Bump to 22.05 #600
Bump to 22.05 #600
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* made GALAXY_ROOT a symbolic link to the full extracted tarball (e.g. /galaxyproject-galaxy-abcde12345) so that the exact commit hash that generated the tarball is preserved * added C++ build toolchain to the ansible provision step because some binaries that Galaxy depends on are not currently available
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Hey @chambm, is there anything I can do to help with this effort? I'm not super familiar with all of the really specific ways to provision Galaxy, but maybe there's boring things I could help with? |
| @@ -222,7 +223,7 @@ RUN mkdir -p /shed_tools $EXPORT_DIR/ftp/ \ | |||
| && python /usr/local/bin/setup_postgresql.py --dbuser galaxy --dbpassword galaxy --db-name galaxy --dbpath $PG_DATA_DIR_DEFAULT --dbversion $PG_VERSION \ | |||
| && service postgresql start \ | |||
| && service postgresql stop \ | |||
| && apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && rm -rf ~/.cache/ \ | |||
| && apt-get autoremove -y make g++ gcc && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && rm -rf ~/.cache/ \ | |||
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It looks like pysam is expecting make (and likely gcc) to exist still. Although I would have expected the Galaxy environment to have a precompiled build of pysam already.
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Any help is welcome, but its a larger project. We need to migrate to the new FastAPI Framework and need to get rid of uwsgi .... which is replacing a lot of the startup magic here. |
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Is the FastAPI framework a new way of managing the Galaxy server (vs using ephemeris tools), or is it something else? |
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FastAPI is a API framework (https://fastapi.tiangolo.com/) Galaxy is using this framework now for its backend. With this framework we can now use gunicorn and friends to run Galaxy backend processes instead of the previously used uwsgi. |
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