galaxy-commits June 2018

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170 discussions

[galaxyproject/galaxy] 031ce6: Fix delete "Collection Only" option in history men...
by GitHub 06 Jun '18

06 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 031ce67e996edc3c363bca1fbaf8572e92b5cbc7 https://github.com/galaxyproject/galaxy/commit/031ce67e996edc3c363bca1fbaf8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li-edit.js Log Message: ----------- Fix delete "Collection Only" option in history menu. Broken with https://github.com/galaxyproject/galaxy/commit/7cc01380afd017c5cac2af2b2d73…. Commit: d2723428391a9355e5cd8bc34776d8bf589685a9 https://github.com/galaxyproject/galaxy/commit/d2723428391a9355e5cd8bc34776… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li-edit.js Log Message: ----------- Merge pull request #6281 from jmchilton/fix_delete_collection_only_2 Fix delete "Collection Only" option in history menu. Compare: https://github.com/galaxyproject/galaxy/compare/97fd079255da...d2723428391a **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.

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[galaxyproject/galaxy] 644824: Remove todo
by GitHub 06 Jun '18

06 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 644824c499080648dcfce73693b1235b331c2def https://github.com/galaxyproject/galaxy/commit/644824c499080648dcfce73693b1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Remove todo Commit: 8b31cb1b1a90bbc70c5efc352349cea0149a24bb https://github.com/galaxyproject/galaxy/commit/8b31cb1b1a90bbc70c5efc352349… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Fix help text for renaming operation in workflows Commit: 97fd079255dacbb085e89988d78a6f67cc99d342 https://github.com/galaxyproject/galaxy/commit/97fd079255dacbb085e89988d78a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge pull request #6274 from guerler/fix_help Fix help text for renaming operation in workflows Compare: https://github.com/galaxyproject/galaxy/compare/afa62a25e134...97fd079255da **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.

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[galaxyproject/galaxy] 7b741a: Fix `GALAXY_RUN_ALL=1 ./run.sh --daemon`
by GitHub 06 Jun '18

06 Jun '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 7b741a32cddb94442c7663f94c6c3b29e91e4158 https://github.com/galaxyproject/galaxy/commit/7b741a32cddb94442c7663f94c6c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M run.sh Log Message: ----------- Fix `GALAXY_RUN_ALL=1 ./run.sh --daemon` Broken in commit 0ea8107191ea1a3bc8b4b57623c981c06f38092e . Reported by @lparsons in https://github.com/galaxyproject/galaxy/pull/6262#issuecomment-395113621 Commit: a2fe4b0c76fa9cfff9e974b76e4d5ea34679a881 https://github.com/galaxyproject/galaxy/commit/a2fe4b0c76fa9cfff9e974b76e4d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M run.sh Log Message: ----------- Merge pull request #6295 from nsoranzo/release_18.01_followup_on_6262 [18.01] Fix `GALAXY_RUN_ALL=1 ./run.sh --daemon` Compare: https://github.com/galaxyproject/galaxy/compare/a0004db7203e...a2fe4b0c76fa **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.

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[galaxyproject/usegalaxy-playbook] 502a0b: Set $XDG_DATA_HOME for fontconfig fonts, unset $FO...
by GitHub 06 Jun '18

06 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 502a0b338632c8ef8269497ca3c01dbcb54cba88 https://github.com/galaxyproject/usegalaxy-playbook/commit/502a0b338632c8ef… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Set $XDG_DATA_HOME for fontconfig fonts, unset $FONTCONFIG_FILE so that fonts.conf in conda envs will be used **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.

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[galaxyproject/usegalaxy-playbook] e118cc: Main mutable configs for tool installs
by GitHub 06 Jun '18

06 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e118cc1a2487b918444819af42e015f19af75126 https://github.com/galaxyproject/usegalaxy-playbook/commit/e118cc1a2487b918… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 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: ----------- Main mutable configs for tool installs **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.

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[galaxyproject/usegalaxy-playbook] 171251: Test mutable configs for new tool installs
by GitHub 06 Jun '18

06 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1712510e0e33aae6da05a8f802f9d7b001232254 https://github.com/galaxyproject/usegalaxy-playbook/commit/1712510e0e33aae6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Test mutable configs for new tool installs **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.

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[galaxyproject/galaxy] 1ab71f: Only update options if provided in parameter defin...
by GitHub 06 Jun '18

06 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1ab71ff1901d9b3c231947171f4611f6e3dcbf56 https://github.com/galaxyproject/galaxy/commit/1ab71ff1901d9b3c231947171f46… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-options.js Log Message: ----------- Only update options if provided in parameter definition Commit: afa62a25e1340f6ed9340a8b30e7ef53a9364262 https://github.com/galaxyproject/galaxy/commit/afa62a25e1340f6ed9340a8b30e7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-options.js Log Message: ----------- Merge pull request #6289 from guerler/fix_update_handler Only update options if provided in parameter definition Compare: https://github.com/galaxyproject/galaxy/compare/d95dcecbea34...afa62a25e134 **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.

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[galaxyproject/galaxy] b62099: change to a more defensive approach, clarify varna...
by GitHub 06 Jun '18

06 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b62099f4188f5dcdfe9fc955cdd3059a22b76d38 https://github.com/galaxyproject/galaxy/commit/b62099f4188f5dcdfe9fc955cdd3… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- change to a more defensive approach, clarify varnames Commit: e767438afc305b1c426c7c9152a58bd54b7c1f8e https://github.com/galaxyproject/galaxy/commit/e767438afc305b1c426c7c9152a5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- add spaces before inline comment Commit: acb4cdf5843abbfb110b6cc00e6cb1e1acdfac95 https://github.com/galaxyproject/galaxy/commit/acb4cdf5843abbfb110b6cc00e6c… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- Merge pull request #6285 from martenson/grt-defensive [18.05] telescope export: change to a more defensive approach Commit: d95dcecbea3499a55c531f40045661b4e3fe1db4 https://github.com/galaxyproject/galaxy/commit/d95dcecbea3499a55c531f400456… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/d330a79c8d7b...d95dcecbea34 **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.

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[galaxyproject/galaxy] b62099: change to a more defensive approach, clarify varna...
by GitHub 06 Jun '18

06 Jun '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: b62099f4188f5dcdfe9fc955cdd3059a22b76d38 https://github.com/galaxyproject/galaxy/commit/b62099f4188f5dcdfe9fc955cdd3… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- change to a more defensive approach, clarify varnames Commit: e767438afc305b1c426c7c9152a58bd54b7c1f8e https://github.com/galaxyproject/galaxy/commit/e767438afc305b1c426c7c9152a5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- add spaces before inline comment Commit: acb4cdf5843abbfb110b6cc00e6cb1e1acdfac95 https://github.com/galaxyproject/galaxy/commit/acb4cdf5843abbfb110b6cc00e6c… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- Merge pull request #6285 from martenson/grt-defensive [18.05] telescope export: change to a more defensive approach Compare: https://github.com/galaxyproject/galaxy/compare/2b8beb69c4ff...acb4cdf5843a **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.

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[galaxyproject/galaxy] 0ea810: Use separate `pid_log_paster_args` variable
by GitHub 06 Jun '18

06 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0ea8107191ea1a3bc8b4b57623c981c06f38092e https://github.com/galaxyproject/galaxy/commit/0ea8107191ea1a3bc8b4b57623c9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-02 (Sat, 02 Jun 2018) Changed paths: M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh Log Message: ----------- Use separate `pid_log_paster_args` variable to store --pid-file and --log-file options of `./scripts/paster.py` . https://github.com/galaxyproject/galaxy/pull/6239 fixed 3 bugs: - `GALAXY_RUN_ALL=1 ./run.sh` was reusing the same pid and log files for all Galaxy processes; - `./run.sh restart` was always using `paster.pid` and `paster.log` instead of the configured files - `./run.sh status` was always using `paster.pid` but also introduced a regression, i.e. the plain `./run.sh` started writing to the log file instead of the standard output (console). This fixes the regression by using a separate variable for these options instead of conflating them in `paster_args` or `server_args`. Commit: 87719b9f8edaa983ea70e48532367547d6b2ffdb https://github.com/galaxyproject/galaxy/commit/87719b9f8edaa983ea70e4853236… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-02 (Sat, 02 Jun 2018) Changed paths: M run.sh Log Message: ----------- Check for empty pid file when using --wait Fix this error message: ``` Executing: python ./scripts/paster.py serve config/galaxy.ini --daemon --server-name="main" --pid-file="main.pid" --log-file="main.log" Entering daemon mode ../run.sh: 96: [: Illegal number: ..... ``` Commit: c9daa60e91392c7e7e55fde4af38d0a067fc4fb8 https://github.com/galaxyproject/galaxy/commit/c9daa60e91392c7e7e55fde4af38… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-02 (Sat, 02 Jun 2018) Changed paths: M lib/galaxy/dependencies/__init__.py M scripts/common_startup.sh Log Message: ----------- Look for config file inside galaxy.dependencies.optional() Also don't fail if no config file is found, just print a message on stderr. This allows the removal of the code to set `GALAXY_CONFIG_FILE` from `scripts/common_startup.sh` . Commit: aaff4741422ba4442021a47773c7b1824b98a4e6 https://github.com/galaxyproject/galaxy/commit/aaff4741422ba4442021a47773c7… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-02 (Sat, 02 Jun 2018) Changed paths: M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh R scripts/common_startup_variables.sh M scripts/maintenance.sh Log Message: ----------- Use consistent preference order for config files 1) galaxy.yml 2) galaxy.ini 3) universe_wsgi.ini Also: - properly quote variables which may contain spaces - no need to pass the config file to `./scripts/manage_tool_dependencies.py` - simplify `scripts/maintenance.sh` by moving the `cd` up and reusing functions from `scripts/common_startup_functions.sh` Commit: a0004db7203edd6c0a22fc35658fb1f018665a83 https://github.com/galaxyproject/galaxy/commit/a0004db7203edd6c0a22fc35658f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M lib/galaxy/dependencies/__init__.py M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup.sh M scripts/common_startup_functions.sh R scripts/common_startup_variables.sh M scripts/maintenance.sh Log Message: ----------- Merge pull request #6262 from nsoranzo/release_18.01_fix_run_scripts [18.01] Various fixes for the run scripts Commit: 2b8beb69c4ff5ed393026fa8864940e9629369c5 https://github.com/galaxyproject/galaxy/commit/2b8beb69c4ff5ed393026fa88649… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M lib/galaxy/dependencies/__init__.py M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup.sh M scripts/common_startup_functions.sh R scripts/common_startup_variables.sh M scripts/maintenance.sh Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: d330a79c8d7b47db7d0f8ab49e5cdfbb42260611 https://github.com/galaxyproject/galaxy/commit/d330a79c8d7b47db7d0f8ab49e5c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M lib/galaxy/dependencies/__init__.py M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup.sh M scripts/common_startup_functions.sh R scripts/common_startup_variables.sh M scripts/maintenance.sh Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/9c58c51ea68e...d330a79c8d7b **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.

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galaxy-commits June 2018