- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] cbbbc2: update MTS and TTS
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: cbbbc2025f418bf83dfc21931faa6958339fda3f https://github.com/galaxyproject/usegalaxy-playbook/commit/cbbbc2025f418bf8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M production/group_vars/toolshedservers.yml M stage/group_vars/toolshedservers.yml Log Message: ----------- update MTS and TTS

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[galaxyproject/usegalaxy-playbook] ec3aba: things that showed up after updating Galaxy's vers...
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ec3abaa9fee94c4a852f3eb14acea2483b0f03ab https://github.com/galaxyproject/usegalaxy-playbook/commit/ec3abaa9fee94c4a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M production/files/interactive_environments/plugins/.ansible_ie_role_current_version M production/files/interactive_environments/proxy/.ansible_ie_role_current_version Log Message: ----------- things that showed up after updating Galaxy's version

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[galaxyproject/usegalaxy-playbook] c78ef2: install deeptools; update Main to latest 16.01
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c78ef2fec723ea8784b5c2ea9a63c714a1167e63 https://github.com/galaxyproject/usegalaxy-playbook/commit/c78ef2fec723ea87… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-18 (Fri, 18 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 M production/group_vars/all.yml Log Message: ----------- install deeptools; update Main to latest 16.01 Please enter the commit message for your changes. Lines starting

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[galaxyproject/galaxy] 29c78e: Fix virtualenv broken with #1847.
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 29c78e984e52ac08b1b36a03e39b65c6edbe6200 https://github.com/galaxyproject/galaxy/commit/29c78e984e52ac08b1b36a03e39b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M run_reports.sh M run_tool_shed.sh Log Message: ----------- Fix virtualenv broken with #1847. Commit: 5824bc04af9270afbebcb2c8f9b6b3bea371b788 https://github.com/galaxyproject/galaxy/commit/5824bc04af9270afbebcb2c8f9b6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M run_reports.sh M run_tool_shed.sh Log Message: ----------- Fix duplicate print statement reported by @dannon... https://github.com/galaxyproject/galaxy/pull/1890#issuecomment-193873380 Commit: 438661e8945c1bb317f75dabe3db429ea779255d https://github.com/galaxyproject/galaxy/commit/438661e8945c1bb317f75dabe3db… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M run_reports.sh M run_tool_shed.sh Log Message: ----------- Another fix for virtualenv fixes. Commit: 00a7c3af057c0689a53748802740bc2002df375c https://github.com/galaxyproject/galaxy/commit/00a7c3af057c0689a53748802740… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M run_reports.sh M run_tool_shed.sh Log Message: ----------- Merge pull request #1890 from jmchilton/fix_virtualenvs [16.01] Fix virtual env handling broken with #1847. Commit: f277f99aed411fede7d1cb91d3177469922a58ae https://github.com/galaxyproject/galaxy/commit/f277f99aed411fede7d1cb91d317… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/util/log/fluent_log.py Log Message: ----------- Fix handling of time in fluent logger. Commit: 87bcb5f5a1b6801e948b2cc0f5dc676c7faca682 https://github.com/galaxyproject/galaxy/commit/87bcb5f5a1b6801e948b2cc0f5dc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/util/log/fluent_log.py Log Message: ----------- Fix in a different way not requiring signature change; still not thrilled about overlapping kwarg names w/ stdlib module names. Commit: c8e48bfaccb5d10552df4200e616a9eee49206b0 https://github.com/galaxyproject/galaxy/commit/c8e48bfaccb5d10552df4200e616… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Add fluentd configuration to galaxy.ini.sample Commit: 98c65dcee08338ea80a7e34251f8fa4ed6bd8dd5 https://github.com/galaxyproject/galaxy/commit/98c65dcee08338ea80a7e34251f8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/util/log/fluent_log.py M lib/galaxy/webapps/galaxy/api/metrics.py Log Message: ----------- Swap back to the first fix, update metrics api to use new signature. Commit: 19bf334c7763c2418408083b9a7369386e50ad66 https://github.com/galaxyproject/galaxy/commit/19bf334c7763c2418408083b9a73… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/util/log/fluent_log.py M lib/galaxy/webapps/galaxy/api/metrics.py Log Message: ----------- Merge pull request #1945 from dannon/fluent_logging_fix [16.01] Fix handling of time in fluent logger Commit: 53daf30dd284004c7e0b85ce8dbe6daf94622ef1 https://github.com/galaxyproject/galaxy/commit/53daf30dd284004c7e0b85ce8dbe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/util/log/fluent_log.py M lib/galaxy/webapps/galaxy/api/metrics.py M run_reports.sh M run_tool_shed.sh Log Message: ----------- Merge branch 'release_16.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/6fff01c01c59...53daf30dd284

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[galaxyproject/infrastructure-playbook] b55fdb: Add celery beat for sentry, should be the last pie...
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: b55fdbafe09e758a51466cf633f016ebab820039 https://github.com/galaxyproject/infrastructure-playbook/commit/b55fdbafe09… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M taccenv/templates/supervisor/sentry.j2 Log Message: ----------- Add celery beat for sentry, should be the last piece of the puzzle.

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[galaxyproject/usegalaxy-playbook] b3de5c: update Test mutable configs and common_roles subre...
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b3de5c2b03848640a2cbf3210faf165be774a720 https://github.com/galaxyproject/usegalaxy-playbook/commit/b3de5c2b03848640… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M common_roles M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.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 Log Message: ----------- update Test mutable configs and common_roles subrepo that has not been committed

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[galaxyproject/usegalaxy-playbook] 3daa3e: Update sentry DSNs for main/test/shed/testshed
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3daa3eca9dd8f7c5917273c499be973bfa344ba6 https://github.com/galaxyproject/usegalaxy-playbook/commit/3daa3eca9dd8f7c5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M production/secret_vars/galaxyservers.yml M production/secret_vars/toolshedservers.yml M stage/secret_vars/galaxyservers.yml M stage/secret_vars/toolshedservers.yml Log Message: ----------- Update sentry DSNs for main/test/shed/testshed

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[galaxyproject/infrastructure-playbook] 96fd80: Add sentry_memcached to sentry group.
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 96fd80d84b739176bd6888aaffb55f8dc084b183 https://github.com/galaxyproject/infrastructure-playbook/commit/96fd80d84b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M taccenv/templates/supervisor/sentry.j2 Log Message: ----------- Add sentry_memcached to sentry group.

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[galaxyproject/infrastructure-playbook] 0f91b8: Enable and start memcached on statsservers
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 0f91b8b9e33a229423252d6aed2ea6cd692afc85 https://github.com/galaxyproject/infrastructure-playbook/commit/0f91b8b9e33… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M roles/sentry/tasks/main.yml Log Message: ----------- Enable and start memcached on statsservers Commit: dede2824ad219409ab4210d6ab32390754549171 https://github.com/galaxyproject/infrastructure-playbook/commit/dede2824ad2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M roles/sentry/tasks/main.yml M taccenv/templates/supervisor/sentry.j2 Log Message: ----------- Use supervisor instead of systemd Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/51f6f60c38…

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[galaxyproject/galaxy] 89e6a3: Add IUC as a new default bioconda channel
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/iuc_default_conda_channel Home: https://github.com/galaxyproject/galaxy Commit: 89e6a37d43d85ffd46a786e689e5b2fdc6a6c4ae https://github.com/galaxyproject/galaxy/commit/89e6a37d43d85ffd46a786e689e5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Add IUC as a new default bioconda channel

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[galaxyproject/infrastructure-playbook] dede28: Use supervisor instead of systemd
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/memcached_tweak Home: https://github.com/galaxyproject/infrastructure-playbook Commit: dede2824ad219409ab4210d6ab32390754549171 https://github.com/galaxyproject/infrastructure-playbook/commit/dede2824ad2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M roles/sentry/tasks/main.yml M taccenv/templates/supervisor/sentry.j2 Log Message: ----------- Use supervisor instead of systemd

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[galaxyproject/infrastructure-playbook] 0f91b8: Enable and start memcached on statsservers
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/memcached_tweak Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 0f91b8b9e33a229423252d6aed2ea6cd692afc85 https://github.com/galaxyproject/infrastructure-playbook/commit/0f91b8b9e33… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M roles/sentry/tasks/main.yml Log Message: ----------- Enable and start memcached on statsservers

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[galaxyproject/galaxy] f277f9: Fix handling of time in fluent logger.
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: f277f99aed411fede7d1cb91d3177469922a58ae https://github.com/galaxyproject/galaxy/commit/f277f99aed411fede7d1cb91d317… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/util/log/fluent_log.py Log Message: ----------- Fix handling of time in fluent logger. Commit: 87bcb5f5a1b6801e948b2cc0f5dc676c7faca682 https://github.com/galaxyproject/galaxy/commit/87bcb5f5a1b6801e948b2cc0f5dc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/util/log/fluent_log.py Log Message: ----------- Fix in a different way not requiring signature change; still not thrilled about overlapping kwarg names w/ stdlib module names. Commit: c8e48bfaccb5d10552df4200e616a9eee49206b0 https://github.com/galaxyproject/galaxy/commit/c8e48bfaccb5d10552df4200e616… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Add fluentd configuration to galaxy.ini.sample Commit: 98c65dcee08338ea80a7e34251f8fa4ed6bd8dd5 https://github.com/galaxyproject/galaxy/commit/98c65dcee08338ea80a7e34251f8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/util/log/fluent_log.py M lib/galaxy/webapps/galaxy/api/metrics.py Log Message: ----------- Swap back to the first fix, update metrics api to use new signature. Commit: 19bf334c7763c2418408083b9a7369386e50ad66 https://github.com/galaxyproject/galaxy/commit/19bf334c7763c2418408083b9a73… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/util/log/fluent_log.py M lib/galaxy/webapps/galaxy/api/metrics.py Log Message: ----------- Merge pull request #1945 from dannon/fluent_logging_fix [16.01] Fix handling of time in fluent logger Compare: https://github.com/galaxyproject/galaxy/compare/00a7c3af057c...19bf334c7763

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[galaxyproject/infrastructure-playbook] 51f6f6: Install memcached for sentry
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 51f6f60c38b89591912b731b0b28f18290ab54ed https://github.com/galaxyproject/infrastructure-playbook/commit/51f6f60c38b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M taccenv/group_vars/statsservers.yml Log Message: ----------- Install memcached for sentry

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[galaxyproject/galaxy] 87bb98: Add "new" state to list of dataset states in saved...
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 87bb98eed23634c2684e6b246051e871068aca0c https://github.com/galaxyproject/galaxy/commit/87bb98eed23634c2684e6b246051… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Add "new" state to list of dataset states in saved history list. Commit: 6fff01c01c59a1ebe9a4906c47e1f550d2019f6f https://github.com/galaxyproject/galaxy/commit/6fff01c01c59a1ebe9a4906c47e1… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #1949 from blankenberg/history-list-new-hda Add "new" state to list of dataset states in saved history list. Compare: https://github.com/galaxyproject/galaxy/compare/2bc3da6b4988...6fff01c01c59

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[galaxyproject/galaxy] 6a123b: Use database query rather than dataset iteration t...
by GitHub 17 Mar '16

17 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6a123b12e9a6fd2c8ace506d6a6318504aa6fa81 https://github.com/galaxyproject/galaxy/commit/6a123b12e9a6fd2c8ace506d6a63… Author: jgoecks <jgoecks(a)gwu.edu> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Use database query rather than dataset iteration to compute dataset counts in saved histories grid. Commit: 4520a619abd638d49d07c8deac1a120f6181fad0 https://github.com/galaxyproject/galaxy/commit/4520a619abd638d49d07c8deac1a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Minor style tweaks to pass flake8 Commit: 8c1defe60e6b1195eb2a2fbaba167fec11ed5bce https://github.com/galaxyproject/galaxy/commit/8c1defe60e6b1195eb2a2fbaba16… Author: Jeremy Goecks <jgoecks(a)users.noreply.github.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #2 from dannon/history-grid-state-optimization Minor style tweaks to pass flake8 Commit: 78da8df812393778841e97465993e3ce7199f45f https://github.com/galaxyproject/galaxy/commit/78da8df812393778841e97465993… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Oops. Commit: 38d7bbb712cd2523e3c9ba31df5f49c2b9f2ce83 https://github.com/galaxyproject/galaxy/commit/38d7bbb712cd2523e3c9ba31df5f… Author: Jeremy Goecks <jgoecks(a)users.noreply.github.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #3 from dannon/history-grid-state-optimization It's a function, not a true-y value :/ Commit: 2bc3da6b4988d5fbb5c3aa1e2562452a654f7c6a https://github.com/galaxyproject/galaxy/commit/2bc3da6b4988d5fbb5c3aa1e2562… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #1948 from jgoecks/history-grid-state-optimization Use database query rather than dataset iteration to compute dataset c… Compare: https://github.com/galaxyproject/galaxy/compare/c7d1f009a163...2bc3da6b4988

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[galaxyproject/galaxy] b7b04e: Fix tool downloads
by GitHub 17 Mar '16

17 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b7b04ee92033ca9a2e961e296f74378753ab0563 https://github.com/galaxyproject/galaxy/commit/b7b04ee92033ca9a2e961e296f74… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix tool downloads Commit: c7d1f009a163f8e74905c5c4ee5cc2e2288051c9 https://github.com/galaxyproject/galaxy/commit/c7d1f009a163f8e74905c5c4ee5c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1935 from guerler/fix_downloads_000 Fix tool downloads in tool form Compare: https://github.com/galaxyproject/galaxy/compare/cef58abb55e2...c7d1f009a163

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[galaxyproject/galaxy] 80562a: Fix API method broken in 6e13c3999.
by GitHub 17 Mar '16

17 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 80562acfe8979433620da5ad416705c7c845aad5 https://github.com/galaxyproject/galaxy/commit/80562acfe8979433620da5ad4167… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/model/__init__.py Log Message: ----------- Fix API method broken in 6e13c3999. Commit: 381afd7576309409d788a6cf7cfe97f4f1421b04 https://github.com/galaxyproject/galaxy/commit/381afd7576309409d788a6cf7cfe… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Prevent server error if name or owner are missing. Commit: ad6edac562bd2fcfb0c49dc88bde692ced67ae02 https://github.com/galaxyproject/galaxy/commit/ad6edac562bd2fcfb0c49dc88bde… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Also prevent server error when repository is not found. Commit: cef58abb55e261c05de97b9d99906cc60b6416ba https://github.com/galaxyproject/galaxy/commit/cef58abb55e261c05de97b9d9990… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/model/__init__.py Log Message: ----------- Merge pull request #1943 from davebx/ts_api_bug Fix API method broken in 6e13c3999. Compare: https://github.com/galaxyproject/galaxy/compare/89b25edc313d...cef58abb55e2

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[galaxyproject/galaxy] 13f05d: Allow testing element counts in tool output collec...
by GitHub 17 Mar '16

17 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 13f05d2d79a01e0fdde34eb8f7a2a02917a7c607 https://github.com/galaxyproject/galaxy/commit/13f05d2d79a01e0fdde34eb8f7a2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/tools/parser/interface.py M test/functional/test_toolbox.py M test/functional/tools/collection_creates_list.xml Log Message: ----------- Allow testing element counts in tool output collections. Commit: 89b25edc313d4dd411af4f94d8dc830f2b37b945 https://github.com/galaxyproject/galaxy/commit/89b25edc313d4dd411af4f94d8dc… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/tools/parser/interface.py M test/functional/test_toolbox.py M test/functional/tools/collection_creates_list.xml Log Message: ----------- Merge pull request #1942 from jmchilton/element_count_test Allow testing element counts in tool output collections. Compare: https://github.com/galaxyproject/galaxy/compare/7fad23614b2a...89b25edc313d

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[galaxyproject/galaxy] 3e5aa6: More debugging for transiently failing tool test.
by GitHub 17 Mar '16

17 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3e5aa68ccfd1dcb117cc4131134cbe0c410a21cb https://github.com/galaxyproject/galaxy/commit/3e5aa68ccfd1dcb117cc4131134c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M test/base/twilltestcase.py M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py Log Message: ----------- More debugging for transiently failing tool test. Commit: 7fad23614b2aaf4de1de4dc07829394ecf1d00c3 https://github.com/galaxyproject/galaxy/commit/7fad23614b2aaf4de1de4dc07829… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M test/base/twilltestcase.py M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py Log Message: ----------- Merge pull request #1939 from jmchilton/transient_ts_test More debugging for transiently failing tool shed test. Compare: https://github.com/galaxyproject/galaxy/compare/29b6d545cf22...7fad23614b2a

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[galaxyproject/galaxy] 46728c: Add bam.iobio as a display application.
by GitHub 16 Mar '16

16 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 46728c5728bde2f5587578b1ddd430c4d78757df https://github.com/galaxyproject/galaxy/commit/46728c5728bde2f5587578b1ddd4… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M config/datatypes_conf.xml.sample M config/tool_data_table_conf.xml.sample A display_applications/iobio/bam.xml M lib/galaxy/datatypes/display_applications/application.py A tool-data/bam_iobio.loc.sample Log Message: ----------- Add bam.iobio as a display application. Commit: 0c57453c96f1619a9891d1d659610c44fd12e698 https://github.com/galaxyproject/galaxy/commit/0c57453c96f1619a9891d1d65961… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M config/datatypes_conf.xml.sample M config/tool_data_table_conf.xml.sample A tool-data/vcf_iobio.loc.sample Log Message: ----------- Add vcf.iobio as a display application. Commit: 915993bbd8f82afef9b68f5d8820437a07f6f264 https://github.com/galaxyproject/galaxy/commit/915993bbd8f82afef9b68f5d8820… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: A display_applications/iobio/vcf.xml Log Message: ----------- Add display_applications/iobio/vcf.xml. Commit: e6bb45b29ab20ef64834ca6c2908ae72c44beed8 https://github.com/galaxyproject/galaxy/commit/e6bb45b29ab20ef64834ca6c2908… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M tool-data/vcf_iobio.loc.sample Log Message: ----------- typo Commit: 29b6d545cf229518840e29d7468d65e4221db95a https://github.com/galaxyproject/galaxy/commit/29b6d545cf229518840e29d7468d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M config/datatypes_conf.xml.sample M config/tool_data_table_conf.xml.sample A display_applications/iobio/bam.xml A display_applications/iobio/vcf.xml M lib/galaxy/datatypes/display_applications/application.py A tool-data/bam_iobio.loc.sample A tool-data/vcf_iobio.loc.sample Log Message: ----------- Merge pull request #1926 from blankenberg/iobio-display Add iobio external display applications for BAM and VCF. Compare: https://github.com/galaxyproject/galaxy/compare/aae2006079a9...29b6d545cf22

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[galaxyproject/galaxy] 84865c: Retrieve authentification also for long urls from ...
by GitHub 16 Mar '16

16 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 84865c893e1c089eefed69aeb0300afa7419d500 https://github.com/galaxyproject/galaxy/commit/84865c893e1c089eefed69aeb030… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-11 (Fri, 11 Mar 2016) Changed paths: M lib/tool_shed/tool_shed_registry.py Log Message: ----------- Retrieve authentification also for long urls from shed_auth Commit: aae2006079a9e0e5fc744ae2026e6deaa7d1a2f3 https://github.com/galaxyproject/galaxy/commit/aae2006079a9e0e5fc744ae2026e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M lib/tool_shed/tool_shed_registry.py Log Message: ----------- Merge pull request #1912 from mvdbeek/relax_password_manager_matching Retrieve authentification also for long urls Compare: https://github.com/galaxyproject/galaxy/compare/e86969b4cbe3...aae2006079a9

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[galaxyproject/galaxy] 497694: Fix icon sizes
by GitHub 16 Mar '16

16 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4976945ab0f4388f5b6ed6916bb7ef123c28c0e9 https://github.com/galaxyproject/galaxy/commit/4976945ab0f4388f5b6ed6916bb7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form.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/layout/menu.js M static/scripts/mvc/tool/tool-form.js M static/style/blue/base.css Log Message: ----------- Fix icon sizes Commit: e86969b4cbe3fb22a13aca9fdc17fc668f862ceb https://github.com/galaxyproject/galaxy/commit/e86969b4cbe3fb22a13aca9fdc17… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form.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/layout/menu.js M static/scripts/mvc/tool/tool-form.js M static/style/blue/base.css Log Message: ----------- Merge pull request #1934 from guerler/fix_icon_size_000 Fix icon sizes Compare: https://github.com/galaxyproject/galaxy/compare/46dc26eeda4c...e86969b4cbe3

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[galaxyproject/galaxy] 18a4ed: FTP directory not existing should be a warning, no...
by GitHub 16 Mar '16

16 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 18a4edc1ca1bd491f644e6ee8ca011950cb15797 https://github.com/galaxyproject/galaxy/commit/18a4edc1ca1bd491f644e6ee8ca0… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- FTP directory not existing should be a warning, not an exception Commit: 5c45746e4203d22edfa03c10de6cbf830ff3bf5f https://github.com/galaxyproject/galaxy/commit/5c45746e4203d22edfa03c10de6c… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M lib/galaxy/model/custom_types.py Log Message: ----------- Metadata above max size should be a warning. Commit: 46dc26eeda4c6bb98a951536da1ed9cf4c7e8f75 https://github.com/galaxyproject/galaxy/commit/46dc26eeda4c6bb98a951536da1e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M lib/galaxy/model/custom_types.py M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Merge pull request #1936 from mvdbeek/more_warnings_less_errors More warnings, less errors Compare: https://github.com/galaxyproject/galaxy/compare/9a0f971596a3...46dc26eeda4c

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[galaxyproject/galaxy] 29c78e: Fix virtualenv broken with #1847.
by GitHub 15 Mar '16

15 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 29c78e984e52ac08b1b36a03e39b65c6edbe6200 https://github.com/galaxyproject/galaxy/commit/29c78e984e52ac08b1b36a03e39b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M run_reports.sh M run_tool_shed.sh Log Message: ----------- Fix virtualenv broken with #1847. Commit: 5824bc04af9270afbebcb2c8f9b6b3bea371b788 https://github.com/galaxyproject/galaxy/commit/5824bc04af9270afbebcb2c8f9b6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M run_reports.sh M run_tool_shed.sh Log Message: ----------- Fix duplicate print statement reported by @dannon... https://github.com/galaxyproject/galaxy/pull/1890#issuecomment-193873380 Commit: 438661e8945c1bb317f75dabe3db429ea779255d https://github.com/galaxyproject/galaxy/commit/438661e8945c1bb317f75dabe3db… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M run_reports.sh M run_tool_shed.sh Log Message: ----------- Another fix for virtualenv fixes. Commit: 00a7c3af057c0689a53748802740bc2002df375c https://github.com/galaxyproject/galaxy/commit/00a7c3af057c0689a53748802740… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M run_reports.sh M run_tool_shed.sh Log Message: ----------- Merge pull request #1890 from jmchilton/fix_virtualenvs [16.01] Fix virtual env handling broken with #1847. Compare: https://github.com/galaxyproject/galaxy/compare/9a343efe8b7d...00a7c3af057c

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