- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] bc95f2: Fix the --log-file option in the job handlers
by GitHub 11 Jul '18

11 Jul '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: bc95f2563601635cfa1daa686b3d5c4e3ebb51ea https://github.com/galaxyproject/galaxy/commit/bc95f2563601635cfa1daa686b3d… Author: Devon Ryan <dpryan79(a)gmail.com> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Fix the --log-file option in the job handlers (cherry picked from commit 97c344a17a0188a687629103feefcdf03af8e768) Commit: 23666c94a22b816bc5238e4a22c759a11265f7aa https://github.com/galaxyproject/galaxy/commit/23666c94a22b816bc5238e4a22c7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #6477 from natefoo/backport-pr-6351 [18.01] Fix the --log-file option in the job handlers Compare: https://github.com/galaxyproject/galaxy/compare/36706e9eb387...23666c94a22b **NOTE:** This service 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] 8077d5: Update common_startup_functions.sh
by GitHub 11 Jul '18

11 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8077d59fd9772ef6d1d9175e8edef4c8f95ace5a https://github.com/galaxyproject/galaxy/commit/8077d59fd9772ef6d1d9175e8ede… Author: Nadia Goué <nadia.goue(a)gmail.com> Date: 2018-07-10 (Tue, 10 Jul 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Update common_startup_functions.sh Not to override tool_shed config file. Commit: f33770096c038d420696c822bd3ab8c397156f14 https://github.com/galaxyproject/galaxy/commit/f33770096c038d420696c822bd3a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Merge pull request #6481 from nagoue/patch-1 Update common_startup_functions.sh Compare: https://github.com/galaxyproject/galaxy/compare/f25af28f6667...f33770096c03 **NOTE:** This service 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] fb449b: fix the logging init
by GitHub 11 Jul '18

11 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fb449b49906197fbb611833acf06ee13e5b34e48 https://github.com/galaxyproject/galaxy/commit/fb449b49906197fbb611833acf06… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M scripts/grt/upload.py Log Message: ----------- fix the logging init - properly initialiaze the logger - change level for some of the logs - add some debug and critical logs Commit: 390aedf8c8c28db739a78dc7c41e9275a735369b https://github.com/galaxyproject/galaxy/commit/390aedf8c8c28db739a78dc7c41e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M scripts/grt/grt.yml.sample M scripts/grt/upload.py Log Message: ----------- add all sample tool_conf data source tools to GRT sanitization Commit: ab760f5d27bb248a9c78d79a002b5ab2c68fa5d3 https://github.com/galaxyproject/galaxy/commit/ab760f5d27bb248a9c78d79a002b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-10 (Tue, 10 Jul 2018) Changed paths: M scripts/grt/export.py M scripts/grt/grt.yml.sample Log Message: ----------- revert the datasource tool sanitation, set default # for export Commit: f25af28f6667fa3984fd64bd5c17d906c5e1510a https://github.com/galaxyproject/galaxy/commit/f25af28f6667fa3984fd64bd5c17… Author: Helena Rasche <erasche(a)users.noreply.github.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M scripts/grt/export.py M scripts/grt/grt.yml.sample M scripts/grt/upload.py Log Message: ----------- Merge pull request #6478 from martenson/telescope-logging GRT: fix the upload logging init Compare: https://github.com/galaxyproject/galaxy/compare/038da2e3e65b...f25af28f6667 **NOTE:** This service 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] 6ca7db: Fix for show params server error for https://githu...
by GitHub 10 Jul '18

10 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6ca7db806b953a183fa192bcc0739540599348fa https://github.com/galaxyproject/galaxy/commit/6ca7db806b953a183fa192bcc073… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-07-10 (Tue, 10 Jul 2018) Changed paths: M templates/show_params.mako Log Message: ----------- Fix for show params server error for https://github.com/galaxyproject/galaxy/pull/6480 Commit: 038da2e3e65b8bb21fcf77a186f02db1aae563f2 https://github.com/galaxyproject/galaxy/commit/038da2e3e65b8bb21fcf77a186f0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-10 (Tue, 10 Jul 2018) Changed paths: M templates/show_params.mako Log Message: ----------- Merge pull request #6486 from blankenberg/show-param Fix for show params server error Compare: https://github.com/galaxyproject/galaxy/compare/0860fdf13497...038da2e3e65b **NOTE:** This service 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/usegalaxy-playbook] aaf8aa: add intermine to Test configs
by GitHub 10 Jul '18

10 Jul '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: aaf8aae9226a9dac206dc28524b8a3ce1ce89c6f https://github.com/galaxyproject/usegalaxy-playbook/commit/aaf8aae9226a9dac… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-10 (Tue, 10 Jul 2018) Changed paths: M env/test/files/galaxy/config/tool_conf.xml M env/test/files/galaxy/config/tool_data_table_conf.xml M env/test/files/galaxy/var/integrated_tool_panel.xml Log Message: ----------- add intermine to Test configs **NOTE:** This service 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/usegalaxy-playbook] 4a97ec: install imtermine exchange converter, update Test
by GitHub 10 Jul '18

10 Jul '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4a97eced1ece9f8351168aa1d132c50d4628ad0e https://github.com/galaxyproject/usegalaxy-playbook/commit/4a97eced1ece9f83… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-10 (Tue, 10 Jul 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- install imtermine exchange converter, update Test **NOTE:** This service 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] 9f0018: Add more information to the dataset template
by GitHub 10 Jul '18

10 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9f001807df651ec2792902aa82dd48ea0f937205 https://github.com/galaxyproject/galaxy/commit/9f001807df651ec2792902aa82dd… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-07-10 (Tue, 10 Jul 2018) Changed paths: M templates/show_params.mako Log Message: ----------- Add more information to the dataset template Commit: 04db42343ce9840a078f0f0178a667e20c982b17 https://github.com/galaxyproject/galaxy/commit/04db42343ce9840a078f0f0178a6… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-07-10 (Tue, 10 Jul 2018) Changed paths: M templates/show_params.mako Log Message: ----------- Address review comments Commit: 4bf2d60d6cdc1ef20a275aaf37d602c33005a865 https://github.com/galaxyproject/galaxy/commit/4bf2d60d6cdc1ef20a275aaf37d6… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-10 (Tue, 10 Jul 2018) Changed paths: M templates/show_params.mako Log Message: ----------- Use horizontal <th> Commit: 0860fdf134978f634707bf3f6aa18e1517f89bbb https://github.com/galaxyproject/galaxy/commit/0860fdf134978f634707bf3f6aa1… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-10 (Tue, 10 Jul 2018) Changed paths: M templates/show_params.mako Log Message: ----------- Merge pull request #6480 from erasche/more-job-info Add more information to the dataset template Compare: https://github.com/galaxyproject/galaxy/compare/ce09f53e24ff...0860fdf13497 **NOTE:** This service 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] 019f08: Allow including paths in inputs json files.
by GitHub 10 Jul '18

10 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 019f088543736cecf74febd414782d7a207acd9c https://github.com/galaxyproject/galaxy/commit/019f088543736cecf74febd41478… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/inputs_as_json_with_paths.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Allow including paths in inputs json files. Commit: 6af48d90dbb64b9aa01b9876ae5b10cbe17e5f09 https://github.com/galaxyproject/galaxy/commit/6af48d90dbb64b9aa01b9876ae5b… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- data_stype to data_style Commit: ce09f53e24ff992d7f39fc94d01b75a1cbcee1fe https://github.com/galaxyproject/galaxy/commit/ce09f53e24ff992d7f39fc94d01b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/inputs_as_json_with_paths.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6468 from jmchilton/allow_including_paths_in_inputs_json Allow including paths in inputs json files. Compare: https://github.com/galaxyproject/galaxy/compare/60fc4baa4c3a...ce09f53e24ff **NOTE:** This service 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/usegalaxy-playbook] f9cadc: Update SnpEff build to 4.3+T.galaxy3
by GitHub 10 Jul '18

10 Jul '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f9cadc3a86a865fd95d60b4e4c6394156ce1df95 https://github.com/galaxyproject/usegalaxy-playbook/commit/f9cadc3a86a865fd… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Update SnpEff build to 4.3+T.galaxy3 **NOTE:** This service 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/usegalaxy-playbook] 9454f7: Markdown missing code closing tag
by GitHub 09 Jul '18

09 Jul '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9454f715b8c2c9797fee64379c86164504a0788e https://github.com/galaxyproject/usegalaxy-playbook/commit/9454f715b8c2c979… Author: Mark Esler <eslerm(a)umn.edu> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M roles/galaxyproject.galaxy/README.md Log Message: ----------- Markdown missing code closing tag Commit: 39e34574fa086c1ad0745da177ebf401585c73eb https://github.com/galaxyproject/usegalaxy-playbook/commit/39e34574fa086c1a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M roles/galaxyproject.galaxy/README.md Log Message: ----------- Merge pull request #148 from eslerm/patch-1 Markdown missing code closing tag Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/bd52ea967973...… **NOTE:** This service 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