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

[galaxyproject/infrastructure-playbook] a03d2b: jenkins is dead, long live jenkins
by GitHub 19 Nov '15

19 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: a03d2b5c15aa7c645ef2a8d2fce464567b53a56f https://github.com/galaxyproject/infrastructure-playbook/commit/a03d2b5c15a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: A galaxyenv/host_vars/leeroy.galaxyproject.org.yml R galaxyenv/host_vars/n2.galaxyproject.org.yml M galaxyenv/host_vars/westvleteren.galaxyproject.org.yml M galaxyenv/inventory M galaxyenv/secret_group_vars/all.yml A galaxyenv/secret_host_vars/leeroy.galaxyproject.org.yml R galaxyenv/secret_host_vars/n2.galaxyproject.org.yml M galaxyenv/secret_host_vars/orval.galaxyproject.org.yml M galaxyenv/secret_host_vars/westvleteren.galaxyproject.org.yml M roles/linuxbrew/tasks/main.yml Log Message: ----------- jenkins is dead, long live jenkins

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[galaxyproject/galaxy] a3fee0: Style: fix state-success-bg change that was not re...
by GitHub 19 Nov '15

19 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a3fee086c6dee9a688ffb7da13f71c1210cb76da https://github.com/galaxyproject/galaxy/commit/a3fee086c6dee9a688ffb7da13f7… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M client/galaxy/style/less/galaxy_bootstrap/variables.less Log Message: ----------- Style: fix state-success-bg change that was not reverted during 5fd4daf Commit: 5191c2136a9131005533faff4b0c1267f1ce35c1 https://github.com/galaxyproject/galaxy/commit/5191c2136a9131005533faff4b0c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M client/galaxy/style/less/galaxy_bootstrap/variables.less Log Message: ----------- Merge pull request #1129 from carlfeberhard/fix.styles Style: fix state-success-bg change that was not reverted during 5fd4daf Compare: https://github.com/galaxyproject/galaxy/compare/d2bab13fa92a...5191c2136a91

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[galaxyproject/galaxy] b25b8c: Revise and fix waiting for tool tests.
by GitHub 19 Nov '15

19 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b25b8c3f243e87a196a6cb0fa23328ee7c7e26f7 https://github.com/galaxyproject/galaxy/commit/b25b8c3f243e87a196a6cb0fa233… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/test.py M test/base/twilltestcase.py A test/functional/tools/maxseconds.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Revise and fix waiting for tool tests. - maxseconds on test tag stopped being respected at some point, fix that. - maxseconds on test tag stopped being parsed at some later point, fix that. - Revise default behavior so it can be overridden with yet another testing environment variable GALAXY_TEST_DEFAULT_WAIT. - Add test case to ensure there is no future regression of these behaviors. Commit: d2bab13fa92a87a3c4959d782ba0bf061ecf07db https://github.com/galaxyproject/galaxy/commit/d2bab13fa92a87a3c4959d782ba0… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/test.py M test/base/twilltestcase.py A test/functional/tools/maxseconds.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #1119 from jmchilton/maxseconds Revise and fix waiting for tool tests. Compare: https://github.com/galaxyproject/galaxy/compare/7ab070e9df6e...d2bab13fa92a

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[galaxyproject/galaxy] 72faca: Document GIE proxy config for nginx, mention the A...
by GitHub 18 Nov '15

18 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 72faca1a3a81b6104c776353ee7b4dc03d6ae9be https://github.com/galaxyproject/galaxy/commit/72faca1a3a81b6104c776353ee7b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Document GIE proxy config for nginx, mention the Ansible role. Commit: 7ab070e9df6ebf0658c966942d38779fbc9d16f1 https://github.com/galaxyproject/galaxy/commit/7ab070e9df6ebf0658c966942d38… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Merge pull request #1123 from natefoo/ie-docfix Add nginx config for GIE proxy to documentation Compare: https://github.com/galaxyproject/galaxy/compare/f770128915df...7ab070e9df6e

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[galaxyproject/galaxy] e7d535: Fixes #932
by GitHub 18 Nov '15

18 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e7d5355f7b064fb0eb4063e905d6b32df1ed7a12 https://github.com/galaxyproject/galaxy/commit/e7d5355f7b064fb0eb4063e905d6… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-26 (Mon, 26 Oct 2015) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Fixes #932 But probably at great cost? This seems like basic functionality that I'm changing though a proper HTTPException is obviously the 'right thing to do'(tm) Commit: f770128915df3fa9d8a3a9fe2c4a210fbd9ac2c6 https://github.com/galaxyproject/galaxy/commit/f770128915df3fa9d8a3a9fe2c4a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Merge pull request #991 from erasche/fix-932 Fixes #932 Compare: https://github.com/galaxyproject/galaxy/compare/e4e44be27b7b...f770128915df

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[galaxyproject/galaxy] bafb8a: Add uniprotxml datatype
by GitHub 18 Nov '15

18 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bafb8a9a4d31191a102e5d8c442cbfc82d3ad97e https://github.com/galaxyproject/galaxy/commit/bafb8a9a4d31191a102e5d8c442c… Author: Jim Johnson <jj(a)umn.edu> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add uniprotxml datatype Commit: 4e6c46fa25cd7f23625d2029b57aad0e67bb732a https://github.com/galaxyproject/galaxy/commit/4e6c46fa25cd7f23625d2029b57a… Author: Jim Johnson <jj(a)umn.edu> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Add UniProtXML datatype to proteomics.py Commit: 2a7bba5abaeef0c71c6b86bbbcaf4cdbb0cf7a31 https://github.com/galaxyproject/galaxy/commit/2a7bba5abaeef0c71c6b86bbbcaf… Author: Jim Johnson <jj(a)umn.edu> Date: 2015-11-02 (Mon, 02 Nov 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add UniProtXML sniffer tag Commit: e4e44be27b7b3ddf778eb95559b4d0f11e4aecb7 https://github.com/galaxyproject/galaxy/commit/e4e44be27b7b3ddf778eb95559b4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Merge pull request #1004 from jj-umn/uniprotxml_datatype UniProtXML datatype Compare: https://github.com/galaxyproject/galaxy/compare/7fef50f45fb6...e4e44be27b7b

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[galaxyproject/galaxy] 28065b: Fix the issue where too many datasets are linked t...
by GitHub 18 Nov '15

18 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 28065b6ee7eaa15a7607c17316050939781b8cff https://github.com/galaxyproject/galaxy/commit/28065b6ee7eaa15a7607c1731605… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2015-10-09 (Fri, 09 Oct 2015) Changed paths: M lib/galaxy/web/base/controllers/admin.py Log Message: ----------- Fix the issue where too many datasets are linked to a certain role and the page will not load - or takes too long for the proxy Commit: 7fef50f45fb6484fcb600cfd167e43d1a735a9d2 https://github.com/galaxyproject/galaxy/commit/7fef50f45fb6484fcb600cfd167e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/web/base/controllers/admin.py Log Message: ----------- Merge pull request #881 from scholtalbers/role-page-fix Fix the issue where too many datasets are linked to a certain role Compare: https://github.com/galaxyproject/galaxy/compare/ee2b34c387d9...7fef50f45fb6

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[galaxyproject/usegalaxy-playbook] 15e3e5: Set $HOME for Galaxy processes.
by GitHub 18 Nov '15

18 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 15e3e529e1c9dddbf9d2dc8dde8f1e9c55076f2f https://github.com/galaxyproject/usegalaxy-playbook/commit/15e3e529e1c9dddb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M templates/supervisor/galaxy.conf.j2 Log Message: ----------- Set $HOME for Galaxy processes. Commit: 1cb189cec659569cebbb2053ac62feb79f76c13b https://github.com/galaxyproject/usegalaxy-playbook/commit/1cb189cec659569c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Test mutable configs Commit: 9fe17d3e77e75e7af7ad2394287f2b4050c40fe9 https://github.com/galaxyproject/usegalaxy-playbook/commit/9fe17d3e77e75e7a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: A roles/galaxyprojectdotorg.interactive_environments/README.md A roles/galaxyprojectdotorg.interactive_environments/defaults/main.yml A roles/galaxyprojectdotorg.interactive_environments/handlers/main.yml A roles/galaxyprojectdotorg.interactive_environments/meta/.galaxy_install_info A roles/galaxyprojectdotorg.interactive_environments/meta/main.yml A roles/galaxyprojectdotorg.interactive_environments/tasks/docker_ssl.yml A roles/galaxyprojectdotorg.interactive_environments/tasks/extract_component.yml A roles/galaxyprojectdotorg.interactive_environments/tasks/install_dependencies.yml A roles/galaxyprojectdotorg.interactive_environments/tasks/main.yml A roles/galaxyprojectdotorg.interactive_environments/tasks/supervisor.yml A roles/galaxyprojectdotorg.interactive_environments/tasks/synchronize_components.yml A roles/galaxyprojectdotorg.interactive_environments/tasks/webserver_conf.yml A roles/galaxyprojectdotorg.interactive_environments/templates/_prefix.j2 A roles/galaxyprojectdotorg.interactive_environments/templates/config.ini.j2 A roles/galaxyprojectdotorg.interactive_environments/templates/ipython_apache.conf.j2 A roles/galaxyprojectdotorg.interactive_environments/templates/ipython_nginx.conf.j2 A roles/galaxyprojectdotorg.interactive_environments/templates/proxy_supervisor.conf.j2 Log Message: ----------- Add the interactive_environments role Commit: 9d483c5c7cfb38539cabd9fecdaca23857cef6e6 https://github.com/galaxyproject/usegalaxy-playbook/commit/9d483c5c7cfb3853… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M galaxy.yml A stage/files/interactive_environments/plugins/.ansible_ie_role_current_version A stage/files/interactive_environments/plugins/common/templates/ie.mako A stage/files/interactive_environments/plugins/interactive_environments.dtd A stage/files/interactive_environments/plugins/ipython/config/ipython.ini.sample A stage/files/interactive_environments/plugins/ipython/config/ipython.xml A stage/files/interactive_environments/plugins/ipython/static/js/ipython.js A stage/files/interactive_environments/plugins/ipython/templates/ipython.mako A stage/files/interactive_environments/plugins/ipython/templates/notebook.ipynb A stage/files/interactive_environments/plugins/rstudio/config/rstudio.ini.sample A stage/files/interactive_environments/plugins/rstudio/config/rstudio.xml A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/base64.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/jsbn.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/prng4.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/rng.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/rsa.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio.big.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio.min.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/base64.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/jsbn.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/prng4.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/rng.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/rsa.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/base64.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/jsbn.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/prng4.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/rng.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/rsa.js A stage/files/interactive_environments/plugins/rstudio/static/js/rstudio.js A stage/files/interactive_environments/plugins/rstudio/templates/rstudio.mako A stage/files/interactive_environments/proxy/.ansible_ie_role_current_version A stage/files/interactive_environments/proxy/Dockerfile A stage/files/interactive_environments/proxy/README.md A stage/files/interactive_environments/proxy/lib/main.js A stage/files/interactive_environments/proxy/lib/mapper.js A stage/files/interactive_environments/proxy/lib/proxy.js A stage/files/interactive_environments/proxy/package.json M stage/group_vars/all.yml M stage/group_vars/galaxyservers.yml M stage/secret_vars/galaxyservers.yml Log Message: ----------- Update Test and use the interactive_environments role to deploy IPython Commit: ac7af1a513fe1c3f3a121398ebfb912734bd5c1e https://github.com/galaxyproject/usegalaxy-playbook/commit/ac7af1a513fe1c3f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: A production/files/interactive_environments/plugins/.ansible_ie_role_current_version A production/files/interactive_environments/plugins/common/templates/ie.mako A production/files/interactive_environments/plugins/interactive_environments.dtd A production/files/interactive_environments/plugins/ipython/config/ipython.ini.sample A production/files/interactive_environments/plugins/ipython/config/ipython.xml A production/files/interactive_environments/plugins/ipython/static/js/ipython.js A production/files/interactive_environments/plugins/ipython/templates/ipython.mako A production/files/interactive_environments/plugins/ipython/templates/notebook.ipynb A production/files/interactive_environments/plugins/rstudio/config/rstudio.ini.sample A production/files/interactive_environments/plugins/rstudio/config/rstudio.xml A production/files/interactive_environments/plugins/rstudio/static/js/crypto/base64.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/jsbn.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/prng4.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/rng.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/rsa.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio.big.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio.min.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/base64.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/jsbn.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/prng4.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/rng.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/rsa.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/base64.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/jsbn.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/prng4.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/rng.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/rsa.js A production/files/interactive_environments/plugins/rstudio/static/js/rstudio.js A production/files/interactive_environments/plugins/rstudio/templates/rstudio.mako A production/files/interactive_environments/proxy/.ansible_ie_role_current_version A production/files/interactive_environments/proxy/Dockerfile A production/files/interactive_environments/proxy/README.md A production/files/interactive_environments/proxy/lib/main.js A production/files/interactive_environments/proxy/lib/mapper.js A production/files/interactive_environments/proxy/lib/proxy.js A production/files/interactive_environments/proxy/package.json M production/group_vars/all.yml M production/group_vars/galaxyservers.yml M production/host_vars/galaxy-web-01.tacc.utexas.edu.yml M production/secret_vars/galaxyservers.yml Log Message: ----------- Deploy the IPython IE on Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/23c400852d03...…

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[galaxyproject/galaxy] fe0f9b: Add BIOM v1 in default datatypes.
by GitHub 18 Nov '15

18 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fe0f9ba905f11cfff4407aa574fa761e5eadf2f5 https://github.com/galaxyproject/galaxy/commit/fe0f9ba905f11cfff4407aa574fa… Author: fescudie <fescudie(a)toulouse.inra.fr> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/text.py Log Message: ----------- Add BIOM v1 in default datatypes. Commit: e834b6e189ff0e4e17b1cd3ac541f96a44ba1249 https://github.com/galaxyproject/galaxy/commit/e834b6e189ff0e4e17b1cd3ac541… Author: fescudie <fescudie(a)toulouse.inra.fr> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Add BIOM v1 in default datatypes Commit: ee2b34c387d9bb6189c8befaa069887b535d413c https://github.com/galaxyproject/galaxy/commit/ee2b34c387d9bb6189c8befaa069… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #950 from fescudie/dev Add BIOM v1 in default datatypes. Compare: https://github.com/galaxyproject/galaxy/compare/c252987b4c5f...ee2b34c387d9

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[galaxyproject/galaxy] 05f3da: Fix macro bug with empty CDATA being None instead ...
by GitHub 18 Nov '15

18 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 05f3da308d6a58dc8528f317fa6ea4ffa1fb7610 https://github.com/galaxyproject/galaxy/commit/05f3da308d6a58dc8528f317fa6e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/util/xml_macros.py M test/unit/tools/test_tool_loader.py Log Message: ----------- Fix macro bug with empty CDATA being None instead of ''. Fixes galaxyproject/planemo#362 thanks for the report @erasche. Test using the following command: ``` nosetests test/unit/tools/test_tool_loader.py ``` Commit: eb16ba3743a7e42cc9ad43f0d7a3eb926ba60cd8 https://github.com/galaxyproject/galaxy/commit/eb16ba3743a7e42cc9ad43f0d7a3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/util/xml_macros.py M test/unit/tools/test_tool_loader.py Log Message: ----------- Merge pull request #1122 from jmchilton/empty_cdata_macro [15.10] Fix macro bug with empty CDATA being None instead of ''. Compare: https://github.com/galaxyproject/galaxy/compare/73f46f4e0814...eb16ba3743a7

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