Guix environment pulls all dependencies in locally so there is no real need to use virtualenv, for example. Let’s try a new enviroment as a shell:
user@penguin2:~/cwl$ ~/.config/guix/current/bin/guix environment guix --ad-hoc cwltool python python-magic
Now when you do
user@penguin2:~/cwl$ which python /usr/bin/python user@penguin2:~/cwl$ which python3 /gnu/store/q1wwvb19dg33lh51y03na1bflwpd31aj-profile/bin/python3 user@penguin2:~/cwl$ which cwltool /home/user/.guix-profile/bin/cwltool
2 out of 3 are wrong! You can see some confusion. This is because we are mixing shells. This can be useful, but you have to be aware! Try Python
user@penguin2:~/cwl$ python3 Python 3.8.2 (default, Jan 1 1970, 00:00:01) >>> import magic
and that works fine!
When things don’t work it is because of the mixing of environments. To create a pure environment try
user@penguin2:~/cwl$ ~/.config/guix/current/bin/guix environment guix --pure --ad-hoc cwltool python python-magic user@penguin2:~/cwl$ which python bash: which: command not found set |grep guix
and you can see that your environment is no longer confused, but limited to the guix paths (to use which we’ll need to include binutils)
user@penguin2:~/cwl$ set|grep guix
CMAKE_PREFIX_PATH=/home/user/.guix-profile/
CPLUS_INCLUDE_PATH=/home/user/.guix-profile/include/c++:/home/user/.guix-profile/include:/gnu/store/q1wwvb19dg33lh51y03na1bflwpd31aj-profile/include/c++:/gnu/store/q1wwvb19dg33lh51y03na1bflwpd31aj-profile/include
C_INCLUDE_PATH=/home/user/.guix-profile/include:/gnu/store/q1wwvb19dg33lh51y03na1bflwpd31aj-profile/include
GUIX_LOCPATH=/home/user/.guix-profile/lib/locale:/gnu/store/q1wwvb19dg33lh51y03na1bflwpd31aj-profile/lib/locale
GUIX_PROFILE=/home/user/.guix-profile
LIBRARY_PATH=/home/user/.guix-profile/lib:/gnu/store/q1wwvb19dg33lh51y03na1bflwpd31aj-profile/lib
NODE_PATH=/home/user/.guix-profile/lib/node_modules:/gnu/store/q1wwvb19dg33lh51y03na1bflwpd31aj-profile/lib/node_modules
PATH=/home/user/.guix-profile/bin:/home/user/.guix-profile/sbin:/home/user/.config/guix/current/bin:/gnu/store/q1wwvb19dg33lh51y03na1bflwpd31aj-profile/bin:/gnu/store/q1wwvb19dg33lh51y03na1bflwpd31aj-profile/sbinand
euser@penguin2:~/cwl$ echo $PATH
/home/user/.guix-profile/bin:/home/user/.guix-profile/sbin:/home/user/.config/guix/current/bin:/gnu/store/q1wwvb19dg33lh51y03na1bflwpd31aj-profile/bin:/gnu/store/q1wwvb19dg33lh51y03na1bflwpd31aj-profile/sbin
user@penguin2:~/cwl$ echo $GUIX_ENVIRONMENT
/gnu/store/q1wwvb19dg33lh51y03na1bflwpd31aj-profileactually the environment is still a bit confused because it keeps the
orginal guix-profile in addition to the new shiny guix environment! This
may be because of your .bashrc or .profile settings.
When you start environment as a container it becomes really clean (that is why I do that a lot), i.e., there is no confusion possible:
user@penguin2:~/cwl$ ~/.config/guix/current/bin/guix environment guix -C --ad-hoc cwltool python python-magic
user@penguin2 ~/cwl [env]$ python3
Python 3.8.2 (default, Jan 1 1970, 00:00:01)
[GCC 7.5.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import magicJust works (tm). Try using set in a container and see.
To have network access in a container use --network switch.
Containers can only access directories that are in the container. To
access paths that are outside the directory you’ll have to mount them
explicitely. This is also a safety feature when you want to run a
webservice in a container, for example. Use the guix environment
--expose and --share switches.
cwltool –no-container –preserve-environment GUIX_ENVIRONMENT \ yamlfa2ttl.cwl –path_fasta ~/bh20-seq-resource/example/sequence.fasta
print(os.environ)
‘PYTHONPATH’: ‘/gnu/store/9k64w8czk2x3gv6j4f5pr7d5lv2f3zfs-profile/lib/python3.8/site-packages’
environ({‘GUIX_ENVIRONMENT’: ‘/gnu/store/9k64w8czk2x3gv6j4f5pr7d5lv2f3zfs-profile’, ‘PATH’: ‘/gnu/store/9k64w8czk2x3gv6j4f5pr7d5lv2f3zfs-profile/bin:/gnu/store/9k64w8czk2x3gv6j4f5pr7d5lv2f3zfs-profile/sbin’, ‘HOME’: ‘/tmp/wv1g6f1c’, ‘TMPDIR’: ‘/tmp/k0mqtin5’}