February 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 29acb1: Show parameter name in DataToolParameter exception
by GitHub 11 Feb '18

11 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 29acb11df5c971a2bc99ae534e36cffa046e2a6c https://github.com/galaxyproject/galaxy/commit/29acb11df5c971a2bc99ae534e36… Author: Peter Cock <p.j.a.cock(a)googlemail.com> Date: 2018-02-07 (Wed, 07 Feb 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Show parameter name in DataToolParameter exception Goal is to replace this kind of output in a failed test run: RunToolException: Error creating a job for these tool inputs - Specify a dataset of the required format / build. with: RunToolException: Error creating a job for these tool inputs - Specify a dataset of the required format / build in parameter 'XXX'. Commit: 587f20cf9c0b6d250bee403cf3baab85e1272dcf https://github.com/galaxyproject/galaxy/commit/587f20cf9c0b6d250bee403cf3ba… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #5465 from peterjc/patch-5 Show parameter name in DataToolParameter exception Compare: https://github.com/galaxyproject/galaxy/compare/d0b4503e0cc2...587f20cf9c0b

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[galaxyproject/ansible-galaxy] d94c2d: Fix pypi index url
by GitHub 09 Feb '18

09 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: d94c2de1a06782aebf88ebbc5c7e0533bd326f09 https://github.com/galaxyproject/ansible-galaxy/commit/d94c2de1a06782aebf88… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-09 (Fri, 09 Feb 2018) Changed paths: M tasks/dependencies.yml Log Message: ----------- Fix pypi index url ping @drosofff, who asked about this on gitter. Commit: ec9cee294f060ef699929f52e848afbcdad899ee https://github.com/galaxyproject/ansible-galaxy/commit/ec9cee294f060ef69992… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-09 (Fri, 09 Feb 2018) Changed paths: M tasks/dependencies.yml Log Message: ----------- Merge pull request #24 from mvdbeek/fix_pypi_url Fix pypi index url Compare: https://github.com/galaxyproject/ansible-galaxy/compare/6544db9b17cc...ec9c…

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[galaxyproject/galaxy] 1ea416: Python3: Update pulsar-galaxy-lib dependency to 0....
by GitHub 09 Feb '18

09 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1ea41622632aeefdac7138ad515659a594887908 https://github.com/galaxyproject/galaxy/commit/1ea41622632aeefdac7138ad5156… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Python3: Update pulsar-galaxy-lib dependency to 0.8.3 Commit: d0b4503e0cc2e3d083330da08672b6ca35d5c4b2 https://github.com/galaxyproject/galaxy/commit/d0b4503e0cc2e3d083330da08672… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-02-09 (Fri, 09 Feb 2018) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge pull request #5494 from nsoranzo/update_pulsar_galaxy_lib Python3: Update pulsar-galaxy-lib dependency to 0.8.3 Compare: https://github.com/galaxyproject/galaxy/compare/b6fe83409ad5...d0b4503e0cc2

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[galaxyproject/galaxy] 6f2a0c: Unify config-rebuild Makefile targets
by GitHub 08 Feb '18

08 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6f2a0cceb03b4277f9ed4e8761cc011e230fa08e https://github.com/galaxyproject/galaxy/commit/6f2a0cceb03b4277f9ed4e8761cc… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M Makefile M config/reports.yml.sample M doc/source/admin/reports_options.rst Log Message: ----------- Unify config-rebuild Makefile targets Rebuild reports sample and RST from schema with the new Makefile target. Commit: b6fe83409ad57e15adcb1b270102827e5e5fc084 https://github.com/galaxyproject/galaxy/commit/b6fe83409ad57e15adcb1b270102… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M Makefile M config/reports.yml.sample M doc/source/admin/reports_options.rst Log Message: ----------- Merge pull request #5488 from nsoranzo/unify_makefile_targets Unify config-rebuild Makefile targets Compare: https://github.com/galaxyproject/galaxy/compare/10ff797ac77d...b6fe83409ad5

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[galaxyproject/usegalaxy-playbook]
by GitHub 08 Feb '18

08 Feb '18

Branch: refs/heads/martenson-patch-1 Home: https://github.com/galaxyproject/usegalaxy-playbook

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[galaxyproject/usegalaxy-playbook] 8a295a: Test mutable configs
by GitHub 08 Feb '18

08 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8a295a1cc22b41985a7b53cb30f0d21054e631b1 https://github.com/galaxyproject/usegalaxy-playbook/commit/8a295a1cc22b4198… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Test mutable configs Commit: f361a5d29332e2f89cfbd0e7ed1e06678f41e8e5 https://github.com/galaxyproject/usegalaxy-playbook/commit/f361a5d29332e2f8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M env/main/group_vars/webservers.yml Log Message: ----------- Merge branch 'master' of github.com:/galaxyproject/usegalaxy-playbook Commit: bbc4b2af277691f56ff4c5edfdb2c0f2592d97ae https://github.com/galaxyproject/usegalaxy-playbook/commit/bbc4b2af277691f5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml M env/main/group_vars/all.yml M env/main/group_vars/galaxyservers/vars.yml M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Enable slow request logging, update Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/a98c020ac2c8...…

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[galaxyproject/usegalaxy-playbook] 39dd10: enable gzipping on main
by GitHub 08 Feb '18

08 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 39dd104bc464869228dbc2afd85b9e829a345b33 https://github.com/galaxyproject/usegalaxy-playbook/commit/39dd104bc4648692… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M env/main/group_vars/webservers.yml Log Message: ----------- enable gzipping on main and unify the gzip_types with Test Commit: a98c020ac2c8a9e84228c05040d57555ec9ecafe https://github.com/galaxyproject/usegalaxy-playbook/commit/a98c020ac2c8a9e8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M env/main/group_vars/webservers.yml Log Message: ----------- Merge pull request #91 from galaxyproject/martenson-patch-1 enable gzipping on main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/182fa5c14203...…

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[galaxyproject/usegalaxy-playbook] 39dd10: enable gzipping on main
by GitHub 08 Feb '18

08 Feb '18

Branch: refs/heads/martenson-patch-1 Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 39dd104bc464869228dbc2afd85b9e829a345b33 https://github.com/galaxyproject/usegalaxy-playbook/commit/39dd104bc4648692… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M env/main/group_vars/webservers.yml Log Message: ----------- enable gzipping on main and unify the gzip_types with Test

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[galaxyproject/galaxy] b5945a: Add IdeasPre datatype subclassed from Rgenetics
by GitHub 08 Feb '18

08 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b5945ad3e3a972acb41c87c2ddeeff222779020c https://github.com/galaxyproject/galaxy/commit/b5945ad3e3a972acb41c87c2ddee… Author: greg <ghv2(a)psu.edu> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py Log Message: ----------- Add IdeasPre datatype subclassed from Rgenetics Commit: 3fdd4edc5c1954dc750dfeff03cb3205ee1b6042 https://github.com/galaxyproject/galaxy/commit/3fdd4edc5c1954dc750dfeff03cb… Author: greg <ghv2(a)psu.edu> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/datatypes/genetics.py Log Message: ----------- Subclass IdeasPre from Html Commit: b463be78a5066c7e6c389c43af2bd863f05e4a80 https://github.com/galaxyproject/galaxy/commit/b463be78a5066c7e6c389c43af2b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt Log Message: ----------- Add nodeenv to dev requirements Commit: 977bbf1481b2fd36512f869c01f0af6ba4099a92 https://github.com/galaxyproject/galaxy/commit/977bbf1481b2fd36512f869c01f0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Install node and yarn in common_startup.sh using nodeenv and the venv's npm. Commit: eba3fb4b35570fc704dbb9a70c733293a2ee4514 https://github.com/galaxyproject/galaxy/commit/eba3fb4b35570fc704dbb9a70c73… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M client/package.json M scripts/common_startup.sh Log Message: ----------- Fix common_startup.sh for galaxy tarballs Do not assume git is installed and the `.git` directory is present. Fix https://github.com/galaxyproject/galaxy/issues/5466 Commit: 3f50b45a4e3016a211dcbd0876bb95acb29cf900 https://github.com/galaxyproject/galaxy/commit/3f50b45a4e3016a211dcbd0876bb… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py Log Message: ----------- Merge pull request #5445 from gregvonkuster/add-ideaspre [18.01] Add support for the ideaspre datatype Commit: d91078024bf3e9404aaca1c8655a5bc2b451ebc8 https://github.com/galaxyproject/galaxy/commit/d91078024bf3e9404aaca1c8655a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M client/package.json M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M scripts/common_startup.sh Log Message: ----------- Merge pull request #5491 from nsoranzo/release_18.01_fix_common_startup_for_bare_clone [18.01] Fix common_startup.sh for galaxy tarballs Commit: 10ff797ac77da470cf2078059b3235cee04570ff https://github.com/galaxyproject/galaxy/commit/10ff797ac77da470cf2078059b32… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M client/package.json M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py M scripts/common_startup.sh Log Message: ----------- Merge branch 'release_18.01' into dev Conflicts: scripts/common_startup.sh Compare: https://github.com/galaxyproject/galaxy/compare/0ca7afb343d8...10ff797ac77d

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[galaxyproject/infrastructure-playbook] db9646: Enable the monitor for influxdb
by GitHub 08 Feb '18

08 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: db9646bca42d6a61e3de2d89fe8d1dfdcea84014 https://github.com/galaxyproject/infrastructure-playbook/commit/db9646bca42… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M roles/stats/templates/influxdb.conf.j2 Log Message: ----------- Enable the monitor for influxdb

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