- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 1aecca: Fix API installation of tool_dependencies
by GitHub 16 Nov '15

16 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1aecca7889681ad9518e26e2a62b470809d2cdd1 https://github.com/galaxyproject/galaxy/commit/1aecca7889681ad9518e26e2a62b… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-11-14 (Sat, 14 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Fix API installation of tool_dependencies This should fix an installation issue with tool_dependencies via the API. Tool dependency repositories to not have any tools specified and with this no metadata associated. It was broken in https://github.com/galaxyproject/galaxy/commit/bb6a784f13ff3f91762244d44884… So I think this should be part of 15.10. Thanks to Greg for fixing this one. Commit: 7e67368424a718f2e156b961aaf0a1a9672df9ce https://github.com/galaxyproject/galaxy/commit/7e67368424a718f2e156b961aaf0… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py Log Message: ----------- Don't fail if a repository is already installed If an repository is already installed `installed_tool_shed_repositories` is None and this does not work with map. Commit: 38f0ed5d043951cc06abeaab9bbf1f4d888e372a https://github.com/galaxyproject/galaxy/commit/38f0ed5d043951cc06abeaab9bbf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M templates/show_params.mako Log Message: ----------- Improve the API attributes on parameters page. Make clear what API ID is and add display of API value for job. Commit: bbe7fbe38c57fd89434eea850621770a1d355231 https://github.com/galaxyproject/galaxy/commit/bbe7fbe38c57fd89434eea850621… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M templates/show_params.mako Log Message: ----------- Merge pull request #1098 from jmchilton/show_param Improve the API attributes on parameters page. Commit: a26526b085c29d41f5662b7f80dee7e3e7a7c294 https://github.com/galaxyproject/galaxy/commit/a26526b085c29d41f5662b7f80de… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Merge pull request #1094 from bgruening/fix_api_ts_installation Fix api TS installation Commit: cfe45d8e0c357cbe191a346a2ae05e1625bb5010 https://github.com/galaxyproject/galaxy/commit/cfe45d8e0c357cbe191a346a2ae0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py Log Message: ----------- Merge pull request #1095 from bgruening/ts_api_fail_if_installed Don't fail if a repository is already installed Compare: https://github.com/galaxyproject/galaxy/compare/3ba139fe1bf8...cfe45d8e0c35

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[galaxyproject/galaxy]
by GitHub 16 Nov '15

16 Nov '15

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

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[galaxyproject/galaxy] 7e6736: Don't fail if a repository is already installed
by GitHub 16 Nov '15

16 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7e67368424a718f2e156b961aaf0a1a9672df9ce https://github.com/galaxyproject/galaxy/commit/7e67368424a718f2e156b961aaf0… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py Log Message: ----------- Don't fail if a repository is already installed If an repository is already installed `installed_tool_shed_repositories` is None and this does not work with map. Commit: cfe45d8e0c357cbe191a346a2ae05e1625bb5010 https://github.com/galaxyproject/galaxy/commit/cfe45d8e0c357cbe191a346a2ae0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py Log Message: ----------- Merge pull request #1095 from bgruening/ts_api_fail_if_installed Don't fail if a repository is already installed Compare: https://github.com/galaxyproject/galaxy/compare/a26526b085c2...cfe45d8e0c35

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[galaxyproject/galaxy] 1aecca: Fix API installation of tool_dependencies
by GitHub 16 Nov '15

16 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1aecca7889681ad9518e26e2a62b470809d2cdd1 https://github.com/galaxyproject/galaxy/commit/1aecca7889681ad9518e26e2a62b… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-11-14 (Sat, 14 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Fix API installation of tool_dependencies This should fix an installation issue with tool_dependencies via the API. Tool dependency repositories to not have any tools specified and with this no metadata associated. It was broken in https://github.com/galaxyproject/galaxy/commit/bb6a784f13ff3f91762244d44884… So I think this should be part of 15.10. Thanks to Greg for fixing this one. Commit: a26526b085c29d41f5662b7f80dee7e3e7a7c294 https://github.com/galaxyproject/galaxy/commit/a26526b085c29d41f5662b7f80de… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Merge pull request #1094 from bgruening/fix_api_ts_installation Fix api TS installation Compare: https://github.com/galaxyproject/galaxy/compare/bbe7fbe38c57...a26526b085c2

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[galaxyproject/galaxy] 38f0ed: Improve the API attributes on parameters page.
by GitHub 16 Nov '15

16 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 38f0ed5d043951cc06abeaab9bbf1f4d888e372a https://github.com/galaxyproject/galaxy/commit/38f0ed5d043951cc06abeaab9bbf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M templates/show_params.mako Log Message: ----------- Improve the API attributes on parameters page. Make clear what API ID is and add display of API value for job. Commit: bbe7fbe38c57fd89434eea850621770a1d355231 https://github.com/galaxyproject/galaxy/commit/bbe7fbe38c57fd89434eea850621… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M templates/show_params.mako Log Message: ----------- Merge pull request #1098 from jmchilton/show_param Improve the API attributes on parameters page. Compare: https://github.com/galaxyproject/galaxy/compare/3ba139fe1bf8...bbe7fbe38c57

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[galaxyproject/galaxy] 75e7e4: Fix 500 error when attempting to update installed ...
by GitHub 15 Nov '15

15 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 75e7e4c2cf7a0cb18b8096c8119e4b0cb207e2a3 https://github.com/galaxyproject/galaxy/commit/75e7e4c2cf7a0cb18b8096c8119e… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-14 (Sat, 14 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Fix 500 error when attempting to update installed repository. Commit: 7150983aab78e4ceb71f8ad2592369523899d768 https://github.com/galaxyproject/galaxy/commit/7150983aab78e4ceb71f8ad25923… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-14 (Sat, 14 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Merge pull request #1093 from martenson/release_15.10 [15.10] Fix 500 error when attempting to update installed repository. Compare: https://github.com/galaxyproject/galaxy/compare/64b084067c73...7150983aab78

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[galaxyproject/galaxy] 7c45bf: Fix 500 error when attempting to update installed ...
by GitHub 14 Nov '15

14 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7c45bf13fad2d60fbee8be409c6879af2ebc25d1 https://github.com/galaxyproject/galaxy/commit/7c45bf13fad2d60fbee8be409c68… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Fix 500 error when attempting to update installed repository. Commit: 321b64d8dcc1917eb107e46124cdb945c5005511 https://github.com/galaxyproject/galaxy/commit/321b64d8dcc1917eb107e46124cd… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Ensure that invalid parameters don't break things. Commit: 87f35ea9752a37da76595db1fee481c391ee686b https://github.com/galaxyproject/galaxy/commit/87f35ea9752a37da76595db1fee4… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Use preexisting library to parse query string. Commit: 3ba139fe1bf8a40df647282a9884eae543a656bc https://github.com/galaxyproject/galaxy/commit/3ba139fe1bf8a40df647282a9884… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-14 (Sat, 14 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Merge pull request #1082 from davebx/hg_middleware Fix 500 error when attempting to update installed repository. Compare: https://github.com/galaxyproject/galaxy/compare/f1abf1e9ab4d...3ba139fe1bf8

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[galaxyproject/usegalaxy-playbook] bfc167: Update SSL certs
by GitHub 14 Nov '15

14 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bfc167bedf63a660d83427562f78960b6bd3963c https://github.com/galaxyproject/usegalaxy-playbook/commit/bfc167bedf63a660… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-14 (Sat, 14 Nov 2015) Changed paths: M common/host_vars/radegast.galaxyproject.org.yml M common/secret_vars/ssl.yml M common_infrastructure.yml M files/ssl/athena.galaxyproject.org_cert.pem R files/ssl/montana.galaxyproject.org_cert.pem A files/ssl/radegast.galaxyproject.org_cert.pem R files/ssl/wildcard_cert.pem M templates/nginx/cloudlaunch.j2 Log Message: ----------- Update SSL certs Commit: 23c400852d03206eb49265dbb6ee0c2517a680c4 https://github.com/galaxyproject/usegalaxy-playbook/commit/23c400852d03206e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-14 (Sat, 14 Nov 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.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 M production/group_vars/all.yml M production/group_vars/galaxyservers.yml M stage/group_vars/all.yml M stage/group_vars/galaxyservers.yml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Merge branch 'master' of github.com:galaxyproject/usegalaxy-playbook Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/57ec60640226...…

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[galaxyproject/galaxy] ce418d: Resolve conflicting label CSS class.
by GitHub 13 Nov '15

13 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ce418d33fe221b27da162717a208381aa8042ea8 https://github.com/galaxyproject/galaxy/commit/ce418d33fe221b27da162717a208… Author: jgoecks <jgoecks(a)gwu.edu> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/trackster.less M static/maps/viz/trackster/tracks.js.map M static/scripts/viz/trackster/tracks.js M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/embed_item.css M static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/trackster.css Log Message: ----------- Resolve conflicting label CSS class. Commit: f1abf1e9ab4dc4f1d3e6987c6bb68ab3b188083c https://github.com/galaxyproject/galaxy/commit/f1abf1e9ab4dc4f1d3e6987c6bb6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/trackster.less M static/maps/viz/trackster/tracks.js.map M static/scripts/viz/trackster/tracks.js M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/embed_item.css M static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/trackster.css Log Message: ----------- Merge pull request #1086 from jgoecks/trackster-pos-label Resolve conflicting label CSS class for trackster. Compare: https://github.com/galaxyproject/galaxy/compare/2dcb92aa0e83...f1abf1e9ab4d

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[galaxyproject/galaxy] ffda4a: Allow dockerized toolshed tests.
by GitHub 13 Nov '15

13 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ffda4aa2cd033e8953ef780fb553afbc77e4a7f4 https://github.com/galaxyproject/galaxy/commit/ffda4aa2cd033e8953ef780fb553… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M lib/galaxy/model/orm/scripts.py M lib/galaxy/webapps/tool_shed/buildapp.py M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/provision.yml M test/docker/base/run_test_wrapper.sh M test/docker/base/start_mysql.sh Log Message: ----------- Allow dockerized toolshed tests. Commit: 096adbf8d0776d4b1085705f2881c2d46ab06611 https://github.com/galaxyproject/galaxy/commit/096adbf8d0776d4b1085705f2881… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M test/docker/base/Dockerfile Log Message: ----------- Collect apt installs in one place. Commit: 1766b896e30ed1b2bc5aa5341cf19d313628c4f4 https://github.com/galaxyproject/galaxy/commit/1766b896e30ed1b2bc5aa5341cf1… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M config/datatypes_conf.xml.sample M doc/source/admin/index.rst A doc/source/admin/useful_scripts.rst M doc/source/dev/faq.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M run_tests.sh A scripts/api/library_upload_dir.py M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge -dev. Commit: 2dcb92aa0e83f9893595b68222fc62cf052a9220 https://github.com/galaxyproject/galaxy/commit/2dcb92aa0e83f9893595b68222fc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M lib/galaxy/model/orm/scripts.py M lib/galaxy/webapps/tool_shed/buildapp.py M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/provision.yml M test/docker/base/run_test_wrapper.sh M test/docker/base/start_mysql.sh Log Message: ----------- Merge pull request #942 from davebx/docker Enable dockerized toolshed tests. Compare: https://github.com/galaxyproject/galaxy/compare/625d49e2de07...2dcb92aa0e83

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