- galaxy-commits - lists.galaxyproject.org

[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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