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 ++++++++++++++++++++++ topics/running_pudb_from_external_environment.gmi | 30 ---------------------- 2 files changed, 30 insertions(+), 30 deletions(-) create mode 100644 topics/pudb/running_pudb_from_external_environment.gmi delete mode 100644 topics/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 python3 -m pudb script.py + +## Tags + +* type: documentation +* keywords: pudb +* status: obsolete diff --git a/topics/running_pudb_from_external_environment.gmi b/topics/running_pudb_from_external_environment.gmi deleted file mode 100644 index a533e22..0000000 --- a/topics/running_pudb_from_external_environment.gmi +++ /dev/null @@ -1,30 +0,0 @@ -# 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 -- cgit v1.2.3