- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] a950df: install SRA tools
by GitHub 05 Mar '16

05 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a950df86eecdada5a4468806ce913b631d32ad4e https://github.com/galaxyproject/usegalaxy-playbook/commit/a950df86eecdada5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-04 (Fri, 04 Mar 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml Log Message: ----------- install SRA tools

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[galaxyproject/galaxy]
by GitHub 05 Mar '16

05 Mar '16

Branch: refs/heads/python26_workaround Home: https://github.com/galaxyproject/galaxy

1 0

[galaxyproject/galaxy] 49d522: Initial commit
by GitHub 05 Mar '16

05 Mar '16

Branch: refs/heads/python26_workaround Home: https://github.com/galaxyproject/galaxy Commit: 49d5222beb9659df7b2d1f043003dd21b1ce95c3 https://github.com/galaxyproject/galaxy/commit/49d5222beb9659df7b2d1f043003… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: A LICENSE A README.md Log Message: ----------- Initial commit Commit: 01d4721c2f08ecbfe3351b76382f3f33f86d8e4a https://github.com/galaxyproject/galaxy/commit/01d4721c2f08ecbfe3351b76382f… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: M README.md A defaults/main.yml A files/install_tool_shed_tools.py A files/shed_tool_list_file.yaml A meta/main.yml A tasks/main.yml A tasks/tools.yml Log Message: ----------- Initial role implementation Commit: 725bd087dd29400fbc37cda223df3d311d2634e7 https://github.com/galaxyproject/galaxy/commit/725bd087dd29400fbc37cda223df… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-08-03 (Mon, 03 Aug 2015) Changed paths: M README.md M defaults/main.yml M tasks/main.yml Log Message: ----------- Rename control-flow variable from install_tools to galaxy_install_tools Commit: 1cda2cc5916ae2e298dcb76bd4c69cf5d83c7229 https://github.com/galaxyproject/galaxy/commit/1cda2cc5916ae2e298dcb76bd4c6… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-08-04 (Tue, 04 Aug 2015) Changed paths: M README.md M defaults/main.yml Log Message: ----------- Add a default to use the localhost Galaxy instance Commit: bfdd53c19e3bb17669bb2b3c9409cf6fe59b7e26 https://github.com/galaxyproject/galaxy/commit/bfdd53c19e3bb17669bb2b3c9409… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-08-04 (Tue, 04 Aug 2015) Changed paths: M README.md M defaults/main.yml A files/README.md A files/dbkeys_list.yaml.sample R files/shed_tool_list_file.yaml A files/tool_list.yaml A files/tool_list.yaml.sample Log Message: ----------- Add/update sample tool list files Commit: 1d2f3526782e7c8efbab3dc0861b6c1df7c14fcb https://github.com/galaxyproject/galaxy/commit/1d2f3526782e7c8efbab3dc0861b… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-08-05 (Wed, 05 Aug 2015) Changed paths: M README.md M defaults/main.yml M files/README.md M files/install_tool_shed_tools.py M tasks/tools.yml Log Message: ----------- Rename variable and corresponding file shed_tool_list_file to tool_list_file Commit: 5a0261ae12929edafcdf01012bf7f36f52497b48 https://github.com/galaxyproject/galaxy/commit/5a0261ae12929edafcdf01012bf7… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-08-06 (Thu, 06 Aug 2015) Changed paths: M files/install_tool_shed_tools.py Log Message: ----------- Replace OptionParser with ArgumentParser Commit: 77748d8b3713083677baebcb6c068c20b486497c https://github.com/galaxyproject/galaxy/commit/77748d8b3713083677baebcb6c06… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-08-06 (Thu, 06 Aug 2015) Changed paths: M files/install_tool_shed_tools.py Log Message: ----------- Add command line options to allow an individual tool to be installed without providing a YAML file Commit: 5c0c23935f79051b6781f9797c0a61ac3aa72ce3 https://github.com/galaxyproject/galaxy/commit/5c0c23935f79051b6781f9797c0a… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-08-06 (Thu, 06 Aug 2015) Changed paths: M README.md Log Message: ----------- Update README Commit: dc4e9a5cfc9d390cfb32130c9b9107b34e008958 https://github.com/galaxyproject/galaxy/commit/dc4e9a5cfc9d390cfb32130c9b91… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-08-06 (Thu, 06 Aug 2015) Changed paths: M files/install_tool_shed_tools.py Log Message: ----------- Remove dev leftovers... Commit: 44e73cacb47841b520cfd3be23ee06f6aff306b3 https://github.com/galaxyproject/galaxy/commit/44e73cacb47841b520cfd3be23ee… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M files/install_tool_shed_tools.py Log Message: ----------- Keep track of tools that installed successfully. Commit: 87c28325bb080685ccbd6c91c0eba065bf22694f https://github.com/galaxyproject/galaxy/commit/87c28325bb080685ccbd6c91c0eb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M README.md M defaults/main.yml M tasks/tools.yml Log Message: ----------- Role-scope variables Commit: 8bd6a3e62a0bc59eb15992686d957d9123ba63c5 https://github.com/galaxyproject/galaxy/commit/8bd6a3e62a0bc59eb15992686d95… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M README.md M defaults/main.yml M tasks/tools.yml Log Message: ----------- Merge pull request #1 from natefoo/master Role-scope variables Commit: 849e1fcf4a7d5dcdfce0bc16205e73c7c60f56e2 https://github.com/galaxyproject/galaxy/commit/849e1fcf4a7d5dcdfce0bc16205e… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M README.md Log Message: ----------- Update README Commit: ab64c06135da40cbff5a34823b7e57655986b3a8 https://github.com/galaxyproject/galaxy/commit/ab64c06135da40cbff5a34823b7e… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M files/install_tool_shed_tools.py Log Message: ----------- Fix one of the Tool Shed ID names Commit: b9b006f749f93e4703e1e691bcf12780e352d587 https://github.com/galaxyproject/galaxy/commit/b9b006f749f93e4703e1e691bcf1… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M README.md M defaults/main.yml A files/manage_bootstrap_user.py A tasks/bootstrap_user.yml M tasks/main.yml A tasks/restart_galaxy.yml Log Message: ----------- Add an option to create (and delete) a bootstrap user as part of the tool installation process Commit: 667667ddeb5023df642bf9e088af76e4a8f7b880 https://github.com/galaxyproject/galaxy/commit/667667ddeb5023df642bf9e088af… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M README.md Log Message: ----------- Update README Commit: f3d963054eeca1afcc06a4480db92e16f17447b3 https://github.com/galaxyproject/galaxy/commit/f3d963054eeca1afcc06a4480db9… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: M files/install_tool_shed_tools.py Log Message: ----------- Update function to grabbing installed tool revisions to be more compatible with the required input for the tool installation function Commit: 7bae7d63c2622b7f531af225392d83bf78fa7e13 https://github.com/galaxyproject/galaxy/commit/7bae7d63c2622b7f531af225392d… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: M files/install_tool_shed_tools.py Log Message: ----------- Match up tools from the tool panel and those obtained from the /api/tool_shed_repositories endpoint to create a more complete list of tools installed on a Galaxy instance Commit: 759d064897969fc39525aef7a9493f0d145e3ca5 https://github.com/galaxyproject/galaxy/commit/759d064897969fc39525aef7a949… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: M files/install_tool_shed_tools.py Log Message: ----------- A bit of code cleanup Commit: 952b3aba536bb6923e7a7f8846c04204bc8b7c51 https://github.com/galaxyproject/galaxy/commit/952b3aba536bb6923e7a7f8846c0… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-08-25 (Tue, 25 Aug 2015) Changed paths: M files/install_tool_shed_tools.py Log Message: ----------- Add an option to omit tools based on their name from the returned list of installed tools Commit: 8dc2e7ce2a0821c3dba9feb972ba4fa22181c4c7 https://github.com/galaxyproject/galaxy/commit/8dc2e7ce2a0821c3dba9feb972ba… Author: nuwan_ag <nuwan.ag(a)gmail.com> Date: 2015-09-09 (Wed, 09 Sep 2015) Changed paths: M tasks/bootstrap_user.yml M tasks/main.yml Log Message: ----------- Fix execution order and short-circuit issue when installing tools Commit: b4c010cd4f04f2cbc6799aaa4fdd3954bbb23918 https://github.com/galaxyproject/galaxy/commit/b4c010cd4f04f2cbc6799aaa4fdd… Author: nuwan_ag <nuwan.ag(a)gmail.com> Date: 2015-09-09 (Wed, 09 Sep 2015) Changed paths: M tasks/main.yml Log Message: ----------- Passed variable instead of value Commit: 6e4d52ff185160c93fe30b9a164356a4fe7e918b https://github.com/galaxyproject/galaxy/commit/6e4d52ff185160c93fe30b9a1643… Author: nuwan_ag <nuwan.ag(a)gmail.com> Date: 2015-09-09 (Wed, 09 Sep 2015) Changed paths: M tasks/bootstrap_user.yml Log Message: ----------- Fixed conditional evaluation when variable is undefined Commit: 86226744f50730cfe7326b8943367ce526a5a719 https://github.com/galaxyproject/galaxy/commit/86226744f50730cfe7326b894336… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-09-09 (Wed, 09 Sep 2015) Changed paths: M tasks/bootstrap_user.yml M tasks/main.yml Log Message: ----------- Merge pull request #4 from nuwang/master Fix execution order and short-circuit issue when installing tools Commit: e9550624506a1666073dd9ea5acbc0a11805752c https://github.com/galaxyproject/galaxy/commit/e9550624506a1666073dd9ea5acb… Author: nuwan_ag <nuwan.ag(a)gmail.com> Date: 2015-09-19 (Sat, 19 Sep 2015) Changed paths: M tasks/bootstrap_user.yml Log Message: ----------- Remove bootstrap user from galaxy admin list Commit: 63c17f002d039479cd85a448464443ac11cf9652 https://github.com/galaxyproject/galaxy/commit/63c17f002d039479cd85a4484644… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-09-19 (Sat, 19 Sep 2015) Changed paths: M tasks/bootstrap_user.yml Log Message: ----------- Merge pull request #6 from nuwang/master Remove bootstrap user from galaxy admin list Commit: 0bc968146425d2e8025a6b90db511ec71faa65e0 https://github.com/galaxyproject/galaxy/commit/0bc968146425d2e8025a6b90db51… Author: nuwan_ag <nuwan.ag(a)gmail.com> Date: 2015-09-20 (Sun, 20 Sep 2015) Changed paths: M defaults/main.yml M tasks/tools.yml Log Message: ----------- Added setting for ignoring tool errors. Default is no Commit: ca8724e2e522e361b781922184e37d20c76a98f2 https://github.com/galaxyproject/galaxy/commit/ca8724e2e522e361b781922184e3… Author: nuwan_ag <nuwan.ag(a)gmail.com> Date: 2015-09-20 (Sun, 20 Sep 2015) Changed paths: M tasks/tools.yml Log Message: ----------- Fixed syntax error Commit: bb278077f692b60104b4c71a5864b04819c16c7b https://github.com/galaxyproject/galaxy/commit/bb278077f692b60104b4c71a5864… Author: nuwan_ag <nuwan.ag(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M defaults/main.yml M tasks/tools.yml Log Message: ----------- Added support for multiple tool list files. Removed ignore_tool_errors when installing tools Commit: 0f175fda7bc85d5fec136a6bb9102bee0f2326b8 https://github.com/galaxyproject/galaxy/commit/0f175fda7bc85d5fec136a6bb910… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M defaults/main.yml M tasks/tools.yml Log Message: ----------- Merge pull request #7 from nuwang/master Added support for multiple tool list files Commit: c259caa75621dadea8280dfa7d06db9df1c122bd https://github.com/galaxyproject/galaxy/commit/c259caa75621dadea8280dfa7d06… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M files/install_tool_shed_tools.py Log Message: ----------- Allow specifying tool_panel_section_label. Commit: f4f8f4ef3c901e5716aa3dbe355bf0b2e1ca2dee https://github.com/galaxyproject/galaxy/commit/f4f8f4ef3c901e5716aa3dbe355b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M files/install_tool_shed_tools.py Log Message: ----------- Merge pull request #8 from mvdbeek/master Allow specifying tool_panel_section_label. Commit: bfbcff5dfd2f7e69418c77cbf66d6679b03e5cb5 https://github.com/galaxyproject/galaxy/commit/bfbcff5dfd2f7e69418c77cbf66d… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M files/install_tool_shed_tools.py Log Message: ----------- Integrate tool_panel_section_label from PR #8 into the logic Commit: 5bba9cb3eccf7f84fdef7667116c79ea4cd28d8c https://github.com/galaxyproject/galaxy/commit/5bba9cb3eccf7f84fdef7667116c… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M files/install_tool_shed_tools.py Log Message: ----------- Merge branch 'master' of https://github.com/galaxyproject/ansible-tools Commit: 9d3b025e0dc45a82accd8553fd450bf9306f0211 https://github.com/galaxyproject/galaxy/commit/9d3b025e0dc45a82accd8553fd45… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M files/install_tool_shed_tools.py M files/tool_list.yaml.sample Log Message: ----------- Add docs to the sample file for using tool_panel_section_label; update logging message Commit: 514edd4fdfc4f5255433bf075583c6ef3ad771ae https://github.com/galaxyproject/galaxy/commit/514edd4fdfc4f5255433bf075583… Author: Fabio Rocha Jimenez Vieira <fabiorjvieira(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M files/install_tool_shed_tools.py Log Message: ----------- Reactivate data manager options. Commit: fa7b4dc22410c87063184a0fa98006077c380cc3 https://github.com/galaxyproject/galaxy/commit/fa7b4dc22410c87063184a0fa980… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-12-26 (Sat, 26 Dec 2015) Changed paths: M files/install_tool_shed_tools.py Log Message: ----------- Merge pull request #9 from fabiorjvieira/master Reactivate data manager options. Commit: 8eba7171b1f9c0752dd7929d20dc7fde0655057b https://github.com/galaxyproject/galaxy/commit/8eba7171b1f9c0752dd7929d20dc… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-01-02 (Sat, 02 Jan 2016) Changed paths: M files/install_tool_shed_tools.py Log Message: ----------- fallback for already installed tools Commit: 88ebe3d88c4570475e968b204122f79c4c68987c https://github.com/galaxyproject/galaxy/commit/88ebe3d88c4570475e968b204122… Author: Enis Afgan <afgane(a)gmail.com> Date: 2016-01-02 (Sat, 02 Jan 2016) Changed paths: M files/install_tool_shed_tools.py Log Message: ----------- Merge pull request #10 from galaxyproject/already_installed fallback for already installed tools Commit: 2e34d84b5a79e5f909f640c78e6853f5f2313ff5 https://github.com/galaxyproject/galaxy/commit/2e34d84b5a79e5f909f640c78e68… Author: Enis Afgan <afgane(a)gmail.com> Date: 2016-01-02 (Sat, 02 Jan 2016) Changed paths: M files/install_tool_shed_tools.py Log Message: ----------- A couple of minor style changes for PR #10 Commit: 5b2bbf6cd6f88cb2ffaef0db2d6e7c7510391b62 https://github.com/galaxyproject/galaxy/commit/5b2bbf6cd6f88cb2ffaef0db2d6e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-01-06 (Wed, 06 Jan 2016) Changed paths: M defaults/main.yml M files/install_tool_shed_tools.py M tasks/tools.yml Log Message: ----------- Install tools from tool_list individually Commit: d26cfa4851d5865b048761a0df16ed621ea2b448 https://github.com/galaxyproject/galaxy/commit/d26cfa4851d5865b048761a0df16… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-01-06 (Wed, 06 Jan 2016) Changed paths: M defaults/main.yml M tasks/tools.yml Log Message: ----------- Attempt to discover tool install state Commit: 7328b2034b6bd6c8c0a549cf30fc6d5873f6b5bf https://github.com/galaxyproject/galaxy/commit/7328b2034b6bd6c8c0a549cf30fc… Author: Enis Afgan <afgane(a)gmail.com> Date: 2016-01-06 (Wed, 06 Jan 2016) Changed paths: M defaults/main.yml M files/install_tool_shed_tools.py M tasks/tools.yml Log Message: ----------- Merge pull request #11 from mvdbeek/install_individual_tools Install tools from tool_list individually Commit: dbf5183aa7bf633e9cf6ddad2741fbea6046fbd8 https://github.com/galaxyproject/galaxy/commit/dbf5183aa7bf633e9cf6ddad2741… Author: Enis Afgan <afgane(a)gmail.com> Date: 2016-01-06 (Wed, 06 Jan 2016) Changed paths: M defaults/main.yml M files/install_tool_shed_tools.py M tasks/tools.yml Log Message: ----------- Add some docs for PR #11 Commit: 809fab5df7a5508ace55bc175a69c99b256ab9e7 https://github.com/galaxyproject/galaxy/commit/809fab5df7a5508ace55bc175a69… Author: Fabio Rocha Jimenez Vieira <fabiorjvieira(a)gmail.com> Date: 2016-01-12 (Tue, 12 Jan 2016) Changed paths: M tasks/bootstrap_user.yml M tasks/restart_galaxy.yml Log Message: ----------- Check if galaxy is managed by supervisor and avoid bootstrap procedure to remove the previous admin. Commit: ca01aeea836f128a8cc54f2a7a514062170b7509 https://github.com/galaxyproject/galaxy/commit/ca01aeea836f128a8cc54f2a7a51… Author: Fabio Rocha Jimenez Vieira <fabiorjvieira(a)gmail.com> Date: 2016-01-12 (Tue, 12 Jan 2016) Changed paths: M tasks/bootstrap_user.yml M tasks/restart_galaxy.yml Log Message: ----------- fix bootstrap user misplaced whens. Commit: 81ad20a35c43cfd97d534e5c952f4e29cab387d7 https://github.com/galaxyproject/galaxy/commit/81ad20a35c43cfd97d534e5c952f… Author: Fabio Rocha Jimenez Vieira <fabiorjvieira(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M tasks/bootstrap_user.yml Log Message: ----------- Fixing bootstrap user porcedure (bootstrap_user.yml) when there is already a admin in galaxy config file. Commit: 3d0040e9237e4000289b8d06cb83526deb9d4a3d https://github.com/galaxyproject/galaxy/commit/3d0040e9237e4000289b8d06cb83… Author: Fabio Rocha Jimenez Vieira <fabiorjvieira(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M tasks/bootstrap_user.yml Log Message: ----------- Bootstrap user procedure fixed (bootstrap_user.yml). It is ok when there is already a admin in galaxy config file. Commit: dee138f1269ce71cc12ac7b346c2afa7505e86ad https://github.com/galaxyproject/galaxy/commit/dee138f1269ce71cc12ac7b346c2… Author: Enis Afgan <afgane(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M tasks/bootstrap_user.yml M tasks/restart_galaxy.yml Log Message: ----------- Merge pull request #14 from fabiorjvieira/master Fix "bootstrap user" and "restart galaxy" tasks Commit: be1300a8fbd501a8d985c8bb9b22604a4807c786 https://github.com/galaxyproject/galaxy/commit/be1300a8fbd501a8d985c8bb9b22… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M files/install_tool_shed_tools.py Log Message: ----------- Use last item of response to determine if install has finished. Commit: 8ce34d1e0931dd70369d717aabb1057100e41f34 https://github.com/galaxyproject/galaxy/commit/8ce34d1e0931dd70369d717aabb1… Author: Enis Afgan <afgane(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M files/install_tool_shed_tools.py Log Message: ----------- Merge pull request #16 from ARTbio/wait_for_install Use last item of response to determine if install has finished. Commit: 429fa4e01b9e03b65f5e28e71f0982c2dc10c746 https://github.com/galaxyproject/galaxy/commit/429fa4e01b9e03b65f5e28e71f09… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-01-31 (Sun, 31 Jan 2016) Changed paths: M files/install_tool_shed_tools.py Log Message: ----------- Wait for tool installation to finish before timeout. Commit: 15c12fce58f8dbeb449355c9149ea7a565d649b7 https://github.com/galaxyproject/galaxy/commit/15c12fce58f8dbeb449355c9149e… Author: Enis Afgan <afgane(a)gmail.com> Date: 2016-01-31 (Sun, 31 Jan 2016) Changed paths: M files/install_tool_shed_tools.py Log Message: ----------- Merge pull request #17 from mvdbeek/timeout Wait for tool installation to finish before timeout. Commit: a96e604b9078a9c7bff7bbea8764d16c6ede0b71 https://github.com/galaxyproject/galaxy/commit/a96e604b9078a9c7bff7bbea8764… Author: Enis Afgan <afgane(a)gmail.com> Date: 2016-01-31 (Sun, 31 Jan 2016) Changed paths: M files/install_tool_shed_tools.py Log Message: ----------- Remove unused code; style cleanup Commit: 2dac7b89e1c890a44430d6c217521679cfb3d2eb https://github.com/galaxyproject/galaxy/commit/2dac7b89e1c890a44430d6c21752… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M defaults/main.yml A files/install_workflow.py M tasks/main.yml A tasks/workflows.yml Log Message: ----------- Install workflow (for admin user currently) Commit: 9f4767b448395188259c02fbd44fdc2a1335c63d https://github.com/galaxyproject/galaxy/commit/9f4767b448395188259c02fbd44f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M tasks/workflows.yml Log Message: ----------- Workfow path needs to be quoted Commit: 6c075e8e91f231edd787905b6267de2b36ec2f79 https://github.com/galaxyproject/galaxy/commit/6c075e8e91f231edd787905b6267… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M defaults/main.yml A files/sample-workflow.ga Log Message: ----------- Add sample workflow Commit: 7eb4129adf3303c572f430b28295c51896a8bcec https://github.com/galaxyproject/galaxy/commit/7eb4129adf3303c572f430b28295… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M defaults/main.yml M tasks/main.yml Log Message: ----------- Boolean to control workflow installation, empty list of workflows Commit: dd1444344ae6b26118d3d69d2dc13e1155862e8b https://github.com/galaxyproject/galaxy/commit/dd1444344ae6b26118d3d69d2dc1… Author: Enis Afgan <afgane(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M defaults/main.yml A files/install_workflow.py A files/sample-workflow.ga M tasks/main.yml A tasks/workflows.yml Log Message: ----------- Merge pull request #18 from ARTbio/install_workflow Install workflow Commit: 9ea6a81fe4bf27de285e81d33d8cfbc40f842f98 https://github.com/galaxyproject/galaxy/commit/9ea6a81fe4bf27de285e81d33d8c… Author: Cameron Jack <cameron.jack(a)anu.edu.au> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M files/install_workflow.py Log Message: ----------- Adds UUID checking to avoid duplicate installs Commit: 27e9c783e3624064505be1e2f650795a5d98d141 https://github.com/galaxyproject/galaxy/commit/27e9c783e3624064505be1e2f650… Author: Cameron Jack <cameron.jack(a)anu.edu.au> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M files/install_workflow.py Log Message: ----------- Adds UUID checking to avoid duplicate workflows Commit: d2f157cc0eb177107e97df6a2d372d7735787960 https://github.com/galaxyproject/galaxy/commit/d2f157cc0eb177107e97df6a2d37… Author: Enis Afgan <afgane(a)gmail.com> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M files/install_workflow.py Log Message: ----------- Merge pull request #19 from cameron-jack/master UUID checking to avoid duplicate workflows Commit: eec47f7a6988d4472bc99789fcc7ba894b74c17b https://github.com/galaxyproject/galaxy/commit/eec47f7a6988d4472bc99789fcc7… Author: Enis Afgan <afgane(a)gmail.com> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M files/install_workflow.py Log Message: ----------- Use .get methods when retrieving uuid keys Commit: 90c816bd40a4971dda8bd96d865efb1dee131566 https://github.com/galaxyproject/galaxy/commit/90c816bd40a4971dda8bd96d865e… Author: Enis Afgan <afgane(a)gmail.com> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M files/install_workflow.py Log Message: ----------- Make sure the opened workflow file gets closed after it's been loaded Commit: c2aa72da4180cd6d25b25f8b79730c8fa5f863fd https://github.com/galaxyproject/galaxy/commit/c2aa72da4180cd6d25b25f8b7973… Author: Enis Afgan <afgane(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M files/manage_bootstrap_user.py Log Message: ----------- Fix logging in the bootstrap user management script Commit: a335ceecfcc3cd633c562ef8381e9ba30e3aceff https://github.com/galaxyproject/galaxy/commit/a335ceecfcc3cd633c562ef8381e… Author: Enis Afgan <afgane(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M defaults/main.yml M tasks/bootstrap_user.yml Log Message: ----------- Explicitly set the bootstrap user username Commit: 15e9c0925d4e79f82e553205b170855066094df6 https://github.com/galaxyproject/galaxy/commit/15e9c0925d4e79f82e553205b170… Author: Enis Afgan <afgane(a)gmail.com> Date: 2016-02-10 (Wed, 10 Feb 2016) Changed paths: M files/manage_bootstrap_user.py Log Message: ----------- Minor bootstrap user script cleanup Commit: 836b5240653d1cfc9ea39e587841b2f12270c2b2 https://github.com/galaxyproject/galaxy/commit/836b5240653d1cfc9ea39e587841… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-04 (Fri, 04 Mar 2016) Changed paths: M files/install_tool_shed_tools.py Log Message: ----------- Workaround missing logging functionality in python2.6 Compare: https://github.com/galaxyproject/galaxy/compare/49d5222beb96^...836b5240653d

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[galaxyproject/usegalaxy-playbook] 73a7f9: update tools on Main
by GitHub 05 Mar '16

05 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 73a7f96b704e852c2d83dee574f7d720ad29bb71 https://github.com/galaxyproject/usegalaxy-playbook/commit/73a7f96b704e852c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-04 (Fri, 04 Mar 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_data_manager_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- update tools on Main Commit: a9d612d91dcdc7ff64a70642dba6a84882a3ee63 https://github.com/galaxyproject/usegalaxy-playbook/commit/a9d612d91dcdc7ff… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-04 (Fri, 04 Mar 2016) Changed paths: M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml Log Message: ----------- Manage labels on Main (new/updated) Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/2841ee2db805...…

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[galaxyproject/galaxy] a29ae8: Fix regex validator
by GitHub 05 Mar '16

05 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a29ae884087216963a1cb909bb208b3d9ab16573 https://github.com/galaxyproject/galaxy/commit/a29ae884087216963a1cb909bb20… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-04 (Fri, 04 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Fix regex validator Commit: f9afe5927b6b97e6d1e75b58387e1a38696abd17 https://github.com/galaxyproject/galaxy/commit/f9afe5927b6b97e6d1e75b58387e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-04 (Fri, 04 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Merge pull request #1862 from guerler/fix_regex_validator_000 Fix regex validator Compare: https://github.com/galaxyproject/galaxy/compare/b4eae046cd75...f9afe5927b6b

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[galaxyproject/galaxy] 7ca03b: Fix typos.
by GitHub 04 Mar '16

04 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7ca03bbf047d989359dcf1eee460e4586e200f54 https://github.com/galaxyproject/galaxy/commit/7ca03bbf047d989359dcf1eee460… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix typos. Commit: 501a10c3f1ab7102e0a83d4afdd97f78a1a0bc21 https://github.com/galaxyproject/galaxy/commit/501a10c3f1ab7102e0a83d4afdd9… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M lib/galaxy/datatypes/tabular.py M lib/galaxy/external_services/result_handlers/basic.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/context.py M lib/galaxy/model/metadata.py M lib/galaxy/model/search.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/util/dbkeys.py M lib/galaxy/util/json.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/workflow/modules.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/workflow_util.py M scripts/functional_tests.py M scripts/transfer.py M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/tool_shed/base/twilltestcase.py M tools/data_source/upload.py Log Message: ----------- Do not import dumps and loads from galaxy.util.json . Commit: b4eae046cd759a906ccf1e8cd9297a5dc305f57d https://github.com/galaxyproject/galaxy/commit/b4eae046cd759a906ccf1e8cd929… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-04 (Fri, 04 Mar 2016) Changed paths: M lib/galaxy/datatypes/tabular.py M lib/galaxy/external_services/result_handlers/basic.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/context.py M lib/galaxy/model/metadata.py M lib/galaxy/model/search.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/dbkeys.py M lib/galaxy/util/json.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/workflow/modules.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/workflow_util.py M scripts/functional_tests.py M scripts/transfer.py M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/tool_shed/base/twilltestcase.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #1840 from nsoranzo/galaxy_util_json Do not import dumps and loads from galaxy.util.json . Compare: https://github.com/galaxyproject/galaxy/compare/84daaec66e87...b4eae046cd75

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[galaxyproject/galaxy] a10934: Fix repeat prefix
by GitHub 04 Mar '16

04 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a10934741dc53b545effdbd407f6b05584bc64de https://github.com/galaxyproject/galaxy/commit/a10934741dc53b545effdbd407f6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Fix repeat prefix Commit: 84daaec66e875055e5513619e9fa4c7368bda229 https://github.com/galaxyproject/galaxy/commit/84daaec66e875055e5513619e9fa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-04 (Fri, 04 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Merge pull request #1848 from guerler/fix_prefix_000 Fix repeat prefix Compare: https://github.com/galaxyproject/galaxy/compare/6da3c56ec9e6...84daaec66e87

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[galaxyproject/galaxy] 1c73b8: also update rrda when repairing or updating a repo...
by GitHub 04 Mar '16

04 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1c73b8c1a335881d2b1573cc954d1c0ed1438c65 https://github.com/galaxyproject/galaxy/commit/1c73b8c1a335881d2b1573cc954d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py Log Message: ----------- also update rrda when repairing or updating a repository Commit: 887e2577c98244a223cbc8ef0523fa8d1a4ae352 https://github.com/galaxyproject/galaxy/commit/887e2577c98244a223cbc8ef0523… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-04 (Fri, 04 Mar 2016) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Add logging before removing outdated dependencies Commit: 6da3c56ec9e6e644847eee417e2b3f4b5b5078c0 https://github.com/galaxyproject/galaxy/commit/6da3c56ec9e6e644847eee417e2b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-04 (Fri, 04 Mar 2016) Changed paths: M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #1850 from mvdbeek/old_rrda_fix also update rrda when repairing or updating a repository Compare: https://github.com/galaxyproject/galaxy/compare/45bffbcd1915...6da3c56ec9e6

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[galaxyproject/galaxy] 26d556: Update more scripts to respect GALAXY_VIRTUAL_ENV.
by GitHub 03 Mar '16

03 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 26d5561b4ff48eb770970bee5f2ba49d425e9902 https://github.com/galaxyproject/galaxy/commit/26d5561b4ff48eb770970bee5f2b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M manage_tools.sh M run_reports.sh M run_tool_shed.sh Log Message: ----------- Update more scripts to respect GALAXY_VIRTUAL_ENV. Drop explicit sourcing in run_reports and run_tool_shed since they source common_startup. Commit: 97793ab81ab5601466fa89bba7b3250118e95de4 https://github.com/galaxyproject/galaxy/commit/97793ab81ab5601466fa89bba7b3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M manage_tools.sh M run_reports.sh M run_tool_shed.sh Log Message: ----------- Merge pull request #1847 from jmchilton/more_virtualenv_fixes [16.01] Update more scripts to respect GALAXY_VIRTUAL_ENV. Compare: https://github.com/galaxyproject/galaxy/compare/0fbd22c9a306...97793ab81ab5

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[galaxyproject/galaxy] 8dd247: Minor followup to 1846
by GitHub 03 Mar '16

03 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8dd24734e3fd9dd64bc4bd93736c9ef571930cbf https://github.com/galaxyproject/galaxy/commit/8dd24734e3fd9dd64bc4bd93736c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M client/galaxy/scripts/onload.js M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/onload.js Log Message: ----------- Minor followup to 1846 Commit: 45bffbcd19158e6f147398d07d3f691f18d50247 https://github.com/galaxyproject/galaxy/commit/45bffbcd19158e6f147398d07d3f… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M client/galaxy/scripts/onload.js M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/onload.js Log Message: ----------- Merge pull request #1853 from dannon/style_nits Minor style followup to 1846 Compare: https://github.com/galaxyproject/galaxy/compare/02ed07ca82e1...45bffbcd1915

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