Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0ea8107191ea1a3bc8b4b57623c981c06f38092e https://github.com/galaxyproject/galaxy/commit/0ea8107191ea1a3bc8b4b57623c98... Author: Nicola Soranzo <nicola.soranzo@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/87719b9f8edaa983ea70e48532367... Author: Nicola Soranzo <nicola.soranzo@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/c9daa60e91392c7e7e55fde4af38d... Author: Nicola Soranzo <nicola.soranzo@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/aaff4741422ba4442021a47773c7b... Author: Nicola Soranzo <nicola.soranzo@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/a0004db7203edd6c0a22fc35658fb... Author: Nate Coraor <nate@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/2b8beb69c4ff5ed393026fa886494... Author: Nicola Soranzo <nicola.soranzo@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/d330a79c8d7b47db7d0f8ab49e5cd... Author: Nicola Soranzo <nicola.soranzo@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.