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

[galaxyproject/galaxy] 05f02c: Fix for not respecting tool errors when trying to ...
by GitHub 25 Sep '15

25 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 05f02cf9b47c551347299c1a940fc00561d2f71f https://github.com/galaxyproject/galaxy/commit/05f02cf9b47c551347299c1a940f… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix for not respecting tool errors when trying to execute tools where the error occurs within a repeat. Commit: 1a17dbb68d23c3ba775a654e1d03d4e131c2c4fe https://github.com/galaxyproject/galaxy/commit/1a17dbb68d23c3ba775a654e1d03… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #798 from blankenberg/tool_error_fixes [15.07] Fix for not respecting tool errors when trying to execute tools Commit: 759b67dfa8cc59fb1e263d16acfeadd0ab196556 https://github.com/galaxyproject/galaxy/commit/759b67dfa8cc59fb1e263d16acfe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge branch 'release_15.07' Commit: 6d5ee0b6c8c2eb8b343a4473e253bb14e34b1da0 https://github.com/galaxyproject/galaxy/commit/6d5ee0b6c8c2eb8b343a4473e253… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge branch 'master' into dev Compare: https://github.com/galaxyproject/galaxy/compare/0260d753c76d...6d5ee0b6c8c2

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[galaxyproject/galaxy] 05f02c: Fix for not respecting tool errors when trying to ...
by GitHub 25 Sep '15

25 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 05f02cf9b47c551347299c1a940fc00561d2f71f https://github.com/galaxyproject/galaxy/commit/05f02cf9b47c551347299c1a940f… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix for not respecting tool errors when trying to execute tools where the error occurs within a repeat. Commit: 1a17dbb68d23c3ba775a654e1d03d4e131c2c4fe https://github.com/galaxyproject/galaxy/commit/1a17dbb68d23c3ba775a654e1d03… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #798 from blankenberg/tool_error_fixes [15.07] Fix for not respecting tool errors when trying to execute tools Commit: 759b67dfa8cc59fb1e263d16acfeadd0ab196556 https://github.com/galaxyproject/galaxy/commit/759b67dfa8cc59fb1e263d16acfe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge branch 'release_15.07' Compare: https://github.com/galaxyproject/galaxy/compare/79c58bd9250c...759b67dfa8cc

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[galaxyproject/galaxy] 05f02c: Fix for not respecting tool errors when trying to ...
by GitHub 25 Sep '15

25 Sep '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: 05f02cf9b47c551347299c1a940fc00561d2f71f https://github.com/galaxyproject/galaxy/commit/05f02cf9b47c551347299c1a940f… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix for not respecting tool errors when trying to execute tools where the error occurs within a repeat. Commit: 1a17dbb68d23c3ba775a654e1d03d4e131c2c4fe https://github.com/galaxyproject/galaxy/commit/1a17dbb68d23c3ba775a654e1d03… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #798 from blankenberg/tool_error_fixes [15.07] Fix for not respecting tool errors when trying to execute tools Compare: https://github.com/galaxyproject/galaxy/compare/e00674550830...1a17dbb68d23

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[galaxyproject/galaxy] 3f3c1b: Pin IE versions
by GitHub 25 Sep '15

25 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3f3c1b679bfef5dbd75d7c267d25fd2979f362d1 https://github.com/galaxyproject/galaxy/commit/3f3c1b679bfef5dbd75d7c267d25… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Log Message: ----------- Pin IE versions Commit: 85df2f67c4988700232098d4dc08f2bc5148359d https://github.com/galaxyproject/galaxy/commit/85df2f67c4988700232098d4dc08… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Log Message: ----------- Merge pull request #785 from erasche/pin-gie-images [release_15.07] pin GIE image versions Commit: bf60693ed001099b78189f28d46500b572be9df7 https://github.com/galaxyproject/galaxy/commit/bf60693ed001099b78189f28d465… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Fix problem maintaining input maps when rescheduling workflows. Fixes #776. I suspect the problem has very little to do with dynamic output collections and in fact exhibits itself when workflow rescheduling occurs, it is just that workflow rescheduling is forced when using dynamic output collections. Commit: 0bf60a5205947e4e4f20090a0509474983370df7 https://github.com/galaxyproject/galaxy/commit/0bf60a5205947e4e4f20090a0509… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge pull request #794 from jmchilton/release_15.05.output.fix [15.05] Fix problem maintaining input maps when rescheduling workflows. Commit: e0067455083089dbdf35ac4b93ff94d91b689889 https://github.com/galaxyproject/galaxy/commit/e0067455083089dbdf35ac4b93ff… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Commit: 79c58bd9250c174ca5347bcc6cdd33f08074cecc https://github.com/galaxyproject/galaxy/commit/79c58bd9250c174ca5347bcc6cdd… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/workflow/run.py Log Message: ----------- Merge branch 'release_15.07' Commit: 0260d753c76d7305f6c1f05d08af43e61faa7641 https://github.com/galaxyproject/galaxy/commit/0260d753c76d7305f6c1f05d08af… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-25 (Fri, 25 Sep 2015) Log Message: ----------- Merge branch 'master' into dev Conflicts: config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Compare: https://github.com/galaxyproject/galaxy/compare/ba43e95f41c3...0260d753c76d

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[galaxyproject/galaxy] 19bc49: Binary sniffing; along with the registry forcing c...
by GitHub 25 Sep '15

25 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 19bc49d207a92288dc402900cfa0125b8da45111 https://github.com/galaxyproject/galaxy/commit/19bc49d207a92288dc402900cfa0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Binary sniffing; along with the registry forcing case insensitivity through lower() which was implemented a while back, the un/sniffable formats lists should as well. This resolves #753 Commit: aff8c708a925205332c4190e3ada5712dc04519e https://github.com/galaxyproject/galaxy/commit/aff8c708a925205332c4190e3ada… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #774 from dannon/stable_sniffers [15.07] Binary sniffing; along with the registry forcing case insensitivity t… Commit: 3f3c1b679bfef5dbd75d7c267d25fd2979f362d1 https://github.com/galaxyproject/galaxy/commit/3f3c1b679bfef5dbd75d7c267d25… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Log Message: ----------- Pin IE versions Commit: 85df2f67c4988700232098d4dc08f2bc5148359d https://github.com/galaxyproject/galaxy/commit/85df2f67c4988700232098d4dc08… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Log Message: ----------- Merge pull request #785 from erasche/pin-gie-images [release_15.07] pin GIE image versions Commit: bf60693ed001099b78189f28d46500b572be9df7 https://github.com/galaxyproject/galaxy/commit/bf60693ed001099b78189f28d465… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Fix problem maintaining input maps when rescheduling workflows. Fixes #776. I suspect the problem has very little to do with dynamic output collections and in fact exhibits itself when workflow rescheduling occurs, it is just that workflow rescheduling is forced when using dynamic output collections. Commit: 0bf60a5205947e4e4f20090a0509474983370df7 https://github.com/galaxyproject/galaxy/commit/0bf60a5205947e4e4f20090a0509… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge pull request #794 from jmchilton/release_15.05.output.fix [15.05] Fix problem maintaining input maps when rescheduling workflows. Commit: e0067455083089dbdf35ac4b93ff94d91b689889 https://github.com/galaxyproject/galaxy/commit/e0067455083089dbdf35ac4b93ff… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Commit: 79c58bd9250c174ca5347bcc6cdd33f08074cecc https://github.com/galaxyproject/galaxy/commit/79c58bd9250c174ca5347bcc6cdd… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/workflow/run.py Log Message: ----------- Merge branch 'release_15.07' Compare: https://github.com/galaxyproject/galaxy/compare/a6715ebceccf...79c58bd9250c

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[galaxyproject/galaxy] bf6069: Fix problem maintaining input maps when rescheduli...
by GitHub 25 Sep '15

25 Sep '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: bf60693ed001099b78189f28d46500b572be9df7 https://github.com/galaxyproject/galaxy/commit/bf60693ed001099b78189f28d465… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Fix problem maintaining input maps when rescheduling workflows. Fixes #776. I suspect the problem has very little to do with dynamic output collections and in fact exhibits itself when workflow rescheduling occurs, it is just that workflow rescheduling is forced when using dynamic output collections. Commit: 0bf60a5205947e4e4f20090a0509474983370df7 https://github.com/galaxyproject/galaxy/commit/0bf60a5205947e4e4f20090a0509… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge pull request #794 from jmchilton/release_15.05.output.fix [15.05] Fix problem maintaining input maps when rescheduling workflows. Commit: e0067455083089dbdf35ac4b93ff94d91b689889 https://github.com/galaxyproject/galaxy/commit/e0067455083089dbdf35ac4b93ff… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Compare: https://github.com/galaxyproject/galaxy/compare/85df2f67c498...e00674550830

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[galaxyproject/galaxy] bf6069: Fix problem maintaining input maps when rescheduli...
by GitHub 25 Sep '15

25 Sep '15

Branch: refs/heads/release_15.05 Home: https://github.com/galaxyproject/galaxy Commit: bf60693ed001099b78189f28d46500b572be9df7 https://github.com/galaxyproject/galaxy/commit/bf60693ed001099b78189f28d465… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Fix problem maintaining input maps when rescheduling workflows. Fixes #776. I suspect the problem has very little to do with dynamic output collections and in fact exhibits itself when workflow rescheduling occurs, it is just that workflow rescheduling is forced when using dynamic output collections. Commit: 0bf60a5205947e4e4f20090a0509474983370df7 https://github.com/galaxyproject/galaxy/commit/0bf60a5205947e4e4f20090a0509… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge pull request #794 from jmchilton/release_15.05.output.fix [15.05] Fix problem maintaining input maps when rescheduling workflows. Compare: https://github.com/galaxyproject/galaxy/compare/6827aed9efb3...0bf60a520594

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[galaxyproject/galaxy] ac8b5e: Fix errors when starting "./run_tests.sh -with_fra...
by GitHub 25 Sep '15

25 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ac8b5eae02155a7364e4131ba88d983c69bd000b https://github.com/galaxyproject/galaxy/commit/ac8b5eae02155a7364e4131ba88d… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/tools/parser/yaml.py M test/functional/tools/disambiguate_cond.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Fix errors when starting "./run_tests.sh -with_framework_test_tools -api" Commit: ba43e95f41c3220df05aac0be7bc117c6acda362 https://github.com/galaxyproject/galaxy/commit/ba43e95f41c3220df05aac0be7bc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/tools/parser/yaml.py M test/functional/tools/disambiguate_cond.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #800 from nsoranzo/functional_tests_fixes Fix errors when starting "./run_tests.sh -with_framework_test_tools -api" Compare: https://github.com/galaxyproject/galaxy/compare/3f91a9a38186...ba43e95f41c3

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[galaxyproject/galaxy] 3fcf32: Add sentry configuration option and doc to galaxy....
by GitHub 25 Sep '15

25 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3fcf3210462a64ca3112295926240d04a99f3d24 https://github.com/galaxyproject/galaxy/commit/3fcf3210462a64ca311229592624… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Add sentry configuration option and doc to galaxy.ini.sample Commit: 3f91a9a381868910a1f5d3e8daf784dc960ffded https://github.com/galaxyproject/galaxy/commit/3f91a9a381868910a1f5d3e8daf7… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #799 from dannon/sample_sentry Add sentry configuration option and doc to galaxy.ini.sample Compare: https://github.com/galaxyproject/galaxy/compare/a5610d6845f4...3f91a9a38186

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[galaxyproject/galaxy] 86c426: Fix unit tests broken with f935d27bdfb4ff66e841de2...
by GitHub 25 Sep '15

25 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 86c4263b344f1bdd3c316a579a30f157f88eadf7 https://github.com/galaxyproject/galaxy/commit/86c4263b344f1bdd3c316a579a30… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M test/unit/jobs/test_job_configuration.py Log Message: ----------- Fix unit tests broken with f935d27bdfb4ff66e841de2667a40d3d65c0175d. Commit: a5610d6845f4bf016a0ac6a9a2d3d17a11e9b83b https://github.com/galaxyproject/galaxy/commit/a5610d6845f4bf016a0ac6a9a2d3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M test/unit/jobs/test_job_configuration.py Log Message: ----------- Merge pull request #797 from jmchilton/java_opts_doc Fix unit tests broken with f935d27bdfb4ff66e841de2667a40d3d65c0175d. Compare: https://github.com/galaxyproject/galaxy/compare/6d3ea7ee0086...a5610d6845f4

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