diff options
| author | Pjotr Prins | 2023-01-25 06:37:37 -0600 |
|---|---|---|
| committer | Pjotr Prins | 2023-01-25 06:37:49 -0600 |
| commit | 9f8de83700a5aa1c19ec8d11b0978e8852b442db (patch) | |
| tree | 4f7737bc95ffc871a7cf8d54f24f2137d764a4af | |
| parent | 9b85f424a37a817641a182da665359b8b2879475 (diff) | |
| download | genenetwork3-9f8de83700a5aa1c19ec8d11b0978e8852b442db.tar.gz | |
Some comments
| -rw-r--r-- | README.md | 18 | ||||
| -rw-r--r-- | gn3/computations/rqtl.py | 2 |
2 files changed, 15 insertions, 5 deletions
@@ -21,8 +21,6 @@ A continuously deployed instance of genenetwork3 is available at redeployed on every commit provided that the [continuous integration tests](https://ci.genenetwork.org/jobs/genenetwork3) pass. - - ## Installation #### GNU Guix packages @@ -35,6 +33,8 @@ There are at least three ways to start GeneNetwork3 with GNU Guix: 2. Create a container with `guix shell -C` 3. Use a profile and shell settings with `source ~/opt/genenetwork3/etc/profile` +At this point we use all three for different purposes. + #### Create an environment: Simply load up the environment (for development purposes): @@ -43,7 +43,7 @@ Simply load up the environment (for development purposes): guix shell -Df guix.scm ``` -Also, make sure you have the [guix-bioinformatics](https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics) channel set up. +Also, make sure you have the guix-bioinformatics channel set up correctly and this should work ```bash guix shell --expose=$HOME/genotype_files/ -Df guix.scm @@ -51,7 +51,15 @@ python3 import redis ``` -#### Run a Guix container +Check if guix and guix-bioinformatics channel are up-to-date with + +``` +guix describe +``` + +#### Run a Guix container with network + +Containers provide full isolation from the underlying distribution. Very useful for figuring out any dependency issues: ``` guix shell -C --network --expose=$HOME/genotype_files/ -Df guix.scm @@ -59,6 +67,8 @@ guix shell -C --network --expose=$HOME/genotype_files/ -Df guix.scm #### Using a Guix profile (or rolling back) +A guix profile is different from a Guix shell - it has less isolation from the underlying distribution. + Create a new profile with ``` diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py index 2f9c4a2..f082482 100644 --- a/gn3/computations/rqtl.py +++ b/gn3/computations/rqtl.py @@ -1,4 +1,4 @@ -"""Procedures related rqtl computations""" +"""Procedures related to R/qtl computations""" import os from bisect import bisect from typing import Dict, List, Tuple, Union |