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

[galaxyproject/usegalaxy-playbook] e1e1ea: Update Main
by GitHub 21 Sep '16

21 Sep '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e1e1eab378ac02231eede28c6c27681514a97db1 https://github.com/galaxyproject/usegalaxy-playbook/commit/e1e1eab378ac0223… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M production/galaxy_version.yml Log Message: ----------- Update Main

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[galaxyproject/usegalaxy-playbook] c0e35d: Move Main install db to SQLite on CVMFS
by GitHub 21 Sep '16

21 Sep '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c0e35d4b6b618a8b49d1caf9f012a5a00b545f4f https://github.com/galaxyproject/usegalaxy-playbook/commit/c0e35d4b6b618a8b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M production/group_vars/galaxyservers.yml M production/secret_vars/galaxyservers.yml Log Message: ----------- Move Main install db to SQLite on CVMFS

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[galaxyproject/usegalaxy-playbook] 7ee3e7: Installed tools on Test
by GitHub 21 Sep '16

21 Sep '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7ee3e7095d1b6253e2cb4f7b73c3019ff03ba5d8 https://github.com/galaxyproject/usegalaxy-playbook/commit/7ee3e7095d1b6253… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Installed tools on Test Commit: 4475976c6dee713d716a62d27db3af42d67a9843 https://github.com/galaxyproject/usegalaxy-playbook/commit/4475976c6dee713d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M files/galaxy/test.galaxyproject.org/config/job_resource_params_conf.xml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Greenfield -> Bridges Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/3d4f123bccb9...…

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[galaxyproject/galaxy] 36b514: Remove unnecessary use of binascii
by GitHub 21 Sep '16

21 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 36b514c6e963b44b27003e7f64f0a9fe019f305e https://github.com/galaxyproject/galaxy/commit/36b514c6e963b44b27003e7f64f0… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/util/checkers.py Log Message: ----------- Remove unnecessary use of binascii Also explicitly specify binary mode for file opening and header strings. Fix import order. Commit: c81ec07c6d39f7dbb080f0db3680d6a29747608a https://github.com/galaxyproject/galaxy/commit/c81ec07c6d39f7dbb080f0db3680… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/util/checkers.py Log Message: ----------- Merge pull request #2946 from nsoranzo/binascii_reduction Remove unnecessary use of binascii Compare: https://github.com/galaxyproject/galaxy/compare/b30d331a811f...c81ec07c6d39

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[galaxyproject/galaxy] 8b3356: Strip stderr message from sacct
by GitHub 21 Sep '16

21 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8b3356b869beba70820235c2d0894cee9e590ffe https://github.com/galaxyproject/galaxy/commit/8b3356b869beba70820235c2d089… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Strip stderr message from sacct Commit: 34d60e2b27ab08a3ebc5201d1c3282d346d40af0 https://github.com/galaxyproject/galaxy/commit/34d60e2b27ab08a3ebc5201d1c32… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2945 from nsoranzo/release_16.07_strip_stderr [16.07] Strip stderr message from sacct Commit: b30d331a811f2c5621ba81ff5bd54dc4ee93d755 https://github.com/galaxyproject/galaxy/commit/b30d331a811f2c5621ba81ff5bd5… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge branch 'release_16.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/7d76bfe046fe...b30d331a811f

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[galaxyproject/galaxy] 8b3356: Strip stderr message from sacct
by GitHub 21 Sep '16

21 Sep '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 8b3356b869beba70820235c2d0894cee9e590ffe https://github.com/galaxyproject/galaxy/commit/8b3356b869beba70820235c2d089… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Strip stderr message from sacct Commit: 34d60e2b27ab08a3ebc5201d1c3282d346d40af0 https://github.com/galaxyproject/galaxy/commit/34d60e2b27ab08a3ebc5201d1c32… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2945 from nsoranzo/release_16.07_strip_stderr [16.07] Strip stderr message from sacct Compare: https://github.com/galaxyproject/galaxy/compare/7627abb3856a...34d60e2b27ab

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[galaxyproject/galaxy] 10b310: Allow naming Dataset/collection inputs during work...
by GitHub 21 Sep '16

21 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 10b310b87142a9f34a1ce5340575d6c351a2279b https://github.com/galaxyproject/galaxy/commit/10b310b87142a9f34a1ce5340575… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/extract.py M templates/webapps/galaxy/workflow/build_from_current_history.mako Log Message: ----------- Allow naming Dataset/collection inputs during workflow extraction. Default name is now the original input dataset name. Commit: 9890cb63f12d2d2e5eccd40e931c5563732efd44 https://github.com/galaxyproject/galaxy/commit/9890cb63f12d2d2e5eccd40e931c… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: M templates/webapps/galaxy/workflow/build_from_current_history.mako Log Message: ----------- Text inputs can't be checked. Commit: 7d76bfe046fef24e25d4d04ef68b8228971aa79c https://github.com/galaxyproject/galaxy/commit/7d76bfe046fef24e25d4d04ef68b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/extract.py M templates/webapps/galaxy/workflow/build_from_current_history.mako Log Message: ----------- Merge pull request #2943 from blankenberg/wf_input_name Allow naming Dataset/collection inputs during workflow extraction. Compare: https://github.com/galaxyproject/galaxy/compare/f799656b1117...7d76bfe046fe

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[galaxyproject/galaxy] 0e0b77: Allow '.' and '_' for public names
by GitHub 21 Sep '16

21 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0e0b773edc85c3e36ae25f38ee929e8a95cc520b https://github.com/galaxyproject/galaxy/commit/0e0b773edc85c3e36ae25f38ee92… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/security/validate_user_input.py M templates/user/info.mako M templates/user/register.mako M test/unit/managers/test_UserManager.py Log Message: ----------- Allow '.' and '_' for public names Fix #2593. Also standardise error messages. Commit: 70db2b7c4ad253b3ce0443d66df3832e4fc2a189 https://github.com/galaxyproject/galaxy/commit/70db2b7c4ad253b3ce0443d66df3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/mobile.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Validate public name when auto-registering a user Commit: 8fb3cd9c5bc52495e6055c0a2a5bb4339e31612b https://github.com/galaxyproject/galaxy/commit/8fb3cd9c5bc52495e6055c0a2a5b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M templates/user/info.mako M templates/user/register.mako M templates/user/username.mako Log Message: ----------- propagate allowed changes to hints Commit: 736df5a0717089f815e0ba02ef7e9502fef36814 https://github.com/galaxyproject/galaxy/commit/736df5a0717089f815e0ba02ef7e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M templates/user/info.mako M templates/user/register.mako M templates/user/username.mako Log Message: ----------- Merge pull request #4 from martenson/nsoranzo-publicnames propagate allowed username changes to form hints Commit: f799656b1117d74afac0cd0c4ad1ca19625ca625 https://github.com/galaxyproject/galaxy/commit/f799656b1117d74afac0cd0c4ad1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/security/validate_user_input.py M lib/galaxy/webapps/galaxy/controllers/mobile.py M lib/galaxy/webapps/galaxy/controllers/user.py M templates/user/info.mako M templates/user/register.mako M templates/user/username.mako M test/unit/managers/test_UserManager.py Log Message: ----------- Merge pull request #2947 from nsoranzo/publicnames Allow '.' and '_' for public names Compare: https://github.com/galaxyproject/galaxy/compare/9ae56b782a24...f799656b1117

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[galaxyproject/galaxy] b58b83: Allow JSONP in api calls
by GitHub 20 Sep '16

20 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b58b83e56e458efd749fb9966cfe087cfbf41c3d https://github.com/galaxyproject/galaxy/commit/b58b83e56e458efd749fb9966cfe… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-19 (Mon, 19 Sep 2016) Changed paths: M lib/galaxy/web/framework/decorators.py Log Message: ----------- Allow JSONP in api calls Commit: ffd0ac78cd3920768ed84f6ab780c13d69532a45 https://github.com/galaxyproject/galaxy/commit/ffd0ac78cd3920768ed84f6ab780… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-19 (Mon, 19 Sep 2016) Changed paths: M lib/galaxy/web/framework/decorators.py Log Message: ----------- Extend JSONP to older decorators Commit: c69a20f76109754c846ac2d42e22ce87cdc96bca https://github.com/galaxyproject/galaxy/commit/c69a20f76109754c846ac2d42e22… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: M lib/galaxy/web/framework/decorators.py Log Message: ----------- API, jsonp: better var name Commit: a312ef29e113f510d7fffa0343824b4491206c0a https://github.com/galaxyproject/galaxy/commit/a312ef29e113f510d7fffa034382… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: M lib/galaxy/web/framework/decorators.py Log Message: ----------- API, jsonp: switch off for certain decorators Commit: 9ae56b782a241c373d3ef4496d9110763b31c951 https://github.com/galaxyproject/galaxy/commit/9ae56b782a241c373d3ef4496d91… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: M lib/galaxy/web/framework/decorators.py Log Message: ----------- Merge pull request #2937 from carlfeberhard/jsonp Allow JSONP to be returned from API endpoints Compare: https://github.com/galaxyproject/galaxy/compare/35d0fed80145...9ae56b782a24

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[galaxyproject/galaxy] 1f53c3: Add missing tabular_to_dbnsfp.py for dbnsfp.tabula...
by GitHub 20 Sep '16

20 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1f53c32ad68235537d8f6c843d1cd81eda5c11c3 https://github.com/galaxyproject/galaxy/commit/1f53c32ad68235537d8f6c843d1c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-19 (Mon, 19 Sep 2016) Changed paths: A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py Log Message: ----------- Add missing tabular_to_dbnsfp.py for dbnsfp.tabular to snpsiftdbnsfp conversion This should have been added in https://bitbucket.org/galaxy/galaxy-central/pull-requests/640/ Actual source code comes from https://github.com/galaxyproject/tools-iuc/blob/master/datatypes/snpsift_db… Commit: b748250193a26ddce4010759b9a22d012d281b81 https://github.com/galaxyproject/galaxy/commit/b748250193a26ddce4010759b9a2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py Log Message: ----------- Merge pull request #2938 from nsoranzo/release_16.04_tabular_to_dbnsfp [16.04] Add missing tabular_to_dbnsfp.py for dbnsfp.tabular to snpsiftdbnsfp conversion Commit: 7627abb3856a4e757b5ed5c55ec05a4f97bd4cac https://github.com/galaxyproject/galaxy/commit/7627abb3856a4e757b5ed5c55ec0… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: 35d0fed80145c7d07c0512ebcb9b4a23c4293072 https://github.com/galaxyproject/galaxy/commit/35d0fed80145c7d07c0512ebcb9b… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py Log Message: ----------- Merge branch 'release_16.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/71cea6604d43...35d0fed80145

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