galaxy-commits May 2016

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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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galaxy-commits May 2016