- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 168ba1: Follow up on @nsoranzo comment...
by GitHub 25 May '16

25 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 168ba1b130cfa306f050aacc3d7d4a0bb260421e https://github.com/galaxyproject/galaxy/commit/168ba1b130cfa306f050aacc3d7d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/tools/parser/xml.py Log Message: ----------- Follow up on @nsoranzo comment... https://github.com/galaxyproject/galaxy/pull/2409#discussion_r64588439 \minor Commit: b16ad40bee213a861085dc7e6a0bb762caee4adf https://github.com/galaxyproject/galaxy/commit/b16ad40bee213a861085dc7e6a0b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/tools/parser/xml.py Log Message: ----------- Merge pull request #2412 from jmchilton/2409_followup Follow up on @nsoranzo comment... Compare: https://github.com/galaxyproject/galaxy/compare/b41e03994e48...b16ad40bee21

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[galaxyproject/galaxy] 4765f5: Enhancements to tool test output verification.
by GitHub 25 May '16

25 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4765f5876eddf8855395b9d1bd8dd82f19ab4ce5 https://github.com/galaxyproject/galaxy/commit/4765f5876eddf8855395b9d1bd8d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/tools/parser/xml.py A lib/galaxy/tools/verify/__init__.py A lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/asserts/tabular.py A lib/galaxy/tools/verify/asserts/text.py A lib/galaxy/tools/verify/asserts/xml.py A lib/galaxy/tools/verify/test_data.py M test/api/test_tools.py M test/api/test_workflows.py R test/base/asserts/__init__.py R test/base/asserts/tabular.py R test/base/asserts/text.py R test/base/asserts/xml.py R test/base/test_data.py M test/base/twilltestcase.py M test/functional/test_toolbox.py A test/functional/tools/composite_output_tests.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Enhancements to tool test output verification. Refactor test verification into galaxy-lib-compat module. - Refactor a bunch class methods in ``test.base.twilltestcase`` into module functions in ``galaxy.tools.verify``. - Move ``test.base.test_data`` to ``galaxy.tools.verify.test_data``. - Move ``test.base.asserts`` to ``galaxy.tools.verify.asserts``. Remove duplication in execution of these methods between composite and normal test outputs. This also entailed reworking the parsing of the composite test outputs to bring them inline with normal outputs. In addition to simplify removing duplication, this means many more tests can be made over composite outputs - such as md5 checks and test assertions. I've added a new framework test tool to verify this. Commit: b41e03994e48abfb15c375f43a5de0cf3605e462 https://github.com/galaxyproject/galaxy/commit/b41e03994e48abfb15c375f43a5d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/tools/parser/xml.py A lib/galaxy/tools/verify/__init__.py A lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/asserts/tabular.py A lib/galaxy/tools/verify/asserts/text.py A lib/galaxy/tools/verify/asserts/xml.py A lib/galaxy/tools/verify/test_data.py M test/api/test_tools.py M test/api/test_workflows.py R test/base/asserts/__init__.py R test/base/asserts/tabular.py R test/base/asserts/text.py R test/base/asserts/xml.py R test/base/test_data.py M test/base/twilltestcase.py M test/functional/test_toolbox.py A test/functional/tools/composite_output_tests.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #2409 from jmchilton/test_assertions_lib Enhancements to tool test output verification. Compare: https://github.com/galaxyproject/galaxy/compare/d72031869d9c...b41e03994e48

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[galaxyproject/galaxy] 5dcd04: UI, datasets: show hid in 'view details' page
by GitHub 25 May '16

25 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5dcd04b0b2955a1908db3f35b3a18969a307dc8a https://github.com/galaxyproject/galaxy/commit/5dcd04b0b2955a1908db3f35b3a1… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M templates/show_params.mako Log Message: ----------- UI, datasets: show hid in 'view details' page Adds the hid to the list of dataset/job information on the show_params/ view details/info page. Commit: d72031869d9c4885cada462bc77de54c9c52ea64 https://github.com/galaxyproject/galaxy/commit/d72031869d9c4885cada462bc77d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Merge pull request #2411 from carlfeberhard/show-params.add-hid UI, datasets: show hid in 'view details' page Compare: https://github.com/galaxyproject/galaxy/compare/7479dddb8562...d72031869d9c

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[galaxyproject/usegalaxy-playbook] 932903: Remove embedded Pulsar from Main job config
by GitHub 25 May '16

25 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 932903a67a949a69009387803136ba6784a7275f https://github.com/galaxyproject/usegalaxy-playbook/commit/932903a67a949a69… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M files/galaxy/usegalaxy.org/config/pulsar_jetstream.yml M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Remove embedded Pulsar from Main job config

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[galaxyproject/infrastructure-playbook] 4033cc: New slurm controller for IU
by GitHub 25 May '16

25 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 4033cc2de2b67cbfc5868ac6661f28adde535d59 https://github.com/galaxyproject/infrastructure-playbook/commit/4033cc2de2b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M jetstreamiuenv/group_vars/all.yml M jetstreamiuenv/group_vars/galaxynodes.yml M jetstreamiuenv/group_vars/slurmclients.yml Log Message: ----------- New slurm controller for IU

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[galaxyproject/infrastructure-playbook] 3d8b05: Move duvel nginx config from private playbook and ...
by GitHub 25 May '16

25 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 3d8b059560f2be93ca6c41993bad02cc48f7f958 https://github.com/galaxyproject/infrastructure-playbook/commit/3d8b059560f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: A galaxyenv/host_vars/duvel.galaxyproject.org.yml M galaxyenv/inventory A galaxyenv/templates/nginx/duvel.j2 A galaxyenv/templates/nginx/jenkins.j2 Log Message: ----------- Move duvel nginx config from private playbook and add an http proxy timeout

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[galaxyproject/usegalaxy-playbook] 8f6768: Update Main
by GitHub 25 May '16

25 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8f676862eb0f770da0e655bfe87e87fbbdc2b49c https://github.com/galaxyproject/usegalaxy-playbook/commit/8f676862eb0f770d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M production/group_vars/all.yml Log Message: ----------- Update Main

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[galaxyproject/galaxy] 5fbb65: Catch all exceptions in slurm's _complete_terminal...
by GitHub 25 May '16

25 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5fbb65e5033d23b9751251a4a935b4c76ffd65d5 https://github.com/galaxyproject/galaxy/commit/5fbb65e5033d23b9751251a4a935… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-24 (Tue, 24 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Catch all exceptions in slurm's _complete_terminal_job() to prevent looping job completion Commit: b6d65da83d77167482a3fe3a706c249abad6dbfa https://github.com/galaxyproject/galaxy/commit/b6d65da83d77167482a3fe3a706c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-24 (Tue, 24 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Fix linting error Commit: 2a29e92ef9d8e560988d6e64d06c5cbbf79098a1 https://github.com/galaxyproject/galaxy/commit/2a29e92ef9d8e560988d6e64d06c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-24 (Tue, 24 May 2016) Changed paths: M lib/galaxy/managers/histories.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- API, history: fix order in most_recently_used - Fix ascending order used in HistoryManager.most_recent to descending - Slightly update the docs to reflect actual value better - Add tests Commit: 47a65160960003244091d4fd441111c257e9e8d9 https://github.com/galaxyproject/galaxy/commit/47a65160960003244091d4fd4411… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/managers/histories.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge pull request #2407 from carlfeberhard/fix.most_recently_used [16.01] API, history: fix order in most_recently_used Commit: 7dcf850ed5203196371fa3d20800b0b864c01158 https://github.com/galaxyproject/galaxy/commit/7dcf850ed5203196371fa3d20800… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2402 from natefoo/slurm-fixes [16.04] Catch all exceptions in slurm's _complete_terminal_job() to prevent looping job completion Commit: 5db5e1395880876ac3066fc91397e7cb1618ea62 https://github.com/galaxyproject/galaxy/commit/5db5e1395880876ac3066fc91397… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/managers/histories.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Conflicts: test/unit/managers/test_HistoryManager.py Commit: 7479dddb8562dc063db16bc4eb3de3d4053548d6 https://github.com/galaxyproject/galaxy/commit/7479dddb8562dc063db16bc4eb3d… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/managers/histories.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c033544a7e73...7479dddb8562

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[galaxyproject/galaxy] 2a29e9: API, history: fix order in most_recently_used
by GitHub 25 May '16

25 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 2a29e92ef9d8e560988d6e64d06c5cbbf79098a1 https://github.com/galaxyproject/galaxy/commit/2a29e92ef9d8e560988d6e64d06c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-24 (Tue, 24 May 2016) Changed paths: M lib/galaxy/managers/histories.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- API, history: fix order in most_recently_used - Fix ascending order used in HistoryManager.most_recent to descending - Slightly update the docs to reflect actual value better - Add tests Commit: 47a65160960003244091d4fd441111c257e9e8d9 https://github.com/galaxyproject/galaxy/commit/47a65160960003244091d4fd4411… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/managers/histories.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge pull request #2407 from carlfeberhard/fix.most_recently_used [16.01] API, history: fix order in most_recently_used Commit: 5db5e1395880876ac3066fc91397e7cb1618ea62 https://github.com/galaxyproject/galaxy/commit/5db5e1395880876ac3066fc91397… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/managers/histories.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Conflicts: test/unit/managers/test_HistoryManager.py Compare: https://github.com/galaxyproject/galaxy/compare/7dcf850ed520...5db5e1395880

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[galaxyproject/galaxy] 3330a2: increase range to 5, Jenkins still fails to push s...
by GitHub 25 May '16

25 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3330a25c7538d375c9c1331353e8608f164076f0 https://github.com/galaxyproject/galaxy/commit/3330a25c7538d375c9c1331353e8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M test/shed_functional/base/twilltestcase.py Log Message: ----------- increase range to 5, Jenkins still fails to push sometimes Commit: c033544a7e7330a93d9d4a7bb2577325090948ab https://github.com/galaxyproject/galaxy/commit/c033544a7e7330a93d9d4a7bb257… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge pull request #2410 from martenson/more-tspus-attempts increase range to 5, Jenkins still fails to push sometimes Compare: https://github.com/galaxyproject/galaxy/compare/caec8c838a7d...c033544a7e73

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[galaxyproject/galaxy] 5fbb65: Catch all exceptions in slurm's _complete_terminal...
by GitHub 25 May '16

25 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 5fbb65e5033d23b9751251a4a935b4c76ffd65d5 https://github.com/galaxyproject/galaxy/commit/5fbb65e5033d23b9751251a4a935… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-24 (Tue, 24 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Catch all exceptions in slurm's _complete_terminal_job() to prevent looping job completion Commit: b6d65da83d77167482a3fe3a706c249abad6dbfa https://github.com/galaxyproject/galaxy/commit/b6d65da83d77167482a3fe3a706c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-24 (Tue, 24 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Fix linting error Commit: 7dcf850ed5203196371fa3d20800b0b864c01158 https://github.com/galaxyproject/galaxy/commit/7dcf850ed5203196371fa3d20800… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2402 from natefoo/slurm-fixes [16.04] Catch all exceptions in slurm's _complete_terminal_job() to prevent looping job completion Compare: https://github.com/galaxyproject/galaxy/compare/8d0e1c51df31...7dcf850ed520

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[galaxyproject/galaxy] 1652e0: Add EDAM topics to tools and expose in API
by GitHub 25 May '16

25 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1652e0ceedfe54cbd340b11c43797e27aba57ff2 https://github.com/galaxyproject/galaxy/commit/1652e0ceedfe54cbd340b11c4379… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-24 (Tue, 24 May 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M test/functional/tools/simple_constructs.yml M tools/stats/gsummary.xml Log Message: ----------- Add EDAM topics to tools and expose in API Commit: caec8c838a7d1256c28a49d34d2ac90ebc164ea4 https://github.com/galaxyproject/galaxy/commit/caec8c838a7d1256c28a49d34d2a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M test/functional/tools/simple_constructs.yml M tools/stats/gsummary.xml Log Message: ----------- Merge pull request #2397 from nsoranzo/edam_topics Add EDAM topics to tools and expose in API Compare: https://github.com/galaxyproject/galaxy/compare/248eed81fac1...caec8c838a7d

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[galaxyproject/galaxy] d728d3: Check variable's presence before calling str metho...
by GitHub 25 May '16

25 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d728d3a373ed2fdc9135ce19437460b3e27ab910 https://github.com/galaxyproject/galaxy/commit/d728d3a373ed2fdc9135ce194374… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-05-24 (Tue, 24 May 2016) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Check variable's presence before calling str methods Commit: 248eed81fac1af60b6ddc86909605056b71162d4 https://github.com/galaxyproject/galaxy/commit/248eed81fac1af60b6ddc8690960… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Merge pull request #2408 from erasche/fix-condor-universe Check variable's presence before calling str methods Compare: https://github.com/galaxyproject/galaxy/compare/fa77c8f45933...248eed81fac1

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[galaxyproject/galaxy] 2a29e9: API, history: fix order in most_recently_used
by GitHub 25 May '16

25 May '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 2a29e92ef9d8e560988d6e64d06c5cbbf79098a1 https://github.com/galaxyproject/galaxy/commit/2a29e92ef9d8e560988d6e64d06c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-24 (Tue, 24 May 2016) Changed paths: M lib/galaxy/managers/histories.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- API, history: fix order in most_recently_used - Fix ascending order used in HistoryManager.most_recent to descending - Slightly update the docs to reflect actual value better - Add tests Commit: 47a65160960003244091d4fd441111c257e9e8d9 https://github.com/galaxyproject/galaxy/commit/47a65160960003244091d4fd4411… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/managers/histories.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge pull request #2407 from carlfeberhard/fix.most_recently_used [16.01] API, history: fix order in most_recently_used Compare: https://github.com/galaxyproject/galaxy/compare/79dd8c82f034...47a651609600

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[galaxyproject/infrastructure-playbook] 55b7fe: Remote Pulsar for Jetstream infra
by GitHub 24 May '16

24 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 55b7fe4eca733df0b60bddf0f135e6c93f66ad33 https://github.com/galaxyproject/infrastructure-playbook/commit/55b7fe4eca7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-24 (Tue, 24 May 2016) Changed paths: M jetstreamiuenv/group_vars/controllers.yml M jetstreamtaccenv/group_vars/controllers.yml M jetstreamtaccenv/inventory M jetstreamtaccenv/playbook.yml M taccenv/playbook.yml Log Message: ----------- Remote Pulsar for Jetstream infra

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[galaxyproject/infrastructure-playbook] 2e5946: Move delirium's nginx configs from the private pla...
by GitHub 24 May '16

24 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 2e5946761f8704d05741a1d9725da03ef34e7bce https://github.com/galaxyproject/infrastructure-playbook/commit/2e5946761f8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-24 (Tue, 24 May 2016) Changed paths: A common_env/secret_group_vars/sslwebservers.yml M common_roles A galaxyenv/files/ssl/wildcard_cert.pem M galaxyenv/host_vars/delirium.galaxyproject.org.yml M galaxyenv/inventory M galaxyenv/playbook.yml A galaxyenv/secret_group_vars/sslwebservers.yml M galaxyenv/secret_host_vars/delirium.galaxyproject.org.yml A galaxyenv/templates/nginx/docs.j2 A galaxyenv/templates/nginx/eggs.j2 A galaxyenv/templates/nginx/galaxy.tools.j2 A galaxyenv/templates/nginx/galaxydomains.j2 A galaxyenv/templates/nginx/lists.j2 A galaxyenv/templates/nginx/toolshed.tools.j2 A galaxyenv/templates/nginx/wheels.j2 A galaxyenv/templates/supervisor/pypiserver.j2 R taccenv/secret_group_vars/ssl.yml A taccenv/secret_group_vars/sslwebservers.yml Log Message: ----------- Move delirium's nginx configs from the private playbook and move wheels to delirium.

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[galaxyproject/galaxy] 9d56ea: Add a new workflow building mode variation which d...
by GitHub 23 May '16

23 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9d56eaf07a4bb6bd53ee22cbe8e22a5b53c29e01 https://github.com/galaxyproject/galaxy/commit/9d56eaf07a4bb6bd53ee22cbe8e2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/api/workflows.py M templates/webapps/galaxy/workflow/editor_tool_form.mako Log Message: ----------- Add a new workflow building mode variation which does access the history Commit: fa77c8f45933bc260f74a47f8efa298c7cc85f7c https://github.com/galaxyproject/galaxy/commit/fa77c8f45933bc260f74a47f8efa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-23 (Mon, 23 May 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/api/workflows.py M templates/webapps/galaxy/workflow/editor_tool_form.mako Log Message: ----------- Merge pull request #2390 from guerler/revise_tool_framework_000 Add a new workflow building mode variation which does access the history Compare: https://github.com/galaxyproject/galaxy/compare/a9c94bd3d70c...fa77c8f45933

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[galaxyproject/galaxy] 7ab5dc: Remove asserts triggering false exceptions when dy...
by GitHub 23 May '16

23 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7ab5dc3d51edf1313ac74ac6ff07d26f507e7449 https://github.com/galaxyproject/galaxy/commit/7ab5dc3d51edf1313ac74ac6ff07… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py M test/unit/tools/test_select_parameters.py Log Message: ----------- Remove asserts triggering false exceptions when dynamic parameters are evaluated for initial tool models Commit: 1c537b4271b5e6b75c0df4fd0fb8e2b01d2de52a https://github.com/galaxyproject/galaxy/commit/1c537b4271b5e6b75c0df4fd0fb8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove conflicting raise/try/pass combo for select parameters Commit: 4893e0e58385f994327bbe819efc4a14e629f7cb https://github.com/galaxyproject/galaxy/commit/4893e0e58385f994327bbe819efc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Insert previously removed assertion into common validation pathway called through from_json Commit: fa380a00cbb779f5b436e29cba2a466db59db62c https://github.com/galaxyproject/galaxy/commit/fa380a00cbb779f5b436e29cba2a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix assertions for drilldown by raising properly displayed value errors instead Commit: a9c94bd3d70cd7cc99a23d971eb37759a660298b https://github.com/galaxyproject/galaxy/commit/a9c94bd3d70cd7cc99a23d971eb3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-23 (Mon, 23 May 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M test/unit/tools/test_select_parameters.py Log Message: ----------- Merge pull request #2374 from guerler/fix_error_log_000 Revise asserts triggering false exceptions for dynamic parameters Compare: https://github.com/galaxyproject/galaxy/compare/7c3622db4002...a9c94bd3d70c

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[galaxyproject/galaxy] 20d6a4: Add EDAM operations to tool class and expose
by GitHub 23 May '16

23 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 20d6a41c13ac5a4d48189fdb056c51ce33f3ff21 https://github.com/galaxyproject/galaxy/commit/20d6a41c13ac5a4d48189fdb056c… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py Log Message: ----------- Add EDAM operations to tool class and expose in api/tools endpoint. Commit: c3ecd1eb7230e5d44c511cb3d9b07f7552ac5369 https://github.com/galaxyproject/galaxy/commit/c3ecd1eb7230e5d44c511cb3d9b0… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M tools/filters/axt_to_concat_fasta.xml M tools/filters/axt_to_fasta.xml M tools/filters/axt_to_lav.xml M tools/filters/bed2gff.xml M tools/filters/bed_to_bigbed.xml M tools/filters/gff2bed.xml M tools/filters/gtf2bedgraph.xml M tools/stats/filtering.xml Log Message: ----------- Annotate tools with edam_operations to demonstrate usage of edam_operations in tool xml. Commit: 42219575e3591352726bdf11f2ab67ae175f5d2b https://github.com/galaxyproject/galaxy/commit/42219575e3591352726bdf11f2ab… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M test/functional/tools/simple_constructs.yml Log Message: ----------- Annotate test yaml tool with edam_operations Commit: 7c3622db400241bcc61dd36a358298cf433705f8 https://github.com/galaxyproject/galaxy/commit/7c3622db400241bcc61dd36a3582… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-23 (Mon, 23 May 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M test/functional/tools/simple_constructs.yml M tools/filters/axt_to_concat_fasta.xml M tools/filters/axt_to_fasta.xml M tools/filters/axt_to_lav.xml M tools/filters/bed2gff.xml M tools/filters/bed_to_bigbed.xml M tools/filters/gff2bed.xml M tools/filters/gtf2bedgraph.xml M tools/stats/filtering.xml Log Message: ----------- Merge pull request #2379 from mvdbeek/edam_operations Add EDAM operations to tools and expose in API Compare: https://github.com/galaxyproject/galaxy/compare/ebd3250253b9...7c3622db4002

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[galaxyproject/galaxy] 39d78c: Drop "Galaxy pip" in favor of manylinux1 wheels (w...
by GitHub 23 May '16

23 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 39d78c7226d8f0417577bdea94b15ac2c77c45a2 https://github.com/galaxyproject/galaxy/commit/39d78c7226d8f0417577bdea94b1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Drop "Galaxy pip" in favor of manylinux1 wheels (which are supported in pip >= 8.1). Commit: 1be90e49b10c607e36cc730ae1bdeb5ed5d967b2 https://github.com/galaxyproject/galaxy/commit/1be90e49b10c607e36cc730ae1bd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Remove unused $GXPIP_VERSION Commit: ebd3250253b9854486042094f9dc9b6d20b0ff38 https://github.com/galaxyproject/galaxy/commit/ebd3250253b9854486042094f9dc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-23 (Mon, 23 May 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #2383 from natefoo/manylinux-support Drop "Galaxy pip" in favor of manylinux1 wheels (which are supported in pip >= 8.1) Compare: https://github.com/galaxyproject/galaxy/compare/04e34f346f19...ebd3250253b9

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[galaxyproject/galaxy] 0e511b: Remove assumed parameter value from error message
by GitHub 23 May '16

23 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0e511b78a4d515f5b8c454e96683b2dc76b1f8df https://github.com/galaxyproject/galaxy/commit/0e511b78a4d515f5b8c454e96683… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove assumed parameter value from error message Commit: 4a2e67036127d8088b96f7f767907f76f3c9012d https://github.com/galaxyproject/galaxy/commit/4a2e67036127d8088b96f7f76790… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Avoid empty strings when converting values to display text Commit: bfca29a98a1fe26131bcf3b181e0b65ad82130c6 https://github.com/galaxyproject/galaxy/commit/bfca29a98a1fe26131bcf3b181e0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add proper validation error for missing single values in data tool parameters Commit: 5918b054130484ec253c0d18b3901141b8c903e3 https://github.com/galaxyproject/galaxy/commit/5918b054130484ec253c0d18b390… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Show default value in error warning only if its different than the initial value Commit: 04e34f346f19fc29c8dd0d0532b676bc782f0a3e https://github.com/galaxyproject/galaxy/commit/04e34f346f19fc29c8dd0d0532b6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-23 (Mon, 23 May 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2391 from guerler/revise_tool_framework_001 Align and improve validation errors and value to text conversions Compare: https://github.com/galaxyproject/galaxy/compare/4461f2458840...04e34f346f19

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[galaxyproject/galaxy] 0c4601: Fix the installed conda version to 3.19.3.
by GitHub 23 May '16

23 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0c4601aaecedf61e77aef4eea9e777829fa5a40d https://github.com/galaxyproject/galaxy/commit/0c4601aaecedf61e77aef4eea9e7… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-05-21 (Sat, 21 May 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Fix the installed conda version to 3.19.3. Commit: 4461f24588400ec861a6159437f0c7c7dc4697d0 https://github.com/galaxyproject/galaxy/commit/4461f24588400ec861a6159437f0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-23 (Mon, 23 May 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #2394 from bgruening/fix_conda_install Fix the installed conda version to 3.19.3. Compare: https://github.com/galaxyproject/galaxy/compare/389fa8ad7da8...4461f2458840

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[galaxyproject/usegalaxy-playbook] 0494df: Updated slide rotation: May 20 GCC2016 deadlines r...
by GitHub 21 May '16

21 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0494dff450343c21e35f1c797b0adc791ce53f1e https://github.com/galaxyproject/usegalaxy-playbook/commit/0494dff450343c21… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2016-05-21 (Sat, 21 May 2016) Changed paths: A files/galaxy/common/static/welcome_img/GCC2016June4Deadlines.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Updated slide rotation: May 20 GCC2016 deadlines replaced with June 4 deadlines.

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[galaxyproject/galaxy]
by GitHub 20 May '16

20 May '16

Branch: refs/heads/fix_pep8 Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/usegalaxy-playbook] bfd90d: Update Pulsar role
by GitHub 20 May '16

20 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bfd90d94d8c005b8c67e35a0bc8b3cfdd56fa62f https://github.com/galaxyproject/usegalaxy-playbook/commit/bfd90d94d8c005b8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M roles/galaxyprojectdotorg.pulsar/README.md M roles/galaxyprojectdotorg.pulsar/defaults/main.yml M roles/galaxyprojectdotorg.pulsar/meta/.galaxy_install_info M roles/galaxyprojectdotorg.pulsar/tasks/main.yml M roles/galaxyprojectdotorg.pulsar/templates/server.ini.j2 Log Message: ----------- Update Pulsar role Commit: cf361e8432ce45b4a0be9cabf66472b397982c70 https://github.com/galaxyproject/usegalaxy-playbook/commit/cf361e8432ce45b4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M galaxy.yml M production/group_vars/all.yml M production/group_vars/galaxyservers.yml M production/group_vars/pulsarservers.yml A production/host_vars/jetstream-tacc0.galaxyproject.org.yml M production/host_vars/login5.stampede.tacc.utexas.edu.yml M production/inventory M pulsar.yml M stage/group_vars/all.yml M stage/group_vars/galaxyservers.yml M stage/group_vars/pulsarservers.yml M stage/host_vars/greenfield.psc.xsede.org.yml A stage/host_vars/jetstream-tacc0.galaxyproject.org.yml M stage/host_vars/login5.stampede.tacc.utexas.edu.yml M stage/inventory M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Switch Test and Main from embedded to remote (RESTful) Pulsar on Jetstream for performance reasons. A few things of note: - /cvmfs/<instance>.galaxyproject.org/config/datatypes_conf.xml is currently created by hand. - Supervisor is configured by hand to run Pulsar on jetstream-tacc0 - jetstream-iu is draining old embedded jobs. No jobs will go to IU until it is set up with remote pulsar and the job config (and dynamic rule) is updated. - Need to set up SSL for Pulsar Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/2f7c3b4a6747...…

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