galaxy-commits January 2017

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[galaxyproject/infrastructure-playbook] 2a9ee5: Add curl package to Jenkins slaves.
by GitHub 06 Jan '17

06 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 2a9ee5c40bc7218875f8312f3a6401d21259b1eb https://github.com/galaxyproject/infrastructure-playbook/commit/2a9ee5c40bc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-22 (Thu, 22 Dec 2016) Changed paths: M galaxyenv/group_vars/jenkinsslaves.yml Log Message: ----------- Add curl package to Jenkins slaves. Commit: a345eb16ccb8bbb01183bcaed37df1e97e6cd549 https://github.com/galaxyproject/infrastructure-playbook/commit/a345eb16ccb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-06 (Fri, 06 Jan 2017) Changed paths: M galaxyenv/group_vars/jenkinsslaves.yml Log Message: ----------- Merge pull request #12 from jmchilton/add_curl_to_jenkins Add curl package to Jenkins slaves. Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/02bc152179…

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[galaxyproject/galaxy] e0e2d6: added nrrd datatype
by GitHub 05 Jan '17

05 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e0e2d6da7e3184282b64784ca2c0c424a2a28b03 https://github.com/galaxyproject/galaxy/commit/e0e2d6da7e3184282b64784ca2c0… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/images.py Log Message: ----------- added nrrd datatype Commit: 325b06928552604ad90c0c2183a724c04eb5e9b9 https://github.com/galaxyproject/galaxy/commit/325b06928552604ad90c0c2183a7… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/datatypes/images.py Log Message: ----------- fixed default extension of nrrd Commit: b28051a8867d1e0be50869eee3ab416d7f2819c3 https://github.com/galaxyproject/galaxy/commit/b28051a8867d1e0be50869eee3ab… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- fixed typo Commit: eb544104787835c63282e1b1342818bf1be6228e https://github.com/galaxyproject/galaxy/commit/eb544104787835c63282e1b13428… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/datatypes/images.py Log Message: ----------- lint fixes Commit: c9a876e659b30e69bd17586e9c9f213c9a81dc1b https://github.com/galaxyproject/galaxy/commit/c9a876e659b30e69bd17586e9c9f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/images.py Log Message: ----------- Merge pull request #3385 from ThomasWollmann/image_datatypes added nrrd image datatype Compare: https://github.com/galaxyproject/galaxy/compare/1ef96f031b81...c9a876e659b3

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[galaxyproject/galaxy] c7c6c5: Fix typo
by GitHub 05 Jan '17

05 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c7c6c565da4d1ab32db3ce14b91eeb057c49da3b https://github.com/galaxyproject/galaxy/commit/c7c6c565da4d1ab32db3ce14b91e… Author: pvanheus <pvh(a)webbedfeet.co.za> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/tools/verify/asserts/text.py Log Message: ----------- Fix typo ouptup instead of output in assertion message Commit: 1ef96f031b81c7f35ce57c1a376875be75d766e3 https://github.com/galaxyproject/galaxy/commit/1ef96f031b81c7f35ce57c1a3768… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/tools/verify/asserts/text.py Log Message: ----------- Merge pull request #3384 from pvanheus/patch-1 Fix typo Compare: https://github.com/galaxyproject/galaxy/compare/a870ac887cf4...1ef96f031b81

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[galaxyproject/galaxy] a870ac: added STL datatype (#2679)
by GitHub 05 Jan '17

05 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a870ac887cf43881906badecb2db7413b25cb96c https://github.com/galaxyproject/galaxy/commit/a870ac887cf43881906badecb2db… Author: ThomasWollmann <ThomasWollmann(a)users.noreply.github.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample M config/plugins/interactive_environments/jupyter/config/jupyter.xml M config/plugins/interactive_environments/rstudio/config/rstudio.xml M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- added STL datatype (#2679) * added STL datatype * added image support to rstudio IE * added image support to jupyter IE * changed boolean to lower case * lint * lint * revert file extension refactoring * upgraded numpy-stl * Update constructive_solid_geometry.py added additional check to refine stl sniffer * Update constructive_solid_geometry.py * removed stl sniffer * cleanup of dependencies * revert file extension refactoring * upgraded numpy-stl * Update constructive_solid_geometry.py added additional check to refine stl sniffer * Update constructive_solid_geometry.py * removed stl sniffer * cleanup of dependencies * lint

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[galaxyproject/usegalaxy-playbook] 1e7c06: Updated slide rotation.
by GitHub 04 Jan '17

04 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1e7c06ad0d5307336246bfccf862248cb19e0a02 https://github.com/galaxyproject/usegalaxy-playbook/commit/1e7c06ad0d530733… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2017-01-04 (Wed, 04 Jan 2017) Changed paths: A files/galaxy/common/static/welcome_img/GAMe2017RegisterNow.png A files/galaxy/common/static/welcome_img/ImmPortGalaxy.png A files/galaxy/common/static/welcome_img/PAG2017.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Updated slide rotation.

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[galaxyproject/galaxy] 968b97: harmonised the use of capital and small letters
by GitHub 04 Jan '17

04 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 968b97a0ac81cd65397c6e2c0de538b2be16c6a7 https://github.com/galaxyproject/galaxy/commit/968b97a0ac81cd65397c6e2c0de5… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2017-01-02 (Mon, 02 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- harmonised the use of capital and small letters Commit: 7588e9df3d7b0d1cc3da0090aa062cea91dce8ea https://github.com/galaxyproject/galaxy/commit/7588e9df3d7b0d1cc3da0090aa06… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2017-01-02 (Mon, 02 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/images.py Log Message: ----------- added image datatypes Commit: 88e838c587e4425f940dc19cd9848e8f12f42b35 https://github.com/galaxyproject/galaxy/commit/88e838c587e4425f940dc19cd984… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2017-01-02 (Mon, 02 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- added tiff subtypes Commit: f4eadd71fd1da0a18863cd7e1718369cdf9af03d https://github.com/galaxyproject/galaxy/commit/f4eadd71fd1da0a18863cd7e1718… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2017-01-02 (Mon, 02 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- harmonised the use of capital and small letters Commit: 47e0d5d8103c22741555faab1063d1ad5b698e03 https://github.com/galaxyproject/galaxy/commit/47e0d5d8103c22741555faab1063… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2017-01-02 (Mon, 02 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/images.py Log Message: ----------- added hamatsu sub datatypes Commit: f46d8ad739aed601f02c07b60c69c29f12c3b189 https://github.com/galaxyproject/galaxy/commit/f46d8ad739aed601f02c07b60c69… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2017-01-03 (Tue, 03 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- harmonised the use of capital and small letters Commit: 560813d908461cbeeeadf04c0fce487ac4ff9b35 https://github.com/galaxyproject/galaxy/commit/560813d908461cbeeeadf04c0fce… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-04 (Wed, 04 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/images.py Log Message: ----------- Merge pull request #3380 from ThomasWollmann/image_datatypes Added image datatypes Compare: https://github.com/galaxyproject/galaxy/compare/7bac8bbc786b...560813d90846

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[galaxyproject/galaxy] 8d4f99: Limit adjusting Galaxy's Python environment to leg...
by GitHub 03 Jan '17

03 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8d4f9955a66c94604634d436a4262cfef395b3e5 https://github.com/galaxyproject/galaxy/commit/8d4f9955a66c94604634d436a426… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-03 (Tue, 03 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/__init__.py A test/functional/tools/python_environment_problem.py A test/functional/tools/python_environment_problem.xml M test/functional/tools/samples_tool_conf.xml M test/unit/jobs/test_command_factory.py M test/unit/tools_support.py Log Message: ----------- Limit adjusting Galaxy's Python environment to legacy tools. Don't expose Galaxy's environment to tools unless there is evidence we need to. This should restrict future bugs by limitting what tools are exposed to Galaxy's internals and will fix bugs related to Conda dependencies masking Galaxy - such as #2994. Should fix #2994. Rebased with language and tool best practice fixes thanks to @mvdbeek. Commit: 7bac8bbc786ba9697cf1e0a0e8597c8d06aa1721 https://github.com/galaxyproject/galaxy/commit/7bac8bbc786ba9697cf1e0a0e859… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-01-03 (Tue, 03 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/__init__.py A test/functional/tools/python_environment_problem.py A test/functional/tools/python_environment_problem.xml M test/functional/tools/samples_tool_conf.xml M test/unit/jobs/test_command_factory.py M test/unit/tools_support.py Log Message: ----------- Merge pull request #3364 from jmchilton/clean_python Limit adjusting Galaxy's Python environment to legacy tools. Compare: https://github.com/galaxyproject/galaxy/compare/85333d4be474...7bac8bbc786b

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[galaxyproject/galaxy]
by GitHub 03 Jan '17

03 Jan '17

Branch: refs/heads/upgrade_conda Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] e350c8: Use a newer conda version by default
by GitHub 03 Jan '17

03 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e350c8b0517410e65f82e0c1276ef727ac6ae0ec https://github.com/galaxyproject/galaxy/commit/e350c8b0517410e65f82e0c1276e… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-01 (Sun, 01 Jan 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Use a newer conda version by default Commit: 85333d4be47478d6e6107316a15776488f987e46 https://github.com/galaxyproject/galaxy/commit/85333d4be47478d6e6107316a157… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-03 (Tue, 03 Jan 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #3378 from galaxyproject/upgrade_conda Use a newer conda version by default Compare: https://github.com/galaxyproject/galaxy/compare/29e5bd4915f8...85333d4be474

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[galaxyproject/galaxy]
by GitHub 03 Jan '17

03 Jan '17

Branch: refs/heads/conda_channel Home: https://github.com/galaxyproject/galaxy

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galaxy-commits January 2017