Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 46e452bfe820ddbb329e694d0eb2b7b755594910
https://github.com/galaxyproject/galaxy/commit/46e452bfe820ddbb329e694d0eb2…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-12 (Sun, 12 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/tools.py
Log Message:
-----------
Fix typo in install_dependencies docstring
Commit: 8b5d408e438c346f04088374d70eaca65e06c292
https://github.com/galaxyproject/galaxy/commit/8b5d408e438c346f04088374d70e…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-12 (Sun, 12 Mar 2017)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M test/integration/test_resolvers.py
Log Message:
-----------
Add API to remove requirements installed by Conda
This is currently limited to the Conda dependency resolver, but other
resolver would only need to implement the resolver.uninstall method and
set can_uninstall_dependencies to True.
To use this endpoint, POST to
<galaxy_url>/tools/<tool_id>/uninstall_dependencies'.
Commit: 3b067ef62a4dfa8af54bc4c75c6260f98d660aeb
https://github.com/galaxyproject/galaxy/commit/3b067ef62a4dfa8af54bc4c75c62…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-12 (Sun, 12 Mar 2017)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Return last non-zero returncode
Commit: d5b5d29137ee1e5577530ed2c56579b9394520b3
https://github.com/galaxyproject/galaxy/commit/d5b5d29137ee1e5577530ed2c565…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-12 (Sun, 12 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M test/integration/test_resolvers.py
Log Message:
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Change endpoint to `api/tools/<tool_id>/dependencies`
A POST will trigger installation and DELETE will trigger uninstalling
the dependencies (Thx for the suggestion @jmchilton).
Commit: 6902e62d38e3c5741a238736f640b5b847c5e8c2
https://github.com/galaxyproject/galaxy/commit/6902e62d38e3c5741a238736f640…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-12 (Sun, 12 Mar 2017)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Fix uninstall when not all dependencies are resolved by all-in-one resolver
Commit: 95106ea3c9ad875ce35b16c6b9bb8556f3d82076
https://github.com/galaxyproject/galaxy/commit/95106ea3c9ad875ce35b16c6b9bb…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-12 (Sun, 12 Mar 2017)
Changed paths:
M lib/galaxy/web/base/controllers/admin.py
M templates/webapps/galaxy/admin/manage_dependencies.mako
Log Message:
-----------
Add UI for Conda dependency uninstall
Commit: fc1df7bad17e53c54bd57602b82bbec22cc0e074
https://github.com/galaxyproject/galaxy/commit/fc1df7bad17e53c54bd57602b82b…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-13 (Mon, 13 Mar 2017)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M templates/webapps/galaxy/admin/manage_dependencies.mako
M test/integration/test_resolvers.py
Log Message:
-----------
Merge pull request #3725 from mvdbeek/remove_env_conda
Add API and UI to remove requirements installed by Conda
Compare: https://github.com/galaxyproject/galaxy/compare/33ff2754cc75...fc1df7bad17e
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 90108e450fd2d13d3010e05a2fcb1224a2549a2a
https://github.com/galaxyproject/galaxy/commit/90108e450fd2d13d3010e05a2fcb…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-08 (Wed, 08 Mar 2017)
Changed paths:
M client/galaxy/scripts/onload.js
M static/maps/onload.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/onload.js
Log Message:
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tool-form needs to not be required at the top level of the Galaxy webapp
Commit: 2134d6c3856edf8358c185178f9efe35a232c03b
https://github.com/galaxyproject/galaxy/commit/2134d6c3856edf8358c185178f9e…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-08 (Wed, 08 Mar 2017)
Changed paths:
M config/plugins/webhooks/demo/search/static/script.js
Log Message:
-----------
Use a redirect (which will get routed, soon) instead of instantiating a toolform within the overlay -- this is much lighter weight
Commit: da9ee941afa604586cfc6dfdacb2594284b3e6f0
https://github.com/galaxyproject/galaxy/commit/da9ee941afa604586cfc6dfdacb2…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-08 (Wed, 08 Mar 2017)
Changed paths:
M config/plugins/webhooks/demo/search/static/script.js
Log Message:
-----------
Standardize tabs/spaces in webhook overlay search
Commit: 3d33586d4a5758e566dc5d1eceda91e97cd3d73a
https://github.com/galaxyproject/galaxy/commit/3d33586d4a5758e566dc5d1eceda…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-08 (Wed, 08 Mar 2017)
Changed paths:
M config/plugins/webhooks/demo/search/static/script.js
Log Message:
-----------
Cleanup pass on formatting/unused vars in webhooks
Commit: 5a7eab0f06b4eb9f877c8e582bb6e078622be1ad
https://github.com/galaxyproject/galaxy/commit/5a7eab0f06b4eb9f877c8e582bb6…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M client/galaxy/scripts/onload.js
M config/plugins/webhooks/demo/search/static/script.js
M static/maps/onload.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/onload.js
Log Message:
-----------
Merge pull request #3731 from dannon/fix_webhook_search_overlay
Fix webhook search overlay interfering with masthead load
Compare: https://github.com/galaxyproject/galaxy/compare/8911e491a56c...5a7eab0f06b4
Branch: refs/heads/master
Home: https://github.com/galaxyproject/infrastructure-playbook
Commit: 3111f6620693c4145f942fc916a9786140cd5314
https://github.com/galaxyproject/infrastructure-playbook/commit/3111f662069…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M common_env/secret_group_vars/sslwebservers.yml
M galaxyenv/files/jenkins/jenkins_server_user_ssh_config
M galaxyenv/files/jenkins/jenkins_slave_user_ssh_config
A galaxyenv/files/ssl/athena.galaxyproject.org_cert.pem
M galaxyenv/host_vars/athena.galaxyproject.org.yml
M galaxyenv/host_vars/chouffe.galaxyproject.org.yml
M galaxyenv/inventory
M galaxyenv/secret_group_vars/all.yml
M galaxyenv/secret_group_vars/jenkinsslaves.yml
M galaxyenv/secret_host_vars/athena.galaxyproject.org.yml
M galaxyenv/secret_host_vars/chouffe.galaxyproject.org.yml
M galaxyenv/secret_host_vars/leeroy.galaxyproject.org.yml
A galaxyenv/templates/nginx/cloudlaunch.j2
A galaxyenv/templates/nginx/galaxyproject.j2
A galaxyenv/templates/nginx/moin.j2
M galaxyenv/templates/nginx/new.j2
M galaxyenv/templates/nginx/wiki_hub_rewrites.conf.j2
Log Message:
-----------
Galaxy site moved to athena
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: 29479b5ca735b13b5b5716c5858f1966e57125a6
https://github.com/galaxyproject/usegalaxy-playbook/commit/29479b5ca735b13b…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
R common/host_vars/athena.galaxyproject.org.yml
M common/inventory
M common/secret_vars/ssl.yml
R files/ssl/athena.galaxyproject.org_cert.pem
R templates/nginx/cloudlaunch.j2
R templates/nginx/galaxyproject.j2
Log Message:
-----------
Move all athena stuff to infrastructure-playbook
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 33ababaeb48e8ecfad487a54e96550ce7e43bc78
https://github.com/galaxyproject/galaxy/commit/33ababaeb48e8ecfad487a54e965…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/queue_worker.py
Log Message:
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Move the user calculate_and_set_disk_usage functionality to the model instead of the queue worker.
Commit: c928f15b4d00bb798453d42a6f6a79042692edfc
https://github.com/galaxyproject/galaxy/commit/c928f15b4d00bb798453d42a6f6a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M lib/galaxy/model/__init__.py
Log Message:
-----------
Robustify calculate_and_set_disk_usage for handling changes during the long calc
Commit: cd6e7f73d8a54698aa63d670e8aba6e45f8eef1b
https://github.com/galaxyproject/galaxy/commit/cd6e7f73d8a54698aa63d670e8ab…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Swap admin recalculate to use model-based recalc-and-set
Commit: 751182640d1a76962cbac872ae31c0ce471872dd
https://github.com/galaxyproject/galaxy/commit/751182640d1a76962cbac872ae31…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Remove now-unused import of pgcalc
Commit: 8002ef31ea6f4cb52d6e907dcdf1d002ced45eb6
https://github.com/galaxyproject/galaxy/commit/8002ef31ea6f4cb52d6e907dcdf1…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M lib/galaxy/queue_worker.py
Log Message:
-----------
Ensure there's a user before calling calculate_and_set_disk_usage
Commit: e088a48323a06e80d55e85944a4c09cf368b8391
https://github.com/galaxyproject/galaxy/commit/e088a48323a06e80d55e85944a4c…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M lib/galaxy/queue_worker.py
Log Message:
-----------
Add error logging to recalculate task.
Commit: 2d964eb50c9f2f2246044a1d7b83e0f920046510
https://github.com/galaxyproject/galaxy/commit/2d964eb50c9f2f2246044a1d7b83…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M lib/galaxy/queue_worker.py
Log Message:
-----------
I have no idea what I would be doing without Nicola.
Commit: 8911e491a56cdc3b8fb327bc702b4843d7d22a4d
https://github.com/galaxyproject/galaxy/commit/8911e491a56cdc3b8fb327bc702b…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/queue_worker.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Merge pull request #3734 from dannon/queue_worker_trim
Quota recalculation logic consolidation
Compare: https://github.com/galaxyproject/galaxy/compare/bcc4e025c36c...8911e491a56c