blob: 7b700b232d919afdebe25d07a1da626bb422059d (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
|
# guix-bioinformatics
Bioinformatics packages for GNU Guix that are used in
http://genenetwork.org/. See
[Guix Notes](https://github.com/pjotrp/guix-notes/blob/master/HACKING.org)
for installing and hacking GNU Guix.
Set the GUIX_PACKAGE_PATH to point to the root of this directory
before running Guix. E.g.
git clone https://github.com/genenetwork/guix-bioinformatics.git
export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/
guix package -A cwl
or using a checked out Guix repo
env GUIX_PACKAGE_PATH=$genenetwork/guix-bioinformatics/ ./pre-inst-env guix package -A cwl
Some of these package definitions should make it upstream into the GNU
Guix repository when tested and stable.
## Install Common Workflow Language (CWL)
Install the common workflow language tool cwltool with
git clone https://github.com/genenetwork/guix-bioinformatics.git
export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/
guix package -i python2-cwltool
cwtool --version
1.0.20150916041152
## Install R/qtl
git clone https://github.com/genenetwork/guix-bioinformatics.git
export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/
guix package -i r-qtl r
R
library(qtl)
## LICENSE
These package descriptions are distributed by the same license as GNU
Guix, i.e. GPL3+
|
