galaxy-commits May 2016

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[galaxyproject/usegalaxy-playbook]
by GitHub 02 May '16

02 May '16

Branch: refs/heads/adjust-panel-search Home: https://github.com/galaxyproject/usegalaxy-playbook

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[galaxyproject/usegalaxy-playbook] a9283c: adjust tool panel search config
by GitHub 02 May '16

02 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a9283c31557a56bc640160f271f46708303917e9 https://github.com/galaxyproject/usegalaxy-playbook/commit/a9283c31557a56bc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-29 (Fri, 29 Apr 2016) Changed paths: M production/group_vars/galaxyservers.yml Log Message: ----------- adjust tool panel search config we need more results with more weight on name and section Commit: f7f51aeaf9a3dd9f04e5c8277db2d4dfa9af402f https://github.com/galaxyproject/usegalaxy-playbook/commit/f7f51aeaf9a3dd9f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M production/group_vars/galaxyservers.yml Log Message: ----------- Merge pull request #19 from galaxyproject/adjust-panel-search adjust tool panel search config Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/9e4ed017dcff...…

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[galaxyproject/galaxy] eb15c1: Prepass on remote user header based on maildomain ...
by GitHub 02 May '16

02 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: eb15c147504ca4e871afed5f0ff005552b54e85f https://github.com/galaxyproject/galaxy/commit/eb15c147504ca4e871afed5f0ff0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Prepass on remote user header based on maildomain and normalize config. This resolves an error reported on -dev with maildomain and user being set incorrectly. Commit: cdea922890683f8db0cd9dae3b6eed5695cfd094 https://github.com/galaxyproject/galaxy/commit/cdea922890683f8db0cd9dae3b6e… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #2195 from dannon/remoteuser_work [16.01] Prepass on remote user header based on maildomain and normalize confi… Commit: d282ed9ce3e80b06cc89e84add4ca9a32489db9a https://github.com/galaxyproject/galaxy/commit/d282ed9ce3e80b06cc89e84add4c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Commit: 5cd6b47d68902c79631d05ee35d63ccf46e4640d https://github.com/galaxyproject/galaxy/commit/5cd6b47d68902c79631d05ee35d6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/7166a8736448...5cd6b47d6890

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[galaxyproject/galaxy] eb15c1: Prepass on remote user header based on maildomain ...
by GitHub 02 May '16

02 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: eb15c147504ca4e871afed5f0ff005552b54e85f https://github.com/galaxyproject/galaxy/commit/eb15c147504ca4e871afed5f0ff0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Prepass on remote user header based on maildomain and normalize config. This resolves an error reported on -dev with maildomain and user being set incorrectly. Commit: cdea922890683f8db0cd9dae3b6eed5695cfd094 https://github.com/galaxyproject/galaxy/commit/cdea922890683f8db0cd9dae3b6e… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #2195 from dannon/remoteuser_work [16.01] Prepass on remote user header based on maildomain and normalize confi… Commit: d282ed9ce3e80b06cc89e84add4ca9a32489db9a https://github.com/galaxyproject/galaxy/commit/d282ed9ce3e80b06cc89e84add4c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Compare: https://github.com/galaxyproject/galaxy/compare/b9b79839d0f8...d282ed9ce3e8

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[galaxyproject/galaxy] eb15c1: Prepass on remote user header based on maildomain ...
by GitHub 02 May '16

02 May '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: eb15c147504ca4e871afed5f0ff005552b54e85f https://github.com/galaxyproject/galaxy/commit/eb15c147504ca4e871afed5f0ff0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Prepass on remote user header based on maildomain and normalize config. This resolves an error reported on -dev with maildomain and user being set incorrectly. Commit: cdea922890683f8db0cd9dae3b6eed5695cfd094 https://github.com/galaxyproject/galaxy/commit/cdea922890683f8db0cd9dae3b6e… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #2195 from dannon/remoteuser_work [16.01] Prepass on remote user header based on maildomain and normalize confi… Compare: https://github.com/galaxyproject/galaxy/compare/9e980862c8b7...cdea92289068

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[galaxyproject/galaxy] d0447f: Add validation check for data_source tools URL par...
by GitHub 02 May '16

02 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d0447fea2bc6dd63f9f13ebbab685d151ecc5db9 https://github.com/galaxyproject/galaxy/commit/d0447fea2bc6dd63f9f13ebbab68… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/tool_runner.py Log Message: ----------- Add validation check for data_source tools URL parameter Commit: f7fa63365368cf3aa8ab81b8bd2762233bcd9490 https://github.com/galaxyproject/galaxy/commit/f7fa63365368cf3aa8ab81b8bd27… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- it's called conda_ensure_channels Commit: 630a004e3797c9e39349af5f62e07326b9fa8f47 https://github.com/galaxyproject/galaxy/commit/630a004e3797c9e39349af5f62e0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-30 (Sat, 30 Apr 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #2255 from bgruening/release_16.04 [16.04] Update `_condarc` automatically Commit: 787b351404950ae33a1b601eab059d32c817a6fd https://github.com/galaxyproject/galaxy/commit/787b351404950ae33a1b601eab05… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-01 (Sun, 01 May 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/tool_runner.py Log Message: ----------- Merge pull request #2208 from guerler/fix_error_message_001 [16.04] Add fixed validation check for data_source tools URL parameter Commit: cef9270527ba9f56ba4c0fb91a0be5be95095b0d https://github.com/galaxyproject/galaxy/commit/cef9270527ba9f56ba4c0fb91a0b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/jobs/command_factory.py Log Message: ----------- Switch Dockerized commands to use sh instead of bash. We switched to bash for the conda and that doesn't get sourced in containers - so we should be a bit pragmatic about this and switch back to /bin/sh for containers which is more common than /bin/bash. xref https://github.com/galaxyproject/galaxy/pull/2278 Update galaxy.ini.sample to mention this as suggested by @bgruening in https://github.com/galaxyproject/galaxy/pull/2282#issuecomment-216232788. Commit: 9290ddc8a72fba1bf8de7ae5788becef56030223 https://github.com/galaxyproject/galaxy/commit/9290ddc8a72fba1bf8de7ae5788b… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.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/form/form-input.js M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Fixes #2230 This sanitizes some instances where tool parameters were included directly into the DOM. workflow/run.mako displayed the parameter as a value in a hidden input. This was base64 encoded as there was no better solution apparent at the time. I'm not sure where this parameter is POSTed to but we should figure that out and b64decode it, or remove the hidden parameter. client/... added the parameter value into the DOM. This was easily sanitized using a standard method. workflow/display.mako included the parameter value directly into the HTML. This was cgi.esacped Conflicts: static/scripts/bundled/libs.bundled.js.map Commit: 5cf329732307b1fb092825dbfdbad0da464c99c7 https://github.com/galaxyproject/galaxy/commit/5cf329732307b1fb092825dbfdba… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/jobs/command_factory.py Log Message: ----------- Merge pull request #2282 from jmchilton/the_containerz_have_no_bash___doh [16.04] Switch Dockerized commands to use sh instead of bash. Commit: b9b79839d0f812c660dcd39a7316af154728e1a2 https://github.com/galaxyproject/galaxy/commit/b9b79839d0f812c660dcd39a7316… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.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/form/form-input.js M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #2284 from martenson/backport-2230-04 [16.04] Backport of 2230 Commit: 7166a8736448a6383c3a1d286c17d5b568f75aef https://github.com/galaxyproject/galaxy/commit/7166a8736448a6383c3a1d286c17… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py 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 Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c667e52642ef...7166a8736448

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[galaxyproject/galaxy] 9290dd: Fixes #2230
by GitHub 02 May '16

02 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 9290ddc8a72fba1bf8de7ae5788becef56030223 https://github.com/galaxyproject/galaxy/commit/9290ddc8a72fba1bf8de7ae5788b… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.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/form/form-input.js M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Fixes #2230 This sanitizes some instances where tool parameters were included directly into the DOM. workflow/run.mako displayed the parameter as a value in a hidden input. This was base64 encoded as there was no better solution apparent at the time. I'm not sure where this parameter is POSTed to but we should figure that out and b64decode it, or remove the hidden parameter. client/... added the parameter value into the DOM. This was easily sanitized using a standard method. workflow/display.mako included the parameter value directly into the HTML. This was cgi.esacped Conflicts: static/scripts/bundled/libs.bundled.js.map Commit: b9b79839d0f812c660dcd39a7316af154728e1a2 https://github.com/galaxyproject/galaxy/commit/b9b79839d0f812c660dcd39a7316… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.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/form/form-input.js M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #2284 from martenson/backport-2230-04 [16.04] Backport of 2230 Compare: https://github.com/galaxyproject/galaxy/compare/5cf329732307...b9b79839d0f8

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[galaxyproject/galaxy] cef927: Switch Dockerized commands to use sh instead of ba...
by GitHub 02 May '16

02 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: cef9270527ba9f56ba4c0fb91a0be5be95095b0d https://github.com/galaxyproject/galaxy/commit/cef9270527ba9f56ba4c0fb91a0b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/jobs/command_factory.py Log Message: ----------- Switch Dockerized commands to use sh instead of bash. We switched to bash for the conda and that doesn't get sourced in containers - so we should be a bit pragmatic about this and switch back to /bin/sh for containers which is more common than /bin/bash. xref https://github.com/galaxyproject/galaxy/pull/2278 Update galaxy.ini.sample to mention this as suggested by @bgruening in https://github.com/galaxyproject/galaxy/pull/2282#issuecomment-216232788. Commit: 5cf329732307b1fb092825dbfdbad0da464c99c7 https://github.com/galaxyproject/galaxy/commit/5cf329732307b1fb092825dbfdba… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/jobs/command_factory.py Log Message: ----------- Merge pull request #2282 from jmchilton/the_containerz_have_no_bash___doh [16.04] Switch Dockerized commands to use sh instead of bash. Compare: https://github.com/galaxyproject/galaxy/compare/787b35140495...5cf329732307

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[galaxyproject/ansible-galaxy] d41b01: Update README.md
by GitHub 02 May '16

02 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: d41b0171b49cbf0050304b085bd549e98b9daea2 https://github.com/galaxyproject/ansible-galaxy/commit/d41b0171b49cbf005030… Author: Rémi Marenco <remi.marenco(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M README.md Log Message: ----------- Update README.md A few minor modifications (typo and changed universe to galaxy) Commit: c20b067bd28202707c493bc6d624f12fe302a8c1 https://github.com/galaxyproject/ansible-galaxy/commit/c20b067bd28202707c49… Author: Rémi Marenco <remi.marenco(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M README.md Log Message: ----------- Update README.md Commit: a219b93cc62543e35d5631ceabe8cafdf2269716 https://github.com/galaxyproject/ansible-galaxy/commit/a219b93cc62543e35d56… Author: Enis Afgan <afgane(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M README.md Log Message: ----------- Merge pull request #12 from remimarenco/patch-1 Update README.md Compare: https://github.com/galaxyproject/ansible-galaxy/compare/e2393aff87eb...a219…

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[galaxyproject/galaxy] 80e697: Fix encoding issues in test/unit/test_objectstore....
by GitHub 02 May '16

02 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 80e6971d5a433590e5368999bea364ba2dc2b9fc https://github.com/galaxyproject/galaxy/commit/80e6971d5a433590e5368999bea3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M test/unit/test_objectstore.py Log Message: ----------- Fix encoding issues in test/unit/test_objectstore.py. Without fix this test fails in Python 3. Commit: c667e52642efe4ff744357f3fda83a593bcbba8c https://github.com/galaxyproject/galaxy/commit/c667e52642efe4ff744357f3fda8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M test/unit/test_objectstore.py Log Message: ----------- Merge pull request #2280 from jmchilton/test_objectstore_fix Fix encoding issues in test/unit/test_objectstore.py. Compare: https://github.com/galaxyproject/galaxy/compare/431c7707b5f5...c667e52642ef

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galaxy-commits May 2016