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

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

06 Jun '18

Branch: refs/heads/release_18.05 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 Compare: https://github.com/galaxyproject/galaxy/compare/a40abcd6e42e...2b8beb69c4ff **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/release_18.01 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 Compare: https://github.com/galaxyproject/galaxy/compare/b137d5cf3461...a0004db7203e **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] 2fb756: Update Test
by GitHub 06 Jun '18

06 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2fb756a1fb63f02200a2803b94f5f79d740af9d6 https://github.com/galaxyproject/usegalaxy-playbook/commit/2fb756a1fb63f022… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- 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.

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[galaxyproject/galaxy] 994d78: Add the newick extension for the Newick datatype, ...
by GitHub 06 Jun '18

06 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 994d78fde08b7463fc41ec376959871a63f799ea https://github.com/galaxyproject/galaxy/commit/994d78fde08b7463fc41ec376959… Author: greg <ghv2(a)psu.edu> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add the newick extension for the Newick datatype, setting the nhx extension as a subclass Commit: 64ce15f6cfd49ee0667e96402cbfaf8e9e358e96 https://github.com/galaxyproject/galaxy/commit/64ce15f6cfd49ee0667e96402cbf… Author: greg <ghv2(a)psu.edu> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/visualization/data_providers/phyloviz/__init__.py Log Message: ----------- Change Newick ext to be newick instead of nhx Commit: 8cecfe30422d7ef8539b34b1237aa9e2acf498d3 https://github.com/galaxyproject/galaxy/commit/8cecfe30422d7ef8539b34b1237a… Author: greg <ghv2(a)psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M config/plugins/visualizations/phylocanvas/config/phylocanvas.xml Log Message: ----------- Add the newick ext to the phylocanvas plugin Commit: 9c58c51ea68eb38232610cac5cf8a3d6634269f2 https://github.com/galaxyproject/galaxy/commit/9c58c51ea68eb38232610cac5cf8… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample M config/plugins/visualizations/phylocanvas/config/phylocanvas.xml M lib/galaxy/datatypes/data.py M lib/galaxy/visualization/data_providers/phyloviz/__init__.py Log Message: ----------- Merge pull request #6206 from gregvonkuster/newick Add the newick extension for the Newick datatype, Compare: https://github.com/galaxyproject/galaxy/compare/1d52f04807a2...9c58c51ea68e **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] 4f2a58: Update Main
by GitHub 05 Jun '18

05 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4f2a58b4312ce839d24805a9384e023651a7fc47 https://github.com/galaxyproject/usegalaxy-playbook/commit/4f2a58b4312ce839… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml M env/main/group_vars/cvmfsstratum0servers.yml Log Message: ----------- Update Main Commit: 25fb3498847ed52e40ac64a9833aa3eea75e2359 https://github.com/galaxyproject/usegalaxy-playbook/commit/25fb3498847ed52e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M env/main/templates/nginx/usegalaxy.j2 M env/test/templates/nginx/galaxy_test.j2 Log Message: ----------- Set X-Frame-Options and X-Content-Type-Options on X-Accel-Redirect requests. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/3d9593709125...… **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] 3ec578: Fix tool search overlay link
by GitHub 05 Jun '18

05 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3ec5787f59eca7843dbb9e48bb6bcf8232fc3115 https://github.com/galaxyproject/galaxy/commit/3ec5787f59eca7843dbb9e48bb6b… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M config/plugins/webhooks/demo/search/script.js Log Message: ----------- Fix tool search overlay link Commit: 1d52f04807a2f887a5d4d26939ebffb5076ba989 https://github.com/galaxyproject/galaxy/commit/1d52f04807a2f887a5d4d26939eb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M config/plugins/webhooks/demo/search/script.js Log Message: ----------- Merge pull request #6279 from scrathat/tool.search.overlay.selector.fix Fix tool search overlay selector Compare: https://github.com/galaxyproject/galaxy/compare/7a7560ad731e...1d52f04807a2 **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] c0c8aa: Fix history shared with me 'view' link
by GitHub 05 Jun '18

05 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c0c8aad528d9164fb7aaf88c3a202c66044c0134 https://github.com/galaxyproject/galaxy/commit/c0c8aad528d9164fb7aaf88c3a20… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Fix history shared with me 'view' link Commit: 692465d4ec9a4493ae1326cbc8b118cf49f5cbff https://github.com/galaxyproject/galaxy/commit/692465d4ec9a4493ae1326cbc8b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Standard quotes. Commit: 8a0427a6e8eeffde3022ed1187b114265b73447f https://github.com/galaxyproject/galaxy/commit/8a0427a6e8eeffde3022ed1187b1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #6257 from dannon/sharing_link_fix [18.05] Fix history shared with me 'view' link Commit: 6dee708ae8cdad5ccc9f7ae095dae736b44a6091 https://github.com/galaxyproject/galaxy/commit/6dee708ae8cdad5ccc9f7ae095da… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- export another tsv file named datasets.tsv Commit: 11575132dc4fba88751a5e2228956dfc1b75bbe2 https://github.com/galaxyproject/galaxy/commit/11575132dc4fba88751a5e222895… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- exports a dataset tsv Commit: aa062f8546379bd35769314fb3470fde02445157 https://github.com/galaxyproject/galaxy/commit/aa062f8546379bd35769314fb347… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- fixed the issues with the last pull Commit: 0c852257bb9f91983a4afe063bf8d64692802e87 https://github.com/galaxyproject/galaxy/commit/0c852257bb9f91983a4afe063bf8… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- delete comment thats no longer necessary Commit: 5b7055fc6f19e2a0489a92bb8f4762a1b6a1ece1 https://github.com/galaxyproject/galaxy/commit/5b7055fc6f19e2a0489a92bb8f47… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- respect blacklisted tools Commit: 4630994fd0479e66357315fc7e2fa2c20367fb84 https://github.com/galaxyproject/galaxy/commit/4630994fd0479e66357315fc7e2f… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- get output datasets as well Commit: ba45c15fffcb9e54dda35759410675d78346394f https://github.com/galaxyproject/galaxy/commit/ba45c15fffcb9e54dda357594106… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- tried to fix some of stylization fails Commit: 948d0767eb9b2e2a6207ead2456a6580e34eaf84 https://github.com/galaxyproject/galaxy/commit/948d0767eb9b2e2a6207ead2456a… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- more style fixes Commit: 191a134bbc511c508d9ee0636030da2e2e68ea44 https://github.com/galaxyproject/galaxy/commit/191a134bbc511c508d9ee0636030… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- got rid of things that are no longer necessary Commit: 6db9fd3d51b91804e24ed393468973ecfb659eef https://github.com/galaxyproject/galaxy/commit/6db9fd3d51b91804e24ed3934689… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- style fix Commit: dd4de3f3b28f1ddd92aaa87c4f2c00657ecbc457 https://github.com/galaxyproject/galaxy/commit/dd4de3f3b28f1ddd92aaa87c4f2c… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- catch dataset_id=None Commit: c37e3844543b1bd425cfd370830bdb235674706f https://github.com/galaxyproject/galaxy/commit/c37e3844543b1bd425cfd370830b… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- style fix Commit: a40abcd6e42e62a7e46e0afa71c04c152ee8db4a https://github.com/galaxyproject/galaxy/commit/a40abcd6e42e62a7e46e0afa71c0… 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: ----------- Merge pull request #6263 from atyryshkina/modify-grt-export [18.05] Fix dataset sizes in GRT export script Commit: 7a7560ad731e7e4ab39e405ef9cf3f2185844850 https://github.com/galaxyproject/galaxy/commit/7a7560ad731e7e4ab39e405ef9cf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py M scripts/grt/export.py Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/5ddb6fc17988...7a7560ad731e **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] 6dee70: export another tsv file named datasets.tsv
by GitHub 05 Jun '18

05 Jun '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 6dee708ae8cdad5ccc9f7ae095dae736b44a6091 https://github.com/galaxyproject/galaxy/commit/6dee708ae8cdad5ccc9f7ae095da… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- export another tsv file named datasets.tsv Commit: 11575132dc4fba88751a5e2228956dfc1b75bbe2 https://github.com/galaxyproject/galaxy/commit/11575132dc4fba88751a5e222895… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- exports a dataset tsv Commit: aa062f8546379bd35769314fb3470fde02445157 https://github.com/galaxyproject/galaxy/commit/aa062f8546379bd35769314fb347… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- fixed the issues with the last pull Commit: 0c852257bb9f91983a4afe063bf8d64692802e87 https://github.com/galaxyproject/galaxy/commit/0c852257bb9f91983a4afe063bf8… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- delete comment thats no longer necessary Commit: 5b7055fc6f19e2a0489a92bb8f4762a1b6a1ece1 https://github.com/galaxyproject/galaxy/commit/5b7055fc6f19e2a0489a92bb8f47… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- respect blacklisted tools Commit: 4630994fd0479e66357315fc7e2fa2c20367fb84 https://github.com/galaxyproject/galaxy/commit/4630994fd0479e66357315fc7e2f… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- get output datasets as well Commit: ba45c15fffcb9e54dda35759410675d78346394f https://github.com/galaxyproject/galaxy/commit/ba45c15fffcb9e54dda357594106… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- tried to fix some of stylization fails Commit: 948d0767eb9b2e2a6207ead2456a6580e34eaf84 https://github.com/galaxyproject/galaxy/commit/948d0767eb9b2e2a6207ead2456a… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- more style fixes Commit: 191a134bbc511c508d9ee0636030da2e2e68ea44 https://github.com/galaxyproject/galaxy/commit/191a134bbc511c508d9ee0636030… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- got rid of things that are no longer necessary Commit: 6db9fd3d51b91804e24ed393468973ecfb659eef https://github.com/galaxyproject/galaxy/commit/6db9fd3d51b91804e24ed3934689… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- style fix Commit: dd4de3f3b28f1ddd92aaa87c4f2c00657ecbc457 https://github.com/galaxyproject/galaxy/commit/dd4de3f3b28f1ddd92aaa87c4f2c… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- catch dataset_id=None Commit: c37e3844543b1bd425cfd370830bdb235674706f https://github.com/galaxyproject/galaxy/commit/c37e3844543b1bd425cfd370830b… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- style fix Commit: a40abcd6e42e62a7e46e0afa71c04c152ee8db4a https://github.com/galaxyproject/galaxy/commit/a40abcd6e42e62a7e46e0afa71c0… 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: ----------- Merge pull request #6263 from atyryshkina/modify-grt-export [18.05] Fix dataset sizes in GRT export script Compare: https://github.com/galaxyproject/galaxy/compare/8a0427a6e8ee...a40abcd6e42e **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] 5d1556: Verify existing of runtime environment for textabl...
by GitHub 05 Jun '18

05 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5d155617952e0fd6ef5e269ca83704f2f2688cab https://github.com/galaxyproject/galaxy/commit/5d155617952e0fd6ef5e269ca837… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Verify existing of runtime environment for textable mode Commit: b0705a4819cb3a1cb541554798f007d4360f3d87 https://github.com/galaxyproject/galaxy/commit/b0705a4819cb3a1cb541554798f0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Combine context test into single function Commit: d91cb1563d2ce9cee78ed33c4cd0709e5da35bdb https://github.com/galaxyproject/galaxy/commit/d91cb1563d2ce9cee78ed33c4cd0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Validate parsed workflow building mode parameter Commit: c4e8f0d21ead864a1800802db44bf01c550257c6 https://github.com/galaxyproject/galaxy/commit/c4e8f0d21ead864a1800802db44b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Make runtime context validator available for use in other inputs e.g. drilldown Commit: 5adac19825263d8c98e8628b7f63f0ca49c76495 https://github.com/galaxyproject/galaxy/commit/5adac19825263d8c98e8628b7f63… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix indention Commit: dfd80d7d71a8c99495e751cdddbc27d31bbfe8d1 https://github.com/galaxyproject/galaxy/commit/dfd80d7d71a8c99495e751cdddbc… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix indentation Commit: 05fe17a590d9bdbf3aff54b3f3db8b5da5f256a2 https://github.com/galaxyproject/galaxy/commit/05fe17a590d9bdbf3aff54b3f3db… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix SelectToolParameter doctests Commit: 5ddb6fc17988c359984115bb6990ae51b9e81118 https://github.com/galaxyproject/galaxy/commit/5ddb6fc17988c359984115bb6990… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #6251 from guerler/check_context Check context for textable mode of select fields Compare: https://github.com/galaxyproject/galaxy/compare/6e0a2213c6bf...5ddb6fc17988 **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] bd0e1f: Remove bundle_to_json() and other unused functions
by GitHub 05 Jun '18

05 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bd0e1f534e33816302fb1e8ed4d44bbbae278c88 https://github.com/galaxyproject/galaxy/commit/bd0e1f534e33816302fb1e8ed4d4… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Remove bundle_to_json() and other unused functions Last usage was removed in commit af4fab16f58c36ea66328725e5bdcfaa3acbacda . Commit: eb67e4a627ea413af87dc341b32932e0b0fea9e0 https://github.com/galaxyproject/galaxy/commit/eb67e4a627ea413af87dc341b329… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Remove unused hg_util.get_config() function Commit: eaec9d248e8557bb8f03808f2e6940749c11314f https://github.com/galaxyproject/galaxy/commit/eaec9d248e8557bb8f03808f2e69… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/util/hg_util.py Log Message: ----------- Use Mercurial CLI instead of API for archive_repository_revision() Commit: c8e483e7b3ff1cf7899ee750eda244fa4e5e9a80 https://github.com/galaxyproject/galaxy/commit/c8e483e7b3ff1cf7899ee750eda2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Remove files only if created If an exception is raised in the `try` block before the files are created, an exception was generated in the `finally` block: ``` File "/home/nicola/software/nsoranzo_galaxy/lib/galaxy/webapps/tool_shed/controllers/repository.py", line 945, in export repositories_archive, error_message = erm.export_repository() File "/home/nicola/software/nsoranzo_galaxy/lib/tool_shed/capsule/capsule_manager.py", line 109, in export_repository if os.path.exists(tmp_export_info): UnboundLocalError: local variable 'tmp_export_info' referenced before assignment ``` Commit: 6e0a2213c6bfb6be656bce9677b09a671d1d4889 https://github.com/galaxyproject/galaxy/commit/6e0a2213c6bfb6be656bce9677b0… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/util/hg_util.py Log Message: ----------- Merge pull request #6273 from nsoranzo/mercurial_api_removal Use Mercurial CLI instead of API for archive_repository_revision() Compare: https://github.com/galaxyproject/galaxy/compare/0ba8090d22c6...6e0a2213c6bf **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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