blankenberg/rerunfix_15.10 [15.10] Fix for updating tool parameter dicts when a new parameter has been added to a section Compare: https://github.com/galaxyproject/galaxy/compare/30b13bb1d6e5...d83e8d358f1b

1 0

[galaxyproject/galaxy] 3de857: Add debug statement in output checker for why job ...
by GitHub 03 Dec '15

03 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3de8579633c4294abb2a3235f90463108c35d324 https://github.com/galaxyproject/galaxy/commit/3de8579633c4294abb2a3235f904… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/jobs/output_checker.py Log Message: ----------- Add debug statement in output checker for why job is failing. Should help tool testing and other Galaxy testing. Commit: c034dc3e33a4c4aeecefcea375ea179621be1af6 https://github.com/galaxyproject/galaxy/commit/c034dc3e33a4c4aeecefcea375ea… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/jobs/output_checker.py Log Message: ----------- Merge pull request #1213 from jmchilton/tool_logging_2 Add debug statement in output checker for why job is failing. Compare: https://github.com/galaxyproject/galaxy/compare/20b96d883d9e...c034dc3e33a4

1 0

[galaxyproject/galaxy] f64d15: Extension point for environment variables.
by GitHub 03 Dec '15

03 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f64d1597b84801dd48c2cdb5bc0c303355786942 https://github.com/galaxyproject/galaxy/commit/f64d1597b84801dd48c2cdb5bc0c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Extension point for environment variables. Commit: ea9f4a0467b6955ccc470da06eaf7c13e7643715 https://github.com/galaxyproject/galaxy/commit/ea9f4a0467b6955ccc470da06eaf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Initialize a ToolOutput.from_work_dir. Commit: 7ce43a0463c3d98b757d78d0600aadf5d7876eb9 https://github.com/galaxyproject/galaxy/commit/7ce43a0463c3d98b757d78d0600a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Refactor run_request for downstream diff improvements. Commit: 77ed5681f8565b12ab1d5e5c7d0302c938e9c73d https://github.com/galaxyproject/galaxy/commit/77ed5681f8565b12ab1d5e5c7d03… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M test/api/test_workflows.py Log Message: ----------- Extend base api workflow _run_jobs helper... ... to allow loading content from test-data files. Commit: 42778e27539d919ff11d67a07368c0b6e4ebae75 https://github.com/galaxyproject/galaxy/commit/42778e27539d919ff11d67a07368… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Improved error handling in workflow run code. Commit: 28501ab676f9df797bae316c3d24e9ae8fd58a9b https://github.com/galaxyproject/galaxy/commit/28501ab676f9df797bae316c3d24… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M test/unit/test_galaxy_mapping.py Log Message: ----------- Refactor workflow manager for extension. Commit: 4584a579a297ffd02bd77584b71a8c17d85d261a https://github.com/galaxyproject/galaxy/commit/4584a579a297ffd02bd77584b71a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix interface declaration for WorkflowModule.get_state. Implementers all take this attribute. Commit: 21213ef70f535e06bc485370686807a6d2850345 https://github.com/galaxyproject/galaxy/commit/21213ef70f535e06bc4853706868… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M test/unit/workflows/test_render.py M test/unit/workflows/workflow_support.py Log Message: ----------- Refactor workflow testing code to quickly bootstrap workflows. Commit: 031a39aba83932fd0291f440a7e58c962deadfe8 https://github.com/galaxyproject/galaxy/commit/031a39aba83932fd0291f440a7e5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: A test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py Log Message: ----------- Basic unit tests for workflow progress tracking. Commit: 8a01b42112ec32e5f978f3a4245127cad3219c45 https://github.com/galaxyproject/galaxy/commit/8a01b42112ec32e5f978f3a42451… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Refactor input_by_connections_name logic into model. Continue to delay calculation of this but auto-compute it if requested and module injection code hasn't been called explicitly. Moves logic internal to class where it belongs also. Commit: cf367ff0c75454837359b74046c05cc7cb456dc5 https://github.com/galaxyproject/galaxy/commit/cf367ff0c75454837359b74046c0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Add another workflow progress test case. This one for replacing a tool input with an input dataset. Commit: 7974c1f33486c0a66803004c5d7885a9d91b9c70 https://github.com/galaxyproject/galaxy/commit/7974c1f33486c0a66803004c5d78… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Add unit tests for workflow progress initialization. Commit: 07c3d10f31e48f783baf05c133b117e7f3e7ee1a https://github.com/galaxyproject/galaxy/commit/07c3d10f31e48f783baf05c133b1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Extend workflow recovery progress test case to include replacement check. Commit: 48340b5829fb5ca346060d9372ba7df7e3effcef https://github.com/galaxyproject/galaxy/commit/48340b5829fb5ca346060d9372ba… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Add TODO items to workflow progress unit tests. Commit: dd5f3aec52d1cec8e2a98dc9cf7134cd9b381d84 https://github.com/galaxyproject/galaxy/commit/dd5f3aec52d1cec8e2a98dc9cf71… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M test/api/test_workflows.py Log Message: ----------- Fix workflow extraction test cases broken with 77ed5681f8565b12ab1d5e5c7d0302c938e9c73d Commit: 20b96d883d9ef33b51d5a32d82ce2d1251daf572 https://github.com/galaxyproject/galaxy/commit/20b96d883d9ef33b51d5a32d82ce… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py M test/unit/test_galaxy_mapping.py M test/unit/workflows/test_render.py A test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge pull request #1202 from jmchilton/workflow_tool_refactoring Small Tool and Workflow Refactoring and Fixes Compare: https://github.com/galaxyproject/galaxy/compare/ffb3de9ede51...20b96d883d9e

1 0

[galaxyproject/galaxy] 51cd41: Fix ScIdx sniff method to handle first line commen...
by GitHub 02 Dec '15

02 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 51cd41be94ea4e5af50201bbd0e85ade21774e69 https://github.com/galaxyproject/galaxy/commit/51cd41be94ea4e5af50201bbd0e8… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Fix ScIdx sniff method to handle first line comment Commit: c04b3a5bb557c836e60c060f68598ea314fc9521 https://github.com/galaxyproject/galaxy/commit/c04b3a5bb557c836e60c060f6859… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Re-add egg imports Commit: 30b13bb1d6e576c4f6e32f4e98b08c9a3a5651eb https://github.com/galaxyproject/galaxy/commit/30b13bb1d6e576c4f6e32f4e98b0… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Merge pull request #1203 from gregvonkuster/release_15.10 [15.10] Fix ScIdx sniff method to handle first line comment Compare: https://github.com/galaxyproject/galaxy/compare/da2cc588e5a5...30b13bb1d6e5

1 0

[galaxyproject/usegalaxy-playbook] d26b97: change Main config; allow importing from FTP folde...
by GitHub 02 Dec '15

02 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d26b9739c642d53ef9c88cc7f24d4bca9c3140c5 https://github.com/galaxyproject/usegalaxy-playbook/commit/d26b9739c642d53e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M production/group_vars/galaxyservers.yml Log Message: ----------- change Main config; allow importing from FTP folder to datalibs

1 0

[galaxyproject/galaxy] 0c22d1: Implement type_source on output collections.
by GitHub 01 Dec '15

01 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0c22d138891604d0df98784ab7edc43e9b541c1d https://github.com/galaxyproject/galaxy/commit/0c22d138891604d0df98784ab7ed… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parser/xml.py A test/functional/tools/collection_type_source.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Implement type_source on output collections. Inherit collection_type from an input, the way metadata and format can be. This commit includes a test tool demonstrating this functionality. The tool test for this tool can be executed using the following command: ``` ./run_tests.sh -framework -id collection_type_source ``` Commit: ffb3de9ede515d10fbdf06519140a726e0cfa7d1 https://github.com/galaxyproject/galaxy/commit/ffb3de9ede515d10fbdf06519140… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parser/xml.py A test/functional/tools/collection_type_source.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #1153 from jmchilton/collection_type_source Implement type_source on output collections. Compare: https://github.com/galaxyproject/galaxy/compare/67c98f54cad4...ffb3de9ede51

1 0

[galaxyproject/galaxy] ff619d: Downgrade Mercurial wheel to 3.4.2 to restore hg p...
by GitHub 01 Dec '15

01 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ff619df3946621b819df03909fc63ce9ee412ced https://github.com/galaxyproject/galaxy/commit/ff619df3946621b819df03909fc6… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt M lib/tool_shed/util/hg_util.py Log Message: ----------- Downgrade Mercurial wheel to 3.4.2 to restore hg push of Tool Shed repositories. Fix #1183. Commit: 657afa89d3ac91e53a84ae132334f137eb07acdc https://github.com/galaxyproject/galaxy/commit/657afa89d3ac91e53a84ae132334… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/tool_shed/util/common_util.py Log Message: ----------- Small fixes. Commit: 194d871e38b3815bba120d6bb40c3eef45660738 https://github.com/galaxyproject/galaxy/commit/194d871e38b3815bba120d6bb40c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Fix Tool Shed export capsule for Mercurial >= 3.4 . Fix the following error: tool_shed.capsule.capsule_manager ERROR 2015-12-01 12:24:37,542 unable to find mercurial command "archive" Traceback (most recent call last): File "/opt/galaxy/lib/tool_shed/capsule/capsule_manager.py", line 88, in export_repository work_dir ) File "/opt/galaxy/lib/tool_shed/capsule/capsule_manager.py", line 148, in generate_repository_archive changeset_revision ) File "/opt/galaxy/lib/tool_shed/util/hg_util.py", line 28, in archive_repository_revision options_dict = get_mercurial_default_options_dict( 'archive' ) File "/opt/galaxy/lib/tool_shed/util/hg_util.py", line 200, in get_mercurial_default_options_dict raise Exception('unable to find mercurial command "%s"' % command) Exception: unable to find mercurial command "archive" Commit: 67c98f54cad4f20413568417e2cbb97bee24b0e5 https://github.com/galaxyproject/galaxy/commit/67c98f54cad4f20413568417e2cb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt M lib/tool_shed/util/common_util.py M lib/tool_shed/util/hg_util.py Log Message: ----------- Merge pull request #1200 from nsoranzo/tool_shed_fixes Tool shed fixes. Compare: https://github.com/galaxyproject/galaxy/compare/84464288b18c...67c98f54cad4

1 0

[galaxyproject/usegalaxy-playbook] 7f140f: Update GCC2016 redirect
by GitHub 01 Dec '15

01 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7f140f63d6095f01123da96fe6aed62f529c0614 https://github.com/galaxyproject/usegalaxy-playbook/commit/7f140f63d6095f01… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M templates/nginx/galaxyproject.j2 Log Message: ----------- Update GCC2016 redirect

1 0

[galaxyproject/infrastructure-playbook] 8597fd: Allow jenkins to log in to mjolnir0 for building w...
by GitHub 01 Dec '15

01 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 8597fdb06f69c4b0cade4b9e8f363aebe3c67704 https://github.com/galaxyproject/infrastructure-playbook/commit/8597fdb06f6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M galaxyenv/group_vars/starforgebuilders.yml M galaxyenv/secret_group_vars/all.yml M galaxyenv/secret_host_vars/leeroy.galaxyproject.org.yml M galaxyenv/secret_host_vars/mjolnir0.galaxyproject.org.yml Log Message: ----------- Allow jenkins to log in to mjolnir0 for building wheels

1 0