- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 7ad55b: try pushing again when we get unexpected exception...
by GitHub 18 Apr '16

18 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 7ad55b7eb8ffb49d4cca299432a78b6362207c1d https://github.com/galaxyproject/galaxy/commit/7ad55b7eb8ffb49d4cca299432a7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M test/shed_functional/base/twilltestcase.py Log Message: ----------- try pushing again when we get unexpected exception... Commit: 76386b5eab770b1f7fdb4afbf776947f8e7359fd https://github.com/galaxyproject/galaxy/commit/76386b5eab770b1f7fdb4afbf776… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M test/shed_functional/base/twilltestcase.py Log Message: ----------- remove unwanted check Commit: a85b5ee762009a95ff20273ece10bad06d76420b https://github.com/galaxyproject/galaxy/commit/a85b5ee762009a95ff20273ece10… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M test/shed_functional/base/twilltestcase.py Log Message: ----------- remove unused import Commit: 1fd326855d5b19b9b0fa7b078d26219618823b7f https://github.com/galaxyproject/galaxy/commit/1fd326855d5b19b9b0fa7b078d26… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M test/shed_functional/base/twilltestcase.py Log Message: ----------- improve on refactoring of the test Commit: 53021ef33ea3e024d6a7b775fb1a8df1be29ea54 https://github.com/galaxyproject/galaxy/commit/53021ef33ea3e024d6a7b775fb1a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge pull request #2186 from martenson/port-tstest-fix [16.04] Port TS push test fix Compare: https://github.com/galaxyproject/galaxy/compare/ab015c67dff7...53021ef33ea3

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[galaxyproject/galaxy] f50504: Refactor checking tool files toward reuse with wor...
by GitHub 18 Apr '16

18 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f505041bdace98df66bff3851d1e03a7a349ddac https://github.com/galaxyproject/galaxy/commit/f505041bdace98df66bff3851d1e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- Refactor checking tool files toward reuse with workflow in planemo. Improve docstrings, import order, and interface definiton in that file as well. Updated with improved conditional pass through ``looks_like_a_cwl_artifact`` as spotted by @nsoranzo. Commit: f1c008b741cc08c4cf8dd982943dc4114f555e37 https://github.com/galaxyproject/galaxy/commit/f1c008b741cc08c4cf8dd982943d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- Merge pull request #2183 from jmchilton/more_looks_like_tool Refactor checking tool files toward reuse with workflows in planemo. Compare: https://github.com/galaxyproject/galaxy/compare/d8e4f571aebc...f1c008b741cc

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[galaxyproject/galaxy] cea9a1: Replace masthead dom to avoid duplication
by GitHub 18 Apr '16

18 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: cea9a12238b681892b8956dd6961383a9a025220 https://github.com/galaxyproject/galaxy/commit/cea9a12238b681892b8956dd6961… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Replace masthead dom to avoid duplication Commit: ab015c67dff7261dfd233901fe6f2ea97db2d727 https://github.com/galaxyproject/galaxy/commit/ab015c67dff7261dfd233901fe6f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Merge pull request #2182 from guerler/fix_masthead_002 [16.04] Remove redundant ui divs, move masthead into #everything Compare: https://github.com/galaxyproject/galaxy/compare/e1d937e430a8...ab015c67dff7

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[galaxyproject/galaxy] 92aff6: Fix for redirecting a non-user when a tool has req...
by GitHub 18 Apr '16

18 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 92aff618cb435f2b4d5805378e4bbcd67ae1f7a4 https://github.com/galaxyproject/galaxy/commit/92aff618cb435f2b4d5805378e4b… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/tool_runner.py Log Message: ----------- Fix for redirecting a non-user when a tool has require_login=True. Commit: e1d937e430a859997b252432cc1b01a509fc68a0 https://github.com/galaxyproject/galaxy/commit/e1d937e430a859997b252432cc1b… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/tool_runner.py Log Message: ----------- Merge pull request #2180 from blankenberg/tool-login-required [16.04] Fix for redirecting a non-user when a tool has require_login=True. Compare: https://github.com/galaxyproject/galaxy/compare/1c38b9723cc2...e1d937e430a8

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[galaxyproject/infrastructure-playbook] 41ab2e: Changing node counts requires a full restart of at...
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 41ab2e608f38e19b7ace504bb7784ee042b358fc https://github.com/galaxyproject/infrastructure-playbook/commit/41ab2e608f3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M roles/slurm/handlers/main.yml M roles/slurm/tasks/main.yml Log Message: ----------- Changing node counts requires a full restart of at least slurmctld (not sure about slurmd)

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[galaxyproject/infrastructure-playbook] 1e5623: Fix Main deps
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 1e56237a2890020820180aa32f14bed1a53b3285 https://github.com/galaxyproject/infrastructure-playbook/commit/1e56237a289… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M jetstreamiuenv/group_vars/galaxynodes.yml M jetstreamtaccenv/group_vars/galaxynodes.yml Log Message: ----------- Fix Main deps

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[galaxyproject/infrastructure-playbook] c6135d: New TACC instances
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c6135dd5663dcc4c623495d5d77bfb174f7c2a03 https://github.com/galaxyproject/infrastructure-playbook/commit/c6135dd5663… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M jetstreamtaccenv/group_vars/slurmclients.yml M jetstreamtaccenv/inventory Log Message: ----------- New TACC instances

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[galaxyproject/galaxy] 03c857: Multi-history: open rerun button in new tab
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 03c85737319dbce1a3c9aa258c7c22d2d97d5c35 https://github.com/galaxyproject/galaxy/commit/03c85737319dbce1a3c9aa258c7c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/multi-panel.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/mvc/history/multi-panel.js Log Message: ----------- Multi-history: open rerun button in new tab Commit: e193e46e30d84d7f844a2941f72ed65af11f69b3 https://github.com/galaxyproject/galaxy/commit/e193e46e30d84d7f844a2941f72e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Place $headers before integrity_check PBS needs the resource selection (which will be filled in using $headers) to appear before anything else (except the shebang), so this changes the order. Commit: 434321915a61f53cd668170da076251a8c15889f https://github.com/galaxyproject/galaxy/commit/434321915a61f53cd668170da076… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh Log Message: ----------- Use "$NCPUS" if defined to set GALAXY_SLOTS On our PBS cluster we do not have $PBS_NCPUS, and $PBS_NODEFILE contains the hostname of the nodes the task runs on. But we do have "$NCPUS" with the correct number of CPUS. Commit: 8e72b3095bacdac90a6fa7dea6125f489826bcfd https://github.com/galaxyproject/galaxy/commit/8e72b3095bacdac90a6fa7dea612… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Merge pull request #2174 from mvdbeek/reorder_job_template [16.01] Backport #2146 #2145 Commit: 3e79a574bea53731c734b568e1c6eeab4199cbdd https://github.com/galaxyproject/galaxy/commit/3e79a574bea53731c734b568e1c6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/multi-panel.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/multi-panel.js Log Message: ----------- Merge #2167 manually to resolve conflicts. Commit: 9e278de3959200a1432cca6ba33bc6e7ddd89b60 https://github.com/galaxyproject/galaxy/commit/9e278de3959200a1432cca6ba33b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Rebuild client. Commit: 1c38b9723cc2ed8c42b55095484814e89e99b436 https://github.com/galaxyproject/galaxy/commit/1c38b9723cc2ed8c42b550954848… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/multi-panel.js Log Message: ----------- Merge 16.01->16.04 Commit: d8e4f571aebc356ff0b943526c9795096420d35a https://github.com/galaxyproject/galaxy/commit/d8e4f571aebc356ff0b943526c97… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/multi-panel.js Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/cdadaa436ccf...d8e4f571aebc

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[galaxyproject/galaxy] 03c857: Multi-history: open rerun button in new tab
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 03c85737319dbce1a3c9aa258c7c22d2d97d5c35 https://github.com/galaxyproject/galaxy/commit/03c85737319dbce1a3c9aa258c7c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/multi-panel.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/mvc/history/multi-panel.js Log Message: ----------- Multi-history: open rerun button in new tab Commit: e193e46e30d84d7f844a2941f72ed65af11f69b3 https://github.com/galaxyproject/galaxy/commit/e193e46e30d84d7f844a2941f72e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Place $headers before integrity_check PBS needs the resource selection (which will be filled in using $headers) to appear before anything else (except the shebang), so this changes the order. Commit: 434321915a61f53cd668170da076251a8c15889f https://github.com/galaxyproject/galaxy/commit/434321915a61f53cd668170da076… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh Log Message: ----------- Use "$NCPUS" if defined to set GALAXY_SLOTS On our PBS cluster we do not have $PBS_NCPUS, and $PBS_NODEFILE contains the hostname of the nodes the task runs on. But we do have "$NCPUS" with the correct number of CPUS. Commit: 8e72b3095bacdac90a6fa7dea6125f489826bcfd https://github.com/galaxyproject/galaxy/commit/8e72b3095bacdac90a6fa7dea612… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Merge pull request #2174 from mvdbeek/reorder_job_template [16.01] Backport #2146 #2145 Commit: 3e79a574bea53731c734b568e1c6eeab4199cbdd https://github.com/galaxyproject/galaxy/commit/3e79a574bea53731c734b568e1c6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/multi-panel.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/multi-panel.js Log Message: ----------- Merge #2167 manually to resolve conflicts. Commit: 9e278de3959200a1432cca6ba33bc6e7ddd89b60 https://github.com/galaxyproject/galaxy/commit/9e278de3959200a1432cca6ba33b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Rebuild client. Commit: 1c38b9723cc2ed8c42b55095484814e89e99b436 https://github.com/galaxyproject/galaxy/commit/1c38b9723cc2ed8c42b550954848… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/multi-panel.js Log Message: ----------- Merge 16.01->16.04 Compare: https://github.com/galaxyproject/galaxy/compare/7488e3b7be05...1c38b9723cc2

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[galaxyproject/galaxy] 03c857: Multi-history: open rerun button in new tab
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 03c85737319dbce1a3c9aa258c7c22d2d97d5c35 https://github.com/galaxyproject/galaxy/commit/03c85737319dbce1a3c9aa258c7c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/multi-panel.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/mvc/history/multi-panel.js Log Message: ----------- Multi-history: open rerun button in new tab Commit: 3e79a574bea53731c734b568e1c6eeab4199cbdd https://github.com/galaxyproject/galaxy/commit/3e79a574bea53731c734b568e1c6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/multi-panel.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/multi-panel.js Log Message: ----------- Merge #2167 manually to resolve conflicts. Commit: 9e278de3959200a1432cca6ba33bc6e7ddd89b60 https://github.com/galaxyproject/galaxy/commit/9e278de3959200a1432cca6ba33b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Rebuild client. Compare: https://github.com/galaxyproject/galaxy/compare/8e72b3095bac...9e278de39592

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[galaxyproject/infrastructure-playbook] 4b0a10: Added new IU instances
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 4b0a104c4decd57882eecf5a77715c625c2b9145 https://github.com/galaxyproject/infrastructure-playbook/commit/4b0a104c4de… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M jetstreamiuenv/group_vars/slurmclients.yml M jetstreamiuenv/inventory Log Message: ----------- Added new IU instances

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[galaxyproject/galaxy] 5ff7f9: Fix running tool tests if remote user middleware i...
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5ff7f9a19fd989ae3b4a011c2c5f3ababfb5b508 https://github.com/galaxyproject/galaxy/commit/5ff7f9a19fd989ae3b4a011c2c5f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M test/base/interactor.py Log Message: ----------- Fix running tool tests if remote user middleware is enabled. Commit: cdadaa436ccf89ff24c9c7b0935c0d41789fbd8a https://github.com/galaxyproject/galaxy/commit/cdadaa436ccf89ff24c9c7b0935c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M test/base/interactor.py Log Message: ----------- Merge pull request #2173 from jmchilton/single_user Fix running tool tests if remote user middleware is enabled. Compare: https://github.com/galaxyproject/galaxy/compare/58f510fda94d...cdadaa436ccf

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[galaxyproject/usegalaxy-playbook] 7c3c7e: Jetstream fixes for Test's job conf
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7c3c7e4b22b1853e1a671cb569242d163088964d https://github.com/galaxyproject/usegalaxy-playbook/commit/7c3c7e4b22b1853e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Jetstream fixes for Test's job conf

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[galaxyproject/galaxy] e193e4: Place $headers before integrity_check
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: e193e46e30d84d7f844a2941f72ed65af11f69b3 https://github.com/galaxyproject/galaxy/commit/e193e46e30d84d7f844a2941f72e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Place $headers before integrity_check PBS needs the resource selection (which will be filled in using $headers) to appear before anything else (except the shebang), so this changes the order. Commit: 434321915a61f53cd668170da076251a8c15889f https://github.com/galaxyproject/galaxy/commit/434321915a61f53cd668170da076… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh Log Message: ----------- Use "$NCPUS" if defined to set GALAXY_SLOTS On our PBS cluster we do not have $PBS_NCPUS, and $PBS_NODEFILE contains the hostname of the nodes the task runs on. But we do have "$NCPUS" with the correct number of CPUS. Commit: 8e72b3095bacdac90a6fa7dea6125f489826bcfd https://github.com/galaxyproject/galaxy/commit/8e72b3095bacdac90a6fa7dea612… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Merge pull request #2174 from mvdbeek/reorder_job_template [16.01] Backport #2146 #2145 Compare: https://github.com/galaxyproject/galaxy/compare/18c00899a30c...8e72b3095bac

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[galaxyproject/galaxy] cde04a: markupsafe.escape() in Python2 does not work on st...
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cde04ad52d40b5d7b26a0c636d9d24bf6adbdc92 https://github.com/galaxyproject/galaxy/commit/cde04ad52d40b5d7b26a0c636d9d… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- markupsafe.escape() in Python2 does not work on str containing non-ASCII characters. Fix #2135. Commit: 34900f87f5bc52bc84efe866371588004a049ebf https://github.com/galaxyproject/galaxy/commit/34900f87f5bc52bc84efe8663715… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M tools/stats/grouping.py M tools/stats/grouping.xml Log Message: ----------- Fix grouping tool broken in 7347d75a4a36d42f8060e11d708291d796b266a5 / fd85979a8651e0907bebce05cdfb59d77f0d0f64, and enhance performance when removing lines. Commit: 18c00899a30cd162cd0bb3a251a49cff2143d3a3 https://github.com/galaxyproject/galaxy/commit/18c00899a30cd162cd0bb3a251a4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #2138 from nsoranzo/release_16.01_fix_for_2135 [16.01] markupsafe.escape() in Python2 does not work on str containing non-ASCII characters Commit: 7f101b8da8d09121a302a6707610434e1e2d3cdf https://github.com/galaxyproject/galaxy/commit/7f101b8da8d09121a302a6707610… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M tools/stats/grouping.py M tools/stats/grouping.xml Log Message: ----------- Merge pull request #2166 from blankenberg/release_16.04 [16.04] Fix grouping tool and enhance performance when removing lines. Commit: 7488e3b7be059eb5759020b148c6bff369a15ea6 https://github.com/galaxyproject/galaxy/commit/7488e3b7be059eb5759020b148c6… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Conflicts: lib/galaxy/web/framework/helpers/grids.py Commit: 58f510fda94d12a1041460a603ac56dd7f0f1928 https://github.com/galaxyproject/galaxy/commit/58f510fda94d12a1041460a603ac… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/web/framework/helpers/grids.py M tools/stats/grouping.py M tools/stats/grouping.xml Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/88db9e6a0f0b...58f510fda94d

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[galaxyproject/galaxy] cde04a: markupsafe.escape() in Python2 does not work on st...
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: cde04ad52d40b5d7b26a0c636d9d24bf6adbdc92 https://github.com/galaxyproject/galaxy/commit/cde04ad52d40b5d7b26a0c636d9d… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- markupsafe.escape() in Python2 does not work on str containing non-ASCII characters. Fix #2135. Commit: 18c00899a30cd162cd0bb3a251a49cff2143d3a3 https://github.com/galaxyproject/galaxy/commit/18c00899a30cd162cd0bb3a251a4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #2138 from nsoranzo/release_16.01_fix_for_2135 [16.01] markupsafe.escape() in Python2 does not work on str containing non-ASCII characters Commit: 7488e3b7be059eb5759020b148c6bff369a15ea6 https://github.com/galaxyproject/galaxy/commit/7488e3b7be059eb5759020b148c6… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Conflicts: lib/galaxy/web/framework/helpers/grids.py Compare: https://github.com/galaxyproject/galaxy/compare/7f101b8da8d0...7488e3b7be05

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[galaxyproject/infrastructure-playbook] f9bc82: Rename partition on Jetstream to multi
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: f9bc8286d623204da6d929035cf078887eece83d https://github.com/galaxyproject/infrastructure-playbook/commit/f9bc8286d62… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M jetstreamiuenv/templates/slurm/slurm.conf.j2 M jetstreamtaccenv/templates/slurm/slurm.conf.j2 Log Message: ----------- Rename partition on Jetstream to multi

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[galaxyproject/galaxy] e78add: Hide hidden data parameters in workflow editor
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e78add7decfb1bb2f262b0a7d4df3d586cffeb8e https://github.com/galaxyproject/galaxy/commit/e78add7decfb1bb2f262b0a7d4df… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-06 (Wed, 06 Apr 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Hide hidden data parameters in workflow editor Commit: c78887c4ae3840d807c22bf2ce6bb8b20c3cef94 https://github.com/galaxyproject/galaxy/commit/c78887c4ae3840d807c22bf2ce6b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Use elif, do not require hidden attribute Commit: 88db9e6a0f0b9fe61bdc66e4fa598af82101c11c https://github.com/galaxyproject/galaxy/commit/88db9e6a0f0b9fe61bdc66e4fa59… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #2120 from guerler/fix_hidden_001 Hide hidden data parameters in workflow editor Compare: https://github.com/galaxyproject/galaxy/compare/411e33194b8c...88db9e6a0f0b

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[galaxyproject/galaxy] 34900f: Fix grouping tool broken in 7347d75a4a36d42f8060e1...
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 34900f87f5bc52bc84efe866371588004a049ebf https://github.com/galaxyproject/galaxy/commit/34900f87f5bc52bc84efe8663715… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M tools/stats/grouping.py M tools/stats/grouping.xml Log Message: ----------- Fix grouping tool broken in 7347d75a4a36d42f8060e11d708291d796b266a5 / fd85979a8651e0907bebce05cdfb59d77f0d0f64, and enhance performance when removing lines. Commit: 7f101b8da8d09121a302a6707610434e1e2d3cdf https://github.com/galaxyproject/galaxy/commit/7f101b8da8d09121a302a6707610… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M tools/stats/grouping.py M tools/stats/grouping.xml Log Message: ----------- Merge pull request #2166 from blankenberg/release_16.04 [16.04] Fix grouping tool and enhance performance when removing lines. Compare: https://github.com/galaxyproject/galaxy/compare/8b49814859dc...7f101b8da8d0

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[galaxyproject/galaxy] 44a337: Add conditional statsd requirement. Wheel is live...
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 44a337ab6f8388a4cc1a69dc44e6e1314a2af2dc https://github.com/galaxyproject/galaxy/commit/44a337ab6f8388a4cc1a69dc44e6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Add conditional statsd requirement. Wheel is live on wheels.galaxyproject.org. Commit: 238b90a7f5e045435b45db3626953308ad8577b0 https://github.com/galaxyproject/galaxy/commit/238b90a7f5e045435b45db362695… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Support configurable statsd prefix (was formerly just 'galaxy', which remains the default) Commit: 411e33194b8cad409b6ad6213699e6260350d3ca https://github.com/galaxyproject/galaxy/commit/411e33194b8cad409b6ad6213699… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #2171 from dannon/mostats Stats prefix configurability and conditional wheel req. Compare: https://github.com/galaxyproject/galaxy/compare/5a747bd127c4...411e33194b8c

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[galaxyproject/galaxy] 5b0f23: Tools with auto_format='true' are connectable with...
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5b0f23562d2f90fadd63798ce9949c12f48f3a34 https://github.com/galaxyproject/galaxy/commit/5b0f23562d2f90fadd63798ce994… Author: yhoogstrate <y.hoogstrate(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Tools with auto_format='true' are connectable with other tools in workflow editor via GUI Commit: 5a747bd127c4c003e95f95c6b8a6320fb49e1bef https://github.com/galaxyproject/galaxy/commit/5a747bd127c4c003e95f95c6b8a6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Merge pull request #2144 from yhoogstrate/galaxy_workflow_autosniff Tools with auto_format='true' connectable in workflow editor Compare: https://github.com/galaxyproject/galaxy/compare/fbf894ef1441...5a747bd127c4

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[galaxyproject/galaxy] cde04a: markupsafe.escape() in Python2 does not work on st...
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: cde04ad52d40b5d7b26a0c636d9d24bf6adbdc92 https://github.com/galaxyproject/galaxy/commit/cde04ad52d40b5d7b26a0c636d9d… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- markupsafe.escape() in Python2 does not work on str containing non-ASCII characters. Fix #2135. Commit: 18c00899a30cd162cd0bb3a251a49cff2143d3a3 https://github.com/galaxyproject/galaxy/commit/18c00899a30cd162cd0bb3a251a4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #2138 from nsoranzo/release_16.01_fix_for_2135 [16.01] markupsafe.escape() in Python2 does not work on str containing non-ASCII characters Compare: https://github.com/galaxyproject/galaxy/compare/68ce6ce49cc8...18c00899a30c

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[galaxyproject/galaxy] 541738: Re-use ``trans`` logic for calculating user_ftp_di...
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 54173807e56e8ae4bef4cc0511249d6b87380de2 https://github.com/galaxyproject/galaxy/commit/54173807e56e8ae4bef4cc051124… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Re-use ``trans`` logic for calculating user_ftp_dir. Commit: f95cbf8f38801f03ba1ea9c065bc1796253d6eaf https://github.com/galaxyproject/galaxy/commit/f95cbf8f38801f03ba1ea9c065bc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/context.py Log Message: ----------- More documentation and flexibility for configuring FTP imports. - Add missing documentation for the ftp_upload_dir_identifier option. - Add ftp_upload_dir_template option to configure how to combine identifier and base directory to generate an ftp upload directory. Commit: 997b53f3ae7586d4a2e90f6cb03f00b844bb4d42 https://github.com/galaxyproject/galaxy/commit/997b53f3ae7586d4a2e90f6cb03f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M tools/data_source/upload.py Log Message: ----------- Implement option to prevent FTP uploads from being deleted on import. - Simply set `ftp_upload_purge` to `False` in galaxy.ini to enable this. - xref http://dev.list.galaxyproject.org/Data-removal-after-ftp-import-td4667111.h… - slight xref http://dev.list.galaxyproject.org/Uploading-files-to-galaxy-from-a-folder-t… Commit: 3ce6fca52c1fce1027566d5dbc50811be614ca28 https://github.com/galaxyproject/galaxy/commit/3ce6fca52c1fce1027566d5dbc50… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- config doc fixes spotted by @nsoranzo Commit: fbf894ef144101dec25237435040c82f945c3525 https://github.com/galaxyproject/galaxy/commit/fbf894ef144101dec25237435040… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/context.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/webapps/galaxy/api/remote_files.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #2168 from jmchilton/ftp_upload More documentation and flexibility for FTP imports. Compare: https://github.com/galaxyproject/galaxy/compare/4ffee71969e7...fbf894ef1441

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[galaxyproject/galaxy] e67506: Implement config.single_user = <email> option.
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e67506802de481c5b604513d947048abe67a7dc8 https://github.com/galaxyproject/galaxy/commit/e67506802de481c5b604513d9470… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Implement config.single_user = <email> option. Let Planemo and other such applications serve a full-fledged Galaxy instance without having to worry about logins, etc.... Commit: 2546030c66fb453f98035ddf176ffb2b103d8d8d https://github.com/galaxyproject/galaxy/commit/2546030c66fb453f98035ddf176f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Do not require use_remote_user to be explicitly set if single_user is set. Based on comments from @erasche - https://github.com/galaxyproject/galaxy/pull/2165#issuecomment-210048830. Commit: 4ffee71969e77be22f28eeac567572ba5b548d4d https://github.com/galaxyproject/galaxy/commit/4ffee71969e77be22f28eeac5675… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #2165 from jmchilton/single_user Implement ``single_user = <email>`` config option. Compare: https://github.com/galaxyproject/galaxy/compare/1e040258193a...4ffee71969e7

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[galaxyproject/galaxy] 128a91: Checks for api_key before checking for header from...
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 128a9112bb1635c1c49ac7dc1a99b531933ea659 https://github.com/galaxyproject/galaxy/commit/128a9112bb1635c1c49ac7dc1a99… Author: MatthewRalston <mrals89(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Checks for api_key before checking for header from SSO. Also fixes the NoneType issue discovered in #972. Commit: 4e12c5e782249c3aea1ddbdd5bd2f363111e78b6 https://github.com/galaxyproject/galaxy/commit/4e12c5e782249c3aea1ddbdd5bd2… Author: MatthewRalston <mrals89(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Fixes NoneType problem in a simpler way. Thanks @nsoranzo. Commit: 6473057f3b63ce615727800babbaf439ed66bb3f https://github.com/galaxyproject/galaxy/commit/6473057f3b63ce615727800babba… Author: Matt Ralston <mrals89(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Adds whitespace Commit: 774487ddcc9c0e793b6b15b26c971c3df5822644 https://github.com/galaxyproject/galaxy/commit/774487ddcc9c0e793b6b15b26c97… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/mvc/citation/citation-model.js Log Message: ----------- Fix citation-model to fail silently/gracefully when a non-parsable bibtex entry is tried Commit: d225aebc8879b3e96963724d3b5b11aec1d50ed5 https://github.com/galaxyproject/galaxy/commit/d225aebc8879b3e96963724d3b5b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/mvc/citation/citation-model.js Log Message: ----------- Merge pull request #1884 from carlfeberhard/release_15.10 [15.10] Fix citation-model to fail silently/gracefully Commit: e2a03646fd7c47a0ead962c9842e74f977dab8eb https://github.com/galaxyproject/galaxy/commit/e2a03646fd7c47a0ead962c9842e… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Fix farbtastic's use of deprecated jquery fns by loading jq-migrate in galaxy.panels.mako Commit: 9cff686d6d94a8d4a47c4c5cdc9d380fe686a8c4 https://github.com/galaxyproject/galaxy/commit/9cff686d6d94a8d4a47c4c5cdc9d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge pull request #1972 from carlfeberhard/release_15.10 [15.10] Fix farbtastic's use of deprecated jquery fns by loading jq-migrate i… Commit: a2114fdd0e234a3253cec79a02e30899ca081359 https://github.com/galaxyproject/galaxy/commit/a2114fdd0e234a3253cec79a02e3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #1801 from MatthewRalston/api_key_patch [15.10] Checks for api_key before checking for header from SSO. Commit: f85aaa4a27a1067a108c05fd1f74fa6060aa4565 https://github.com/galaxyproject/galaxy/commit/f85aaa4a27a1067a108c05fd1f74… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- port of middleware fix for TS (#2106) Commit: c0d65092fbbd1ad7380a0b17d3d9a949145d6170 https://github.com/galaxyproject/galaxy/commit/c0d65092fbbd1ad7380a0b17d3d9… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Merge pull request #2154 from martenson/port-middleware-fix [16.01] Port middleware fix Commit: e26bff23ed05eeeb7bac469b95a4ee6509dd537c https://github.com/galaxyproject/galaxy/commit/e26bff23ed05eeeb7bac469b95a4… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M lib/galaxy/web/framework/middleware/remoteuser.py M static/maps/mvc/citation/citation-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/citation/citation-model.js M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge 'release_15.10' with 'release_16.01' Commit: 570baa5bb6020a2a8b7592dda8e952225ce7beec https://github.com/galaxyproject/galaxy/commit/570baa5bb6020a2a8b7592dda8e9… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Fix bad merge: when HTTP_GX_SECRET is None Commit: 68ce6ce49cc8c3d6f252a52a6bf9ac90f64328a3 https://github.com/galaxyproject/galaxy/commit/68ce6ce49cc8c3d6f252a52a6bf9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M lib/galaxy/web/framework/middleware/remoteuser.py M static/maps/mvc/citation/citation-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/citation/citation-model.js M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge pull request #2169 from carlfeberhard/release_16.01 [16.01] Merge 15.10 with 16.01 Commit: 8b49814859dc4dcc85d5a4b3b8945f3f7e3342f4 https://github.com/galaxyproject/galaxy/commit/8b49814859dc4dcc85d5a4b3b894… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M lib/galaxy/web/framework/middleware/remoteuser.py M static/maps/mvc/citation/citation-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/citation/citation-model.js M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge 16.01 into 16.04 Commit: 1e040258193ae105b1bcc312a0dde832fd3c0716 https://github.com/galaxyproject/galaxy/commit/1e040258193ae105b1bcc312a0dd… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M lib/galaxy/web/framework/middleware/remoteuser.py M static/maps/mvc/citation/citation-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/citation/citation-model.js M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/e81448c62ab5...1e040258193a

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