- galaxy-commits - lists.galaxyproject.org

[galaxyproject/infrastructure-playbook] 577c59: Backup Biostar to westvleteren
by GitHub 20 Oct '15

20 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 577c599fa6ab496e86018e69ef98b56a85d184fd https://github.com/galaxyproject/infrastructure-playbook/commit/577c599fa6a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M common_roles M galaxyenv/host_vars/westvleteren.galaxyproject.org.yml M galaxyenv/inventory M galaxyenv/secret_group_vars/all.yml A galaxyenv/secret_host_vars/biostar.usegalaxy.org.yml M galaxyenv/secret_host_vars/westvleteren.galaxyproject.org.yml M playbook.yml Log Message: ----------- Backup Biostar to westvleteren

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[galaxyproject/galaxy] ffc5b0: Swap naïve spaces for regex
by GitHub 20 Oct '15

20 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ffc5b02db98109fd3df35a0ba7f6a7b7cfd2b3a8 https://github.com/galaxyproject/galaxy/commit/ffc5b02db98109fd3df35a0ba7f6… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- Swap naïve spaces for regex Commit: 6f2b43330d5334bb46c10e1ce2a5675793e76219 https://github.com/galaxyproject/galaxy/commit/6f2b43330d5334bb46c10e1ce2a5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- Merge pull request #951 from erasche/949-followup Swap naïve spaces for regex Compare: https://github.com/galaxyproject/galaxy/compare/5ae2db59049f...6f2b43330d53

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[galaxyproject/galaxy] 8c8ddb: Tools don't start with <tool_dependencies
by GitHub 20 Oct '15

20 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8c8ddb9ce967bf3a47bf4cbdd2173e696228630d https://github.com/galaxyproject/galaxy/commit/8c8ddb9ce967bf3a47bf4cbdd217… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- Tools don't start with <tool_dependencies Tools start with '<tool ' Commit: 5ae2db59049fb38a6fa804ec8c5c8d08dda214b4 https://github.com/galaxyproject/galaxy/commit/5ae2db59049fb38a6fa804ec8c5c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- Merge pull request #949 from erasche/looks-like-a-bug Tools don't start with <tool_dependencies Compare: https://github.com/galaxyproject/galaxy/compare/d29283616ed8...5ae2db59049f

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[galaxyproject/galaxy] b80eb8: Fix tool url building
by GitHub 20 Oct '15

20 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b80eb8d47ce93cb4520459f59a20659d11c81e58 https://github.com/galaxyproject/galaxy/commit/b80eb8d47ce93cb4520459f59a20… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Fix tool url building Commit: d29283616ed83a707012d5c5d65a9efc33ae7a0e https://github.com/galaxyproject/galaxy/commit/d29283616ed83a707012d5c5d65a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Merge pull request #947 from guerler/fix_tool_url_000 Revise tool url building Compare: https://github.com/galaxyproject/galaxy/compare/278c2aa399c4...d29283616ed8

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[galaxyproject/infrastructure-playbook] a15fae: Change backup cron job for Jenkins to not copy the...
by GitHub 19 Oct '15

19 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: a15fae8401e73bfa68e07cfe6bbb81f5850d0737 https://github.com/galaxyproject/infrastructure-playbook/commit/a15fae8401e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M galaxyenv/host_vars/n2.galaxyproject.org.yml Log Message: ----------- Change backup cron job for Jenkins to not copy the workspace.

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[galaxyproject/galaxy] 61f1cd: Added script to upload a directory to a data libra...
by GitHub 19 Oct '15

19 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 61f1cdf5d7e2078569cb4c1efb3c1df3bda6d0e2 https://github.com/galaxyproject/galaxy/commit/61f1cdf5d7e2078569cb4c1efb3c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: A scripts/api/library_upload_dir.py Log Message: ----------- Added script to upload a directory to a data library Commit: a8b727791ffbdcbe70d2b638080101ec2a8a3a4d https://github.com/galaxyproject/galaxy/commit/a8b727791ffbdcbe70d2b6380801… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M doc/source/dev/faq.rst Log Message: ----------- Correct language in galaxy dev doc Commit: decca0e96a43bf9cf23af56d09a966898018b354 https://github.com/galaxyproject/galaxy/commit/decca0e96a43bf9cf23af56d09a9… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M scripts/api/library_upload_dir.py Log Message: ----------- Refactor to accept output of find Commit: aec9961407717f305b4ee3a5fdd6f655f4885944 https://github.com/galaxyproject/galaxy/commit/aec9961407717f305b4ee3a5fdd6… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M scripts/api/library_upload_dir.py Log Message: ----------- Strip newlines Commit: 1f9be2410bb9efe8cd647e240bd45a9e99a3bdce https://github.com/galaxyproject/galaxy/commit/1f9be2410bb9efe8cd647e240bd4… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M doc/source/admin/index.rst A doc/source/admin/useful_scripts.rst Log Message: ----------- Documented use of library upload tool Commit: 33925747b8b3b554b7b1cbb185ab4f15cfa3586b https://github.com/galaxyproject/galaxy/commit/33925747b8b3b554b7b1cbb185ab… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M scripts/api/library_upload_dir.py Log Message: ----------- Allow linking only Commit: 705445a2f2605d45d31fb11ef773460f252b0afd https://github.com/galaxyproject/galaxy/commit/705445a2f2605d45d31fb11ef773… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M doc/source/admin/useful_scripts.rst Log Message: ----------- Correct doc script name Commit: 6be301ca8afcbc3cd1c3c7e3d74d3dee17a6a607 https://github.com/galaxyproject/galaxy/commit/6be301ca8afcbc3cd1c3c7e3d74d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M scripts/api/library_upload_dir.py Log Message: ----------- Support local/non local data and paths including root Commit: 2cca823a787dfcd48b5cfb7ef685d81e9341d189 https://github.com/galaxyproject/galaxy/commit/2cca823a787dfcd48b5cfb7ef685… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M scripts/api/library_upload_dir.py Log Message: ----------- Prepopulate memoization cache Commit: 8a66701d4f622e3a57e39274fb3046dc67640be5 https://github.com/galaxyproject/galaxy/commit/8a66701d4f622e3a57e39274fb30… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M scripts/api/library_upload_dir.py Log Message: ----------- Don't re-upload if already there Commit: 5dd7370b845202b45b30b88c67e8ca98362935a5 https://github.com/galaxyproject/galaxy/commit/5dd7370b845202b45b30b88c67e8… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M doc/source/admin/useful_scripts.rst Log Message: ----------- Add a line of documentation about syncing Commit: 278c2aa399c45aec0eac6e8fa66e47d83e3bace2 https://github.com/galaxyproject/galaxy/commit/278c2aa399c45aec0eac6e8fa66e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M doc/source/admin/index.rst A doc/source/admin/useful_scripts.rst M doc/source/dev/faq.rst A scripts/api/library_upload_dir.py Log Message: ----------- Merge pull request #918 from erasche/library_upload_dir_script Library upload dir script Compare: https://github.com/galaxyproject/galaxy/compare/5a9fd385fa23...278c2aa399c4

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[galaxyproject/infrastructure-playbook] a09e61: Stuff for Jenkins
by GitHub 19 Oct '15

19 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: a09e61e00ca62e4de76684035c69028a1b9502eb https://github.com/galaxyproject/infrastructure-playbook/commit/a09e61e00ca… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M galaxyenv/host_vars/n2.galaxyproject.org.yml M galaxyenv/host_vars/westvleteren.galaxyproject.org.yml M galaxyenv/secret_group_vars/all.yml M 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 Log Message: ----------- Stuff for Jenkins

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[galaxyproject/galaxy] 76da3d: Adding information to help track down remote authe...
by GitHub 19 Oct '15

19 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 76da3df1cc717e24b94b74e0d3f7fd217a48068e https://github.com/galaxyproject/galaxy/commit/76da3df1cc717e24b94b74e0d3f7… Author: Ryan <ngsbioinformatics(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Adding information to help track down remote authentication issues Commit: 022b66b826bcb34407468fbc3f37de570e769606 https://github.com/galaxyproject/galaxy/commit/022b66b826bcb34407468fbc3f37… Author: Ryan <ngsbioinformatics(a)gmail.com> Date: 2015-10-03 (Sat, 03 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Update remoteuser.py Commit: 1c679021b176577723335719701d093b49c266de https://github.com/galaxyproject/galaxy/commit/1c679021b176577723335719701d… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Implement @blankenberg's suggestion. Remove whitespaces. Commit: 9343d189e227592bda13a1363d2ea96cf429108f https://github.com/galaxyproject/galaxy/commit/9343d189e227592bda13a1363d2e… Author: Ryan <ngsbioinformatics(a)gmail.com> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #1 from nsoranzo/patch-3 Implement @blankenberg's suggestion. Commit: 5a9fd385fa23211e4cc616278696459224b3e8b7 https://github.com/galaxyproject/galaxy/commit/5a9fd385fa23211e4cc616278696… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #823 from golharam/patch-1 Adding information to help track down remote authentication issues Compare: https://github.com/galaxyproject/galaxy/compare/347b1596a843...5a9fd385fa23

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[galaxyproject/usegalaxy-playbook] 3e9d83: Swapped GCC2016 Training nomination for November F...
by GitHub 19 Oct '15

19 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3e9d838e4d51c7094fc75078310e76cf579402a2 https://github.com/galaxyproject/usegalaxy-playbook/commit/3e9d838e4d51c709… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: A files/galaxy/common/static/welcome_img/201511_France.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Swapped GCC2016 Training nomination for November French events slide.

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[galaxyproject/galaxy] 20579e: Add a log.warn() if extracted file does not exist ...
by GitHub 19 Oct '15

19 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 20579ebd50c8e11d2f0bac45d3b0f71e1d732466 https://github.com/galaxyproject/galaxy/commit/20579ebd50c8e11d2f0bac45d3b0… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Add a log.warn() if extracted file does not exist when changing permissions. Should help to debug issue reported in PR #792. Commit: 347b1596a843c59e1158798bc3a2d7fa54f95a2b https://github.com/galaxyproject/galaxy/commit/347b1596a843c59e1158798bc3a2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #939 from nsoranzo/debug_for_792 Add a log.warn() if extracted file does not exist when changing permissions. Compare: https://github.com/galaxyproject/galaxy/compare/123bf620df33...347b1596a843

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