From 064af73a670617c76775f8f94f74e3d5d611d18e Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 3 Dec 2023 09:39:35 -0600
Subject: move pudb file

---
 .../running_pudb_from_external_environment.gmi     | 30 ++++++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 topics/pudb/running_pudb_from_external_environment.gmi

(limited to 'topics/pudb/running_pudb_from_external_environment.gmi')

diff --git a/topics/pudb/running_pudb_from_external_environment.gmi b/topics/pudb/running_pudb_from_external_environment.gmi
new file mode 100644
index 0000000..a533e22
--- /dev/null
+++ b/topics/pudb/running_pudb_from_external_environment.gmi
@@ -0,0 +1,30 @@
+# Running pudb From an External Environment
+
+This documentation is now obsolete since pudb was added as a package in GNU Guix
+
+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
+
+## Tags
+
+* type: documentation
+* keywords: pudb
+* status: obsolete
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