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authorPjotr Prins2023-01-25 06:37:37 -0600
committerPjotr Prins2023-01-25 06:37:49 -0600
commit9f8de83700a5aa1c19ec8d11b0978e8852b442db (patch)
tree4f7737bc95ffc871a7cf8d54f24f2137d764a4af
parent9b85f424a37a817641a182da665359b8b2879475 (diff)
downloadgenenetwork3-9f8de83700a5aa1c19ec8d11b0978e8852b442db.tar.gz
Some comments
-rw-r--r--README.md18
-rw-r--r--gn3/computations/rqtl.py2
2 files changed, 15 insertions, 5 deletions
diff --git a/README.md b/README.md
index 6e33e8c..f328e87 100644
--- a/README.md
+++ b/README.md
@@ -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