- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 31f174: Add enhancements to the Galaxy repository install ...
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 31f174a4254e5cc4c85747a76c3908b0170cf358 https://github.com/galaxyproject/galaxy/commit/31f174a4254e5cc4c85747a76c39… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Add enhancements to the Galaxy repository install process to cleanly handle the case described here: https://github.com/galaxyproject/galaxy/issues/667. Specifically, the following scenario is now cleanly handled: Example use case: In a toolshed I have a repository of a tool, say package_new_gene_db_1_2_3, and in revision 1 it depends on package_sqlite_1_0_0: package_new_gene_db_1_2_3 package_sqlite_1_0_0 At some point in time I discover that postgres is a better solution for my gene database, and I upload revision 2: package_new_gene_db_1_2_3 package_postgres__2_0_0 And I remove the dependecy of sqlite. If I go to my galaxy instance and I remove revision 1 and install revision 2, the installation is cleanly handled with theis PR. It should be noted that this enhancement could adversely impact reproducibility if best practices are not followed with regard to defining package dependencies. Since it is now cleanly possible to eliminate dependencies over time, best practices must be followed to ensure that elimination of a dependency does not affect the output of a tool that uses the underlying hierarchy of packages. Commit: a23e644a9cd7ab64f0fa56314ae5ec2b5a768f7a https://github.com/galaxyproject/galaxy/commit/a23e644a9cd7ab64f0fa56314ae5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #1329 from martenson/release_15.10 [15.10] Add enhancements to the Galaxy repository install process Compare: https://github.com/galaxyproject/galaxy/compare/c48965ffcc5d...a23e644a9cd7

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[galaxyproject/galaxy] f95300: Fix typo causing the option "Link files instead of...
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: f953005f72310279fe69a0deb0b9adef973bf6da https://github.com/galaxyproject/galaxy/commit/f953005f72310279fe69a0deb0b9… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Fix typo causing the option "Link files instead of copying" to be ignored. When uploading folders with the new data library interface. Commit: c48965ffcc5d35877f00dcf1941317cf23c3d4f4 https://github.com/galaxyproject/galaxy/commit/c48965ffcc5d35877f00dcf19413… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Merge pull request #1326 from nsoranzo/release_15.10_link_data_only [15.10] Fix typo causing the option "Link files instead of copying" to be ignored. Compare: https://github.com/galaxyproject/galaxy/compare/989f961fb635...c48965ffcc5d

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[galaxyproject/usegalaxy-playbook] b48412: Fix the manual hackery employed by
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b4841230c39de5e87136d371a9a7366b8055689d https://github.com/galaxyproject/usegalaxy-playbook/commit/b4841230c39de5e8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M templates/supervisor/toolshed.conf.j2 Log Message: ----------- Fix the manual hackery employed by 0db21fc8feab6ff45a5346e307f8d178c7fdeef2 by using uwsgi's -H/--home/--virtualenv/--venv/--pyhome

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[galaxyproject/infrastructure-playbook] 633d58: Give radegast the "lite" env and minor related imp...
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 633d582b88ebc48ce23884a30a8ad47d97b0ef03 https://github.com/galaxyproject/infrastructure-playbook/commit/633d582b88e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M galaxyenv/inventory R roles/nfs/defaults/main.yml M roles/nfs/tasks/main.yml A roles/nfs/vars/debian_8.yml A roles/nfs/vars/default.yml Log Message: ----------- Give radegast the "lite" env and minor related improvements to the nfs role

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[galaxyproject/galaxy] 58911e: Remove worklfow casperjs API test.
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 58911edbfb5aa6e858addd9452e90d6ed389b0d2 https://github.com/galaxyproject/galaxy/commit/58911edbfb5aa6e858addd9452e9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: R test/casperjs/api-workflow-tests.js M test/casperjs/casperjs_runner.py Log Message: ----------- Remove worklfow casperjs API test. It has good and more updated coverage in the Python API testing framework. Commit: 86632afdd3b7f2dbfed47671779818835a075496 https://github.com/galaxyproject/galaxy/commit/86632afdd3b7f2dbfed476717798… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: R test/casperjs/api-workflow-tests.js M test/casperjs/casperjs_runner.py Log Message: ----------- Merge pull request #1316 from jmchilton/remove_casper_api_tests Remove worklfow casperjs API test. Compare: https://github.com/galaxyproject/galaxy/compare/b2a3684f03e4...86632afdd3b7

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[galaxyproject/galaxy] 7f7010: Remove left over packed scripts.
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7f7010dbd96b4b9ce494ba320b853e6441162f5e https://github.com/galaxyproject/galaxy/commit/7f7010dbd96b4b9ce494ba320b85… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: R static/scripts/mvc/collection/paired-collection-creator.js R static/scripts/mvc/history/history-panel.js R static/scripts/mvc/upload/upload-row.js R static/scripts/mvc/workflow/workflow.js Log Message: ----------- Remove left over packed scripts. The source files have been deleted. Commit: b2a3684f03e42d3743d02f4d4f039d429bf5e235 https://github.com/galaxyproject/galaxy/commit/b2a3684f03e42d3743d02f4d4f03… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: R static/scripts/mvc/collection/paired-collection-creator.js R static/scripts/mvc/history/history-panel.js R static/scripts/mvc/upload/upload-row.js R static/scripts/mvc/workflow/workflow.js Log Message: ----------- Merge pull request #1323 from jmchilton/fix_deleted_static Remove left over packed scripts. Compare: https://github.com/galaxyproject/galaxy/compare/cc67557df848...b2a3684f03e4

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[galaxyproject/galaxy] 8e2db2: Fix workflow output step entries
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8e2db2944cbd546fa0f6f6cb46bf78d470ab31c8 https://github.com/galaxyproject/galaxy/commit/8e2db2944cbd546fa0f6f6cb46bf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix workflow output step entries Commit: cc67557df8483899e7058f2047607d0e5339c4eb https://github.com/galaxyproject/galaxy/commit/cc67557df8483899e7058f204760… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #1322 from guerler/fix_workflow_outputs Fix workflow output step entries Compare: https://github.com/galaxyproject/galaxy/compare/19cb62660a37...cc67557df848

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[galaxyproject/galaxy] ce5793: Show a more user-friendly error when the webserver...
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ce57930342c2a4f7eb672f95dc0b19c93c2322f8 https://github.com/galaxyproject/galaxy/commit/ce57930342c2a4f7eb672f95dc0b… Author: shane <shane(a)shanedowling.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/config.py Log Message: ----------- Show a more user-friendly error when the webserver port is blocked Commit: a42328f0002955295cfb70bc6e16fcf83e42ad82 https://github.com/galaxyproject/galaxy/commit/a42328f0002955295cfb70bc6e16… Author: shane <shane(a)shanedowling.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/config.py Log Message: ----------- Removing unnecessary line Commit: c14bb93a60dba72db34996cadcf20ee0e19a7f19 https://github.com/galaxyproject/galaxy/commit/c14bb93a60dba72db34996cadcf2… Author: shane <shane(a)shanedowling.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/config.py Log Message: ----------- Tidying code for linter Commit: 541231bb1723b2aac3fede7f45ca0455ca954894 https://github.com/galaxyproject/galaxy/commit/541231bb1723b2aac3fede7f45ca… Author: shane <shane(a)shanedowling.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/config.py M lib/galaxy/util/pastescript/serve.py Log Message: ----------- Config-based port checker has been removed and adding in an exception checker for paste response Commit: 19cb62660a3779a6333696ec645f7fcee3db5bc5 https://github.com/galaxyproject/galaxy/commit/19cb62660a3779a6333696ec645f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/util/pastescript/serve.py Log Message: ----------- Merge pull request #1320 from shano/dev Show a more user-friendly error when the webserver port is blocked Compare: https://github.com/galaxyproject/galaxy/compare/4c3dfc7cd471...19cb62660a37

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[galaxyproject/galaxy] 2acdbe: UI, Citations: fix citation-model's import of bibt...
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2acdbe54f76312cb748693e018d2d505cf95c3a2 https://github.com/galaxyproject/galaxy/commit/2acdbe54f76312cb748693e018d2… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/citation/citation-model.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- UI, Citations: fix citation-model's import of bibtex to use *either* commonjs or global Commit: 4c3dfc7cd471181edc406724ca8f039e6b2a83d1 https://github.com/galaxyproject/galaxy/commit/4c3dfc7cd471181edc406724ca8f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/citation/citation-model.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #1321 from carlfeberhard/fix.citations UI, Citations: fix citation-model's import of bibtex to use *either* … Compare: https://github.com/galaxyproject/galaxy/compare/5bf926bf3ec1...4c3dfc7cd471

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[galaxyproject/infrastructure-playbook] c767b4: Modified authorized users
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c767b40a2d3641c5736e8dd7fd706dbeb2b6d987 https://github.com/galaxyproject/infrastructure-playbook/commit/c767b40a2d3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M galaxyenv/secret_host_vars/orval.galaxyproject.org.yml Log Message: ----------- Modified authorized users

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