- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 98a9c8: Allow testing tags in input collections.
by GitHub 07 Oct '18

07 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 98a9c86badd87a4db4a815490c06c717b67fced0 https://github.com/galaxyproject/galaxy/commit/98a9c86badd87a4db4a815490c06… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/tools/tag_collection_from_file.xml M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Allow testing tags in input collections. Commit: 58ea67eb457ce154e1d119e94c07a81a1e617ba4 https://github.com/galaxyproject/galaxy/commit/58ea67eb457ce154e1d119e94c07… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-07 (Sun, 07 Oct 2018) Changed paths: M lib/galaxy/tools/tag_collection_from_file.xml M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #6823 from jmchilton/tag_input_tests [18.09] Allow testing tags in input collections. Compare: https://github.com/galaxyproject/galaxy/compare/8ea455303ab7...58ea67eb457c **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] c61617: Replace trans.sa_session with sa_session in PSACod...
by GitHub 07 Oct '18

07 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c61617fed6ae59f237cb22fa0f6103508484fc3b https://github.com/galaxyproject/galaxy/commit/c61617fed6ae59f237cb22fa0f61… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py Log Message: ----------- Replace trans.sa_session with sa_session in PSACode. Commit: 12a3f7b54531f667885d1187538c9b06f244744b https://github.com/galaxyproject/galaxy/commit/12a3f7b54531f667885d1187538c… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py Log Message: ----------- Replace trans.sa_session with sa_session in PSAAssociation. Commit: 49bb3a66668f94bed1534b007237f0b1db3b71d9 https://github.com/galaxyproject/galaxy/commit/49bb3a66668f94bed1534b007237… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py Log Message: ----------- Replace trans.sa_session with sa_session in PSANonce. Commit: a4d03f0de07df762055210f0c3812cbe0c0bccaf https://github.com/galaxyproject/galaxy/commit/a4d03f0de07df762055210f0c381… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py Log Message: ----------- Replace trans.sa_session with sa_session in PSAPartial. Commit: 17eac4fe84465706f3b6b8290ae8872d6985afe7 https://github.com/galaxyproject/galaxy/commit/17eac4fe84465706f3b6b8290ae8… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py Log Message: ----------- Replace trans.sa_session with sa_session in UserAuthnzToken. Commit: ebb37f8ff02f246344d73db7c3751b531c4fd38f https://github.com/galaxyproject/galaxy/commit/ebb37f8ff02f246344d73db7c375… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Replace trans with app & sa_session in on_the_fly_config function. Commit: 69bd26e6046c0dd18eaae4cee433d34d26d87d80 https://github.com/galaxyproject/galaxy/commit/69bd26e6046c0dd18eaae4cee433… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Remove `app` from `on_the_fly_config` signature. Commit: 8ed5d8c9414f8b086852a2a347d79e530c231b0c https://github.com/galaxyproject/galaxy/commit/8ed5d8c9414f8b086852a2a347d7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-07 (Sun, 07 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #6826 from VJalili/authnz_trans Remove `trans` from OIDC-related types Compare: https://github.com/galaxyproject/galaxy/compare/7d9093d5ab30...8ed5d8c9414f **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 18b427: Import gxformat2 as an external dependency.
by GitHub 07 Oct '18

07 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 18b4274e651f85db2019faba0674613ef02921aa https://github.com/galaxyproject/galaxy/commit/18b4274e651f85db2019faba0674… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M test/base/populators.py R test/base/workflows_format_2/README.txt R test/base/workflows_format_2/__init__.py R test/base/workflows_format_2/converter.py R test/base/workflows_format_2/interface.py R test/base/workflows_format_2/main.py Log Message: ----------- Import gxformat2 as an external dependency. Commit: 319c29937e30075d0dab45bca87577fd86bc7492 https://github.com/galaxyproject/galaxy/commit/319c29937e30075d0dab45bca875… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py Log Message: ----------- gxformat2 - allow CWL style 'in' declarations for step connections. Makes gxformat2 look a lot closer to CWL workflows with Galaxy tools and state. Commit: c7fa2860d807229ebb29233d99c545534f3d7079 https://github.com/galaxyproject/galaxy/commit/c7fa2860d807229ebb29233d99c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py Log Message: ----------- Toward new format2 syntaxes in test workflows. Commit: d010077830ccdf2c28e978bc65c9871db646f880 https://github.com/galaxyproject/galaxy/commit/d010077830ccdf2c28e978bc65c9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/workflow/modules.py M test/api/test_workflows_from_yaml.py Log Message: ----------- Allow workflow import of workflows with connections that don't have matching empty tool state entries. There is a long conversation in the added doc string. Commit: 7d9093d5ab308301e2ec9e464ce8e7cfbeba77ea https://github.com/galaxyproject/galaxy/commit/7d9093d5ab308301e2ec9e464ce8… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-07 (Sun, 07 Oct 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/populators.py R test/base/workflows_format_2/README.txt R test/base/workflows_format_2/__init__.py R test/base/workflows_format_2/converter.py R test/base/workflows_format_2/interface.py R test/base/workflows_format_2/main.py Log Message: ----------- Merge pull request #6807 from jmchilton/gxformat2_030 Support for Enhancements to gxformat2. Compare: https://github.com/galaxyproject/galaxy/compare/10e984ce85c2...7d9093d5ab30 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 50019e: Refactor method for running format 2 workflows int...
by GitHub 06 Oct '18

06 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 50019e503adf811a54b54011d64ef92b8a610b13 https://github.com/galaxyproject/galaxy/commit/50019e503adf811a54b54011d64e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M test/api/test_workflows.py M test/base/populators.py Log Message: ----------- Refactor method for running format 2 workflows into populators.py for reuse. Commit: 3e774713a902fb59b4164e4deac2688b9678f0ce https://github.com/galaxyproject/galaxy/commit/3e774713a902fb59b4164e4deac2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_workflows_from_yaml.py M test/base/populators.py M test/base/workflows_format_2/main.py M test/functional/tools/disambiguate_cond.xml Log Message: ----------- Fill in needed state defaults when importing manually curated workflows. Commit: 10e984ce85c2d02d95cb96a11d1738fb1d6ab951 https://github.com/galaxyproject/galaxy/commit/10e984ce85c2d02d95cb96a11d17… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/populators.py M test/base/workflows_format_2/main.py M test/functional/tools/disambiguate_cond.xml Log Message: ----------- Merge pull request #6746 from jmchilton/workflow_state_touch_1 Fill in needed state defaults when importing manually crafted workflows. Compare: https://github.com/galaxyproject/galaxy/compare/56ca1cdef4d3...10e984ce85c2 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 0a6de6: Add more detail about container tags
by GitHub 05 Oct '18

05 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0a6de6b8d7581a2ca27bad3388b936c6b560ea93 https://github.com/galaxyproject/galaxy/commit/0a6de6b8d7581a2ca27bad3388b9… Author: pvanheus <pvh(a)sanbi.ac.za> Date: 2018-10-05 (Fri, 05 Oct 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Add more detail about container tags Explain that singularity container tags are now supported and add some detail about how to use them. Commit: 5601d893a3350a3efca0238d672f059d2404be5c https://github.com/galaxyproject/galaxy/commit/5601d893a3350a3efca0238d672f… Author: pvanheus <pvh(a)sanbi.ac.za> Date: 2018-10-05 (Fri, 05 Oct 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Fixes to workding as per nsoranzo Commit: 56ca1cdef4d373958426c5a0028542854edfb48a https://github.com/galaxyproject/galaxy/commit/56ca1cdef4d373958426c5a00285… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-05 (Fri, 05 Oct 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #6818 from pvanheus/patch-7 Add more detail about container tags Compare: https://github.com/galaxyproject/galaxy/compare/973c73ce722a...56ca1cdef4d3 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] a5d794: Add docs about running jobs in containers
by GitHub 05 Oct '18

05 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a5d794dc4d1ee48539aa36c82ec56ac40760e0fa https://github.com/galaxyproject/galaxy/commit/a5d794dc4d1ee48539aa36c82ec5… Author: pvanheus <pvh(a)sanbi.ac.za> Date: 2018-10-05 (Fri, 05 Oct 2018) Changed paths: M doc/source/admin/jobs.md Log Message: ----------- Add docs about running jobs in containers Explain how jobs can be run in containers (something currently documented in the `job_conf.xml.sample_advanced` file) Commit: 973c73ce722ae588d8aca9d5f71c6f6e938f10e4 https://github.com/galaxyproject/galaxy/commit/973c73ce722ae588d8aca9d5f71c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-05 (Fri, 05 Oct 2018) Changed paths: M doc/source/admin/jobs.md Log Message: ----------- Merge pull request #6820 from pvanheus/patch-8 Add docs about running jobs in containers Compare: https://github.com/galaxyproject/galaxy/compare/13d92c007001...973c73ce722a **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 5b8ae3: Update to latest galaxy-lib.
by GitHub 05 Oct '18

05 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5b8ae3e7314dbd96a13e8b32447fff6bdb358ae0 https://github.com/galaxyproject/galaxy/commit/5b8ae3e7314dbd96a13e8b32447f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/cwl/util.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py M lib/galaxy/tools/parser/cwl.py Log Message: ----------- Update to latest galaxy-lib. Commit: 13d92c007001b11a052f21b103c717a430861f66 https://github.com/galaxyproject/galaxy/commit/13d92c007001b11a052f21b103c7… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-05 (Fri, 05 Oct 2018) Changed paths: M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/cwl/util.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py M lib/galaxy/tools/parser/cwl.py Log Message: ----------- Merge pull request #6709 from jmchilton/galaxy-lib-update-20180913 Update to latest galaxy-lib. Compare: https://github.com/galaxyproject/galaxy/compare/997301cfe4c6...13d92c007001 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 4908b9: Fix types on "reserve_memory" / "reserve_cpu"
by GitHub 05 Oct '18

05 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4908b98daaf45aa886a3b0a7badcf90acb949c19 https://github.com/galaxyproject/galaxy/commit/4908b98daaf45aa886a3b0a7badc… Author: pvanheus <pvh(a)sanbi.ac.za> Date: 2018-10-05 (Fri, 05 Oct 2018) Changed paths: M config/containers_conf.yml.sample Log Message: ----------- Fix types on "reserve_memory" / "reserve_cpu" resverve changed to reserve Commit: 997301cfe4c6ab1ec9596330c8267c73d465a3fc https://github.com/galaxyproject/galaxy/commit/997301cfe4c6ab1ec9596330c826… Author: Helena Rasche <erasche(a)users.noreply.github.com> Date: 2018-10-05 (Fri, 05 Oct 2018) Changed paths: M config/containers_conf.yml.sample Log Message: ----------- Merge pull request #6817 from pvanheus/patch-6 Fix typos on "reserve_memory" / "reserve_cpu" Compare: https://github.com/galaxyproject/galaxy/compare/18f351ae31ae...997301cfe4c6 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/infrastructure-playbook] b4e69c: Set a slurm reboot program so `scontrol reboot` wo...
by GitHub 04 Oct '18

04 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: b4e69cd3abb082a412404d48111093d07fdc1513 https://github.com/galaxyproject/infrastructure-playbook/commit/b4e69cd3abb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M env/tacc/templates/slurm/slurm.conf.j2 Log Message: ----------- Set a slurm reboot program so `scontrol reboot` works **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/infrastructure-playbook] 4fcfff: Remove duplicate athena key
by GitHub 04 Oct '18

04 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 4fcfff08ea457d3fc91f8e99628bce66feea5b71 https://github.com/galaxyproject/infrastructure-playbook/commit/4fcfff08ea4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M env/common/group_vars/sslservers/vault.yml Log Message: ----------- Remove duplicate athena key Commit: 6bf8ecf5223028bb96092dd2018896b8b147dab4 https://github.com/galaxyproject/infrastructure-playbook/commit/6bf8ecf5223… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: A roles/dj-wasabi.telegraf/.github/ISSUE_TEMPLATE/bug_report.md A roles/dj-wasabi.telegraf/.github/ISSUE_TEMPLATE/feature_request.md M roles/dj-wasabi.telegraf/.travis.yml M roles/dj-wasabi.telegraf/CHANGELOG.md A roles/dj-wasabi.telegraf/CODE_OF_CONDUCT.md A roles/dj-wasabi.telegraf/CONTRIBUTING.md A roles/dj-wasabi.telegraf/LICENSE A roles/dj-wasabi.telegraf/PULL_REQUEST_TEMPLATE.md M roles/dj-wasabi.telegraf/README.md M roles/dj-wasabi.telegraf/defaults/main.yml M roles/dj-wasabi.telegraf/meta/.galaxy_install_info M roles/dj-wasabi.telegraf/meta/main.yml M roles/dj-wasabi.telegraf/molecule/default/create.yml M roles/dj-wasabi.telegraf/molecule/default/molecule.yml M roles/dj-wasabi.telegraf/molecule/default/playbook.yml M roles/dj-wasabi.telegraf/molecule/default/yaml-lint.yml A roles/dj-wasabi.telegraf/requirements.txt M roles/dj-wasabi.telegraf/tasks/Debian.yml M roles/dj-wasabi.telegraf/tasks/RedHat.yml A roles/dj-wasabi.telegraf/tasks/configure.yml M roles/dj-wasabi.telegraf/tasks/main.yml M roles/dj-wasabi.telegraf/templates/etc-opt-telegraf-telegraf.conf.j2 M roles/dj-wasabi.telegraf/templates/telegraf-extra-plugin.conf.j2 M roles/dj-wasabi.telegraf/templates/telegraf.conf.j2 Log Message: ----------- Update dj-wasabi.telegraf Commit: d0d15fa672f7604a46f7190677b305dbc988c9e3 https://github.com/galaxyproject/infrastructure-playbook/commit/d0d15fa672f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: A env/tacc/group_vars/galaxydbservers.yml M env/tacc/group_vars/galaxyservers.yml A env/tacc/group_vars/maingalaxydbservers.yml A env/tacc/group_vars/testgalaxydbservers.yml M env/tacc/inventory A env/tacc/templates/stats/galaxy_db_slurp.sh.j2 M roles/stats/templates/galaxy_slurp.py.j2 Log Message: ----------- Use telegraf for collecting (some) of the SQL stats, thanks to a protip from @erasche Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/85852a755a… **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0