for lightning-fast Python dependency updates.
To update all dependencies (as done by the GitHub action):
$ make update-dependencies
To update only one package:
./lib/galaxy/dependencies/update.sh -p <PKG>
Pip 20.3 added support for PEP 600, i.e. manylinux wheels using platform
tags of the form "manylinux_${GLIBCMAJOR}_${GLIBCMINOR}_${ARCH}". Fix
installation of dependencies like pysam 0.20.0 wheels, which otherwise need
to be built from source and can fail as reported by @assuntad23 in
https://gist.github.com/assuntad23/3022db63a6878f044a209961dd40e592
Also:
- Install `wheel` to fix warning like `Using legacy setup.py install for
beaker, since package 'wheel' is not installed.`
- Drop unnecessary `defaults` channel from conda commands.
- Fix "SC2223: This default assignment may cause DoS due to globbing. Quote
it." errors reported by `shellcheck -x` .
- Allow specifying Python to use to create virtualenv using GALAXY_PYTHON
environment variable.
- Integrate Python support docs from https://galaxyproject.org/admin/python/
- Update virtualenv installation to use v16.7.9
Having a different Python version on the Galaxy server vs the compute nodes can cause an error including the message `ImportError: cannot import name _remove_dead_weakref`. This adds text to describe the error and its resolution
Nicola Soranzo