- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] b89c6e: When submitting tool error reports, include 'old' ...
by GitHub 21 Sep '15

21 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b89c6e56a5559186d126afdf09ea1565a146f178 https://github.com/galaxyproject/galaxy/commit/b89c6e56a5559186d126afdf09ea… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- When submitting tool error reports, include 'old' tool id as part of subject line. Makes sifting through bug report emails easier, old id is used for brevity, but full guid is still included in text of report. Commit: c7394bd0b31f4ecab36a144897e26871eedde008 https://github.com/galaxyproject/galaxy/commit/c7394bd0b31f4ecab36a144897e2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Merge pull request #761 from blankenberg/error-tool-id When submitting tool error reports, include 'old' tool id as part of subject line. Compare: https://github.com/galaxyproject/galaxy/compare/2bfc12d66694...c7394bd0b31f

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[galaxyproject/galaxy] 311100: Bugfix in test error reporting handling code.
by GitHub 21 Sep '15

21 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 311100ff9e40128b4da158fbb404a0b781765e11 https://github.com/galaxyproject/galaxy/commit/311100ff9e40128b4da158fbb404… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M test/base/interactor.py Log Message: ----------- Bugfix in test error reporting handling code. The code for showing status of histories in error would fail if there are collections in the history. This fixes that and skips over collections. Commit: 2bfc12d666946a3e057aa3801fde2df90c6ab990 https://github.com/galaxyproject/galaxy/commit/2bfc12d666946a3e057aa3801fde… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M test/base/interactor.py Log Message: ----------- Merge pull request #760 from jmchilton/test_error Bugfix in test error reporting handling code. Compare: https://github.com/galaxyproject/galaxy/compare/1f1eed0e0560...2bfc12d66694

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[galaxyproject/usegalaxy-playbook] 897be7: Fix indentation
by GitHub 21 Sep '15

21 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 897be7f26606611a641687244cc388e8940cd47e https://github.com/galaxyproject/usegalaxy-playbook/commit/897be7f26606611a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M stage/secret_vars/galaxyservers.yml Log Message: ----------- Fix indentation

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[galaxyproject/usegalaxy-playbook] 5db56b: Increase Greenfield concurrency for testing.
by GitHub 21 Sep '15

21 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5db56b223d0c5afaa32877ea38f7605b0deb8192 https://github.com/galaxyproject/usegalaxy-playbook/commit/5db56b223d0c5afa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Increase Greenfield concurrency for testing.

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[galaxyproject/galaxy] 134c98: Updates and fixes for dockerized Galaxy testing.
by GitHub 19 Sep '15

19 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 134c985f90a538eef623e6bc58c540228658d599 https://github.com/galaxyproject/galaxy/commit/134c985f90a538eef623e6bc58c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-19 (Sat, 19 Sep 2015) Changed paths: M run_tests.sh M test/docker/README.md M test/docker/base/Dockerfile Log Message: ----------- Updates and fixes for dockerized Galaxy testing. Commit: 1f1eed0e05600e7d89e36a0b152c87d609c85a3d https://github.com/galaxyproject/galaxy/commit/1f1eed0e05600e7d89e36a0b152c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-19 (Sat, 19 Sep 2015) Changed paths: M run_tests.sh M test/docker/README.md M test/docker/base/Dockerfile Log Message: ----------- Merge pull request #759 from jmchilton/dockerize_test Updates and fixes for dockerized Galaxy testing. Compare: https://github.com/galaxyproject/galaxy/compare/2e55eb11e551...1f1eed0e0560

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[galaxyproject/galaxy] 45d5e2: Extend test_map_over_two_collections timeout.
by GitHub 19 Sep '15

19 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 45d5e29c1dcc30e896ed3fc408b2005a35d11ba6 https://github.com/galaxyproject/galaxy/commit/45d5e29c1dcc30e896ed3fc408b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-19 (Sat, 19 Sep 2015) Changed paths: M test/api/test_tools.py Log Message: ----------- Extend test_map_over_two_collections timeout. May be the cause of intermittent test failure on jenkins (https://jenkins.galaxyproject.org/job/G-API/lastCompletedBuild/default/test…) Commit: 69f4ace0bcdaedc4f2077baeaffe605eb7538d79 https://github.com/galaxyproject/galaxy/commit/69f4ace0bcdaedc4f2077baeaffe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-19 (Sat, 19 Sep 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix failing workflow to_dict editor test. Generating form HTML as part of this request requires a history now (since https://github.com/galaxyproject/galaxy/commit/a00461eaf61bdeeea0c42b8098ae…) This is a less than ideal since it should definitely not require a history, but it is also less than idea to be shipping HTML via the API for non-web transactions. So rather than solving the former problem, this solves the latter and just doesn't attach form HTML for API requests. Fixes #734. Commit: 2e55eb11e5513cf76cb970e16ea2102bc557865a https://github.com/galaxyproject/galaxy/commit/2e55eb11e5513cf76cb970e16ea2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-19 (Sat, 19 Sep 2015) Changed paths: M lib/galaxy/managers/workflows.py M test/api/test_tools.py Log Message: ----------- Merge pull request #758 from jmchilton/framework_tests API Test Fixes Compare: https://github.com/galaxyproject/galaxy/compare/c7d7736472d0...2e55eb11e551

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[galaxyproject/galaxy] 2b0267: Workaround for metadata_bam.xml failure.
by GitHub 19 Sep '15

19 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2b02677e85e57792a2aab52333ccc3f24c65393e https://github.com/galaxyproject/galaxy/commit/2b02677e85e57792a2aab52333cc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-19 (Sat, 19 Sep 2015) Changed paths: A test-data/3.bam M test/functional/tools/metadata_bam.xml Log Message: ----------- Workaround for metadata_bam.xml failure. Commit: c6be0bc12c6300f839d4b9dace05f567c493637d https://github.com/galaxyproject/galaxy/commit/c6be0bc12c6300f839d4b9dace05… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-19 (Sat, 19 Sep 2015) Changed paths: R test/functional/tools/compare_bam_as_sam.xml Log Message: ----------- Remove compare_bam_as_sam.xml test. It never passed, it was originally used by me to test failing tests compared output of bams as sam files. Now that we want all these tests to pass we need to rethink how to test that aspect of the testing framework. Commit: c7d7736472d06b4b8df169f6017f7a4afe97d7b3 https://github.com/galaxyproject/galaxy/commit/c7d7736472d06b4b8df169f6017f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-19 (Sat, 19 Sep 2015) Changed paths: A test-data/3.bam R test/functional/tools/compare_bam_as_sam.xml M test/functional/tools/metadata_bam.xml Log Message: ----------- Merge pull request #757 from jmchilton/framework_tests Fix failing framework tests. Compare: https://github.com/galaxyproject/galaxy/compare/31c2d33ede1b...c7d7736472d0

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[galaxyproject/galaxy] cb303a: Fix the fix I added to make the unit tests pass.
by GitHub 18 Sep '15

18 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cb303a46ef71c1b13d7760d2c8b840afff973b9e https://github.com/galaxyproject/galaxy/commit/cb303a46ef71c1b13d7760d2c8b8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M lib/galaxy/managers/hdas.py Log Message: ----------- Fix the fix I added to make the unit tests pass. Commit: 31c2d33ede1b97672ff0a05faa6928a8d05b1422 https://github.com/galaxyproject/galaxy/commit/31c2d33ede1b97672ff0a05faa69… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-09-19 (Sat, 19 Sep 2015) Changed paths: M lib/galaxy/managers/hdas.py Log Message: ----------- Merge pull request #756 from dannon/oops Fix lack of a return in hda manager Compare: https://github.com/galaxyproject/galaxy/compare/ce9fe44b939a...31c2d33ede1b

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[galaxyproject/infrastructure-playbook] be0739: add node to n2 via brew
by GitHub 18 Sep '15

18 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: be07399e8ddafd6ead81aa0ee5e172642b01b7b9 https://github.com/galaxyproject/infrastructure-playbook/commit/be07399e8dd… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M galaxyenv/group_vars/jenkinsservers.yml Log Message: ----------- add node to n2 via brew

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[galaxyproject/infrastructure-playbook] 044fce: add npm to n2
by GitHub 18 Sep '15

18 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 044fce8b07239d2080f8812bef886c6a3369cf8a https://github.com/galaxyproject/infrastructure-playbook/commit/044fce8b072… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M galaxyenv/host_vars/n2.galaxyproject.org.yml Log Message: ----------- add npm to n2

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[galaxyproject/galaxy] 4064d0: add Oxli datatypes
by GitHub 18 Sep '15

18 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4064d0c5980644f29ac06b83f28e7064479f28db https://github.com/galaxyproject/galaxy/commit/4064d0c5980644f29ac06b83f28e… Author: Michael R. Crusoe <crusoe(a)ucdavis.edu> Date: 2015-09-13 (Sun, 13 Sep 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- add Oxli datatypes Commit: cecea3ebc6e9043df85989cd74899779a06c1e41 https://github.com/galaxyproject/galaxy/commit/cecea3ebc6e9043df85989cd7489… Author: Michael R. Crusoe <michael.crusoe(a)gmail.com> Date: 2015-09-13 (Sun, 13 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/oxli_countgraph.oxlicg A lib/galaxy/datatypes/test/oxli_graphlabels.oxligl A lib/galaxy/datatypes/test/oxli_nodegraph.oxling A lib/galaxy/datatypes/test/oxli_stoptags.oxlist A lib/galaxy/datatypes/test/oxli_subset.oxliss A lib/galaxy/datatypes/test/oxli_tagset.oxlits Log Message: ----------- added doctests + 1 fix + cleanup Made helper function a proper @staticmethod fixed error in sniffer (thank you doctests) Moved registration lines after their respective classes Added test data Commit: 383e9e01817483b819e770e22cf9d2d0beebbd5b https://github.com/galaxyproject/galaxy/commit/383e9e01817483b819e770e22cf9… Author: Michael R. Crusoe <michael.crusoe(a)gmail.com> Date: 2015-09-13 (Sun, 13 Sep 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- OxliLabelSet->OxliGraphLabels even in the config Commit: 02df796c7236b51382f7b1f77d50cc1709c76356 https://github.com/galaxyproject/galaxy/commit/02df796c7236b51382f7b1f77d50… Author: Michael R. Crusoe <michael.crusoe(a)gmail.com> Date: 2015-09-13 (Sun, 13 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- drop trailing whitespace Commit: ce9fe44b939a693a87b18ab4dfaa1dfff4a715f4 https://github.com/galaxyproject/galaxy/commit/ce9fe44b939a693a87b18ab4dfaa… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/oxli_countgraph.oxlicg A lib/galaxy/datatypes/test/oxli_graphlabels.oxligl A lib/galaxy/datatypes/test/oxli_nodegraph.oxling A lib/galaxy/datatypes/test/oxli_stoptags.oxlist A lib/galaxy/datatypes/test/oxli_subset.oxliss A lib/galaxy/datatypes/test/oxli_tagset.oxlits Log Message: ----------- Merge pull request #721 from dib-lab/add-oxli-datatypes add Oxli datatypes Compare: https://github.com/galaxyproject/galaxy/compare/304e569730c8...ce9fe44b939a

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[galaxyproject/infrastructure-playbook] ae9fab: add nodejs to n2
by GitHub 18 Sep '15

18 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: ae9faba6bc9f6503852e30770eb5c85e65d01172 https://github.com/galaxyproject/infrastructure-playbook/commit/ae9faba6bc9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M galaxyenv/host_vars/n2.galaxyproject.org.yml Log Message: ----------- add nodejs to n2

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[galaxyproject/galaxy] 304e56: Revert "Fixed broken RData sniffer"
by GitHub 18 Sep '15

18 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 304e569730c84f54176b06a175a49b7bce225325 https://github.com/galaxyproject/galaxy/commit/304e569730c84f54176b06a175a4… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Revert "Fixed broken RData sniffer" This reverts commit b2e9c8a36f9b1ba394b0d27bdc8287880abe27cd.

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[galaxyproject/galaxy] b2e9c8: Fixed broken RData sniffer
by GitHub 18 Sep '15

18 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b2e9c8a36f9b1ba394b0d27bdc8287880abe27cd https://github.com/galaxyproject/galaxy/commit/b2e9c8a36f9b1ba394b0d27bdc82… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Fixed broken RData sniffer

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[galaxyproject/galaxy] 989191: Fix output_format framework test.
by GitHub 18 Sep '15

18 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 989191d3cef70999661668ca9031e6cf39aaca61 https://github.com/galaxyproject/galaxy/commit/989191d3cef70999661668ca9031… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M test/functional/tools/output_format.xml Log Message: ----------- Fix output_format framework test. Commit: 92a152d89c507168a6085cc34acfa13566b6eda9 https://github.com/galaxyproject/galaxy/commit/92a152d89c507168a6085cc34acf… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M test/api/helpers.py Log Message: ----------- Uniform and slight increase the default timeout of API tests. Commit: d585a4a03d6956404830d63fc6b8872fba241d83 https://github.com/galaxyproject/galaxy/commit/d585a4a03d6956404830d63fc6b8… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Clearer error message when setting metadata for BCF and SAM/BAM files. When the shutil.move() fails. Commit: ca733d33f9c52a630a30132d24974ed1143e6945 https://github.com/galaxyproject/galaxy/commit/ca733d33f9c52a630a30132d2497… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py M test/api/helpers.py M test/functional/tools/output_format.xml Log Message: ----------- Merge pull request #752 from nsoranzo/dev Fixes for #744. Compare: https://github.com/galaxyproject/galaxy/compare/3de7bb66993c...ca733d33f9c5

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[galaxyproject/infrastructure-playbook] 6e9b69: correct the linuxbrew tasks
by GitHub 18 Sep '15

18 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 6e9b69584e16bd8fd132368896314759b920a52e https://github.com/galaxyproject/infrastructure-playbook/commit/6e9b69584e1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M roles/linuxbrew/tasks/main.yml Log Message: ----------- correct the linuxbrew tasks

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[galaxyproject/infrastructure-playbook] 0ba7f9: adjust n2 for brew
by GitHub 18 Sep '15

18 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 0ba7f9c94201c66e7ccfe5e83db5acd24d09869c https://github.com/galaxyproject/infrastructure-playbook/commit/0ba7f9c9420… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M galaxyenv/host_vars/n2.galaxyproject.org.yml M playbook.yml M roles/linuxbrew/tasks/main.yml Log Message: ----------- adjust n2 for brew Commit: e10494f3b65859cf71b2b333938773ad6dcbb0b5 https://github.com/galaxyproject/infrastructure-playbook/commit/e10494f3b65… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M roles/linuxbrew/tasks/main.yml Log Message: ----------- Merge branch 'master' of https://github.com/galaxyproject/infrastructure-playbook Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/3769c7f3f6…

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[galaxyproject/infrastructure-playbook] 3769c7: Install linuxbrew required packages.
by GitHub 18 Sep '15

18 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 3769c7f3f62c5c7b8432bc16c0216642509fbfde https://github.com/galaxyproject/infrastructure-playbook/commit/3769c7f3f62… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M roles/linuxbrew/tasks/main.yml Log Message: ----------- Install linuxbrew required packages. Using apt.

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[galaxyproject/infrastructure-playbook] 77bb06: WIP: linuxbrew role for jenkins.
by GitHub 18 Sep '15

18 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 77bb0686461dac5342143a1c6abfd2011ac8e586 https://github.com/galaxyproject/infrastructure-playbook/commit/77bb0686461… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: A galaxyenv/group_vars/jenkinsservers.yml M playbook.yml A roles/linuxbrew/defaults/main.yml A roles/linuxbrew/tasks/main.yml Log Message: ----------- WIP: linuxbrew role for jenkins. Install planemo and bcftools. Commit: 410c6c010c8f0301c7e1f1713933b0270a01c248 https://github.com/galaxyproject/infrastructure-playbook/commit/410c6c010c8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: A galaxyenv/group_vars/jenkinsservers.yml M playbook.yml A roles/linuxbrew/defaults/main.yml A roles/linuxbrew/tasks/main.yml Log Message: ----------- Merge pull request #5 from jmchilton/linuxbrew linuxbrew role for jenkins. Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/a1912b492b…

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[galaxyproject/galaxy] 4fb487: Jobs API docstring {job_id} to {id} convention fix...
by GitHub 18 Sep '15

18 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4fb4873934ea8857a2e4a694194a97137ba7ae35 https://github.com/galaxyproject/galaxy/commit/4fb4873934ea8857a2e4a694194a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Jobs API docstring {job_id} to {id} convention fix. Elsewhere we refer to a member's id as simply 'id' in docs, and this is the parameter name. Commit: 3de7bb66993c0094f8ff138fcb768a75fd5f3a0a https://github.com/galaxyproject/galaxy/commit/3de7bb66993c0094f8ff138fcb76… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Merge pull request #751 from dannon/api_docstrings Jobs API docstring {job_id} to {id} convention fix. Elsewhere we ref… Compare: https://github.com/galaxyproject/galaxy/compare/35621ca118d2...3de7bb66993c

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[galaxyproject/galaxy] 0ea4ad: Remove deprecated objectstore options from sample; ...
by GitHub 18 Sep '15

18 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0ea4ad69a013a51b1327a275864a0471ec55c070 https://github.com/galaxyproject/galaxy/commit/0ea4ad69a013a51b1327a275864a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Remove deprecated objectstore options from sample; the new way is to set object_store_conf and use it. Commit: 35621ca118d278559dee31ff0ac53f77184be7c1 https://github.com/galaxyproject/galaxy/commit/35621ca118d278559dee31ff0ac5… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #748 from dannon/sample_cleanup Remove deprecated objectstore options from sample; the new way is to … Compare: https://github.com/galaxyproject/galaxy/compare/fec26b39c26d...35621ca118d2

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[galaxyproject/infrastructure-playbook] a1912b: add samtools to n2
by GitHub 17 Sep '15

17 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: a1912b492bb16b94f5f2bc285fc7fdd98b094fa0 https://github.com/galaxyproject/infrastructure-playbook/commit/a1912b492bb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M galaxyenv/host_vars/n2.galaxyproject.org.yml Log Message: ----------- add samtools to n2

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[galaxyproject/galaxy] e71826: API, histories: correct copy to copy both non-dele...
by GitHub 17 Sep '15

17 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e71826889f1c4f8f4cab68ac7adab40bf53d3094 https://github.com/galaxyproject/galaxy/commit/e71826889f1c4f8f4cab68ac7ada… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M lib/galaxy/webapps/galaxy/api/histories.py M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/multi-panel.js Log Message: ----------- API, histories: correct copy to copy both non-deleted and deleted contents by default, add all_datasets flag to support copying only non-deleted; UI, histories: separate out history copy dialog for use in multi-panel (and later: the options menu), include deleted filter in choices Commit: de8bdaf44f0d304ce715e7ff43cf43b1b920f28a https://github.com/galaxyproject/galaxy/commit/de8bdaf44f0d304ce715e7ff43cf… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: A client/galaxy/scripts/mvc/history/copy-dialog.js A static/maps/mvc/history/copy-dialog.js.map A static/scripts/mvc/history/copy-dialog.js Log Message: ----------- Fix to e718268: add copy-dialog files Commit: 3f71220bcfd6d17593e1f8d7aa7e09e6e5bd9997 https://github.com/galaxyproject/galaxy/commit/3f71220bcfd6d17593e1f8d7aa7e… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M static/maps/mvc/history/copy-dialog.js.map M static/scripts/mvc/history/copy-dialog.js Log Message: ----------- UI, history: clean up copy dialog Commit: fec26b39c26d1687622dbfc999d244f34afcf264 https://github.com/galaxyproject/galaxy/commit/fec26b39c26d1687622dbfc999d2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: A client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M lib/galaxy/webapps/galaxy/api/histories.py A static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/multi-panel.js.map A static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/multi-panel.js Log Message: ----------- Merge pull request #742 from carlfeberhard/history.copy-dialog History copy dialog & API fix Compare: https://github.com/galaxyproject/galaxy/compare/63e35965401a...fec26b39c26d

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[galaxyproject/galaxy] 150c17: Do not explicitly require pexpect. If anyone wants...
by GitHub 17 Sep '15

17 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 150c17b9e8adc03fe8684962ca76f19bf0c93705 https://github.com/galaxyproject/galaxy/commit/150c17b9e8adc03fe8684962ca76… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/web/framework/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M scripts/transfer.py Log Message: ----------- Do not explicitly require pexpect. If anyone wants to use the old and mostly unused features that depend on it (namely remote sequencer transfers via scp) they can pip install pexpect. Commit: 63e35965401a2eac2ef3308913fb48be89961c10 https://github.com/galaxyproject/galaxy/commit/63e35965401a2eac2ef3308913fb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/web/framework/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M scripts/transfer.py Log Message: ----------- Merge pull request #741 from natefoo/drop-pexpect Do not explicitly require pexpect Compare: https://github.com/galaxyproject/galaxy/compare/d717ec833de5...63e35965401a

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[galaxyproject/galaxy] ce3e79: Use setup.py for all installations instead of the ...
by GitHub 17 Sep '15

17 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ce3e7931f6cb19a4a0c1e7cd2bdcbe301c9060f3 https://github.com/galaxyproject/galaxy/commit/ce3e7931f6cb19a4a0c1e7cd2bdc… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-09-05 (Sat, 05 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Use setup.py for all installations instead of the depreceated easy_install method. Commit: 4e063e793f6ddea0ae4c36183b8b4ad96d193f08 https://github.com/galaxyproject/galaxy/commit/4e063e793f6ddea0ae4c36183b8b… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- add mkdir as safeguard and remove old warning Commit: d717ec833de5615fdb949fdfd0a3c69ab90a7a7f https://github.com/galaxyproject/galaxy/commit/d717ec833de5615fdb949fdfd0a3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #698 from bgruening/pip_install Use setup.py for Python all installations Compare: https://github.com/galaxyproject/galaxy/compare/c74cda3c60b0...d717ec833de5

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