From 512bc12aaac7189253a62b2be105472a34821263 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 22 Dec 2021 11:48:30 +0300
Subject: Add some notes on running pudb for GN3

---
 topics/running_pudb_from_external_environment.gmi | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 topics/running_pudb_from_external_environment.gmi

(limited to 'topics/running_pudb_from_external_environment.gmi')

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
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