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Diffstat (limited to 'topics/running_pudb_from_external_environment.gmi')
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diff --git a/topics/running_pudb_from_external_environment.gmi b/topics/running_pudb_from_external_environment.gmi new file mode 100644 index 0000000..be9bf14 --- /dev/null +++ b/topics/running_pudb_from_external_environment.gmi @@ -0,0 +1,22 @@ +# Running pudb From an External Environment + +Currently (22nd December 2021), it is a tad difficult to get pudb running under the various guix environments without having to update a lot of stuff. This documents a workaround that seems to work for me (@fredm). + +## GeneNetwork3 + +1) Install pudb in a virtual environment: + +* $ python -m venv pudb_env + +2) Activate the environment and install pudb: + +* $ source pudb_env/bin/activate +* $ pip install pudb + +3) Run the GN3 container, exposing the new virtual environment with something like: + +* env GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment -C --network --expose="$HOME/genotype_files/"="${HOME}/genotype_files" --expose="${HOME}/genenetwork/pudb_env/"="${HOME}/pudb_env" --load=guix.scm + +4) Inside the container, run the debugger with something like: + +* env PYTHONPATH="${PYTHONPATH}:${HOME}/pudb_env/lib/python3.8/site-packages" ... python3 -m pudb script.py |