blob: 7ce8ddcb7aae3f6de12e8dced3cb823050ad062d (
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
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
|
#+TITLE: Running the common workflow language on GNU Guix
* Introduction
The common workflow language (CWL) can run workflows defined in a YAML
definition. Some key concepts are that CWL workflows can be analysed
and reasoned on (unlike shell scripts) and CWL workflows are a
separation of concerns: (1) tools/scripts, (2) data and (3) the
workflow, i.e. how it connects up.
CWL is also agnostic about finding underlying tooling. Docker links
are often provided as hints, but with ~--no-container~ a tool just
gets invoked. This is great in the context of GNU Guix environments!
* Install CWL using GNU Guix
You may need to install GNU Guix and see the README on
http://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics
Recent versions of GNU Guix contain =cwl-runner=:
: guix pull
: ~/.config/guix/current/bin/guix package -A cwl
: cwltool 3.0.20201121085451 out gnu/packages/bioinformatics.scm:2627:2
Install with
: guix package -i cwltool
or in a special profile (I tend to do that)
: guix package -i cwltool -p ~/opt/CWL
Set the PATH and you should be able to run cwltool
: . ~/opt/CWL/etc/profile
: cwltool
* Set up a more advanced workflow
Let's run the workflow that was described in [[https://hpc.guix.info/blog/2019/01/creating-a-reproducible-workflow-with-cwl/][creating a reproducible
workflow with GNU Guix]]:
: git clone https://github.com/pjotrp/CWL-workflows
Build the contained trimmomatic (if you are unlucky this may take a
while)
: cd CWL-workflows
: env GUIX_PACKAGE_PATH=. guix build trimmomatic-jar
Now let's rerun the workflow as set up in above [[https://hpc.guix.info/blog/2019/01/creating-a-reproducible-workflow-with-cwl/][BLOG]] (I created a
local version to skip IPFS). Make sure your PATH points to all the
tools and
: cwltool --no-container Workflows/test-workflow.cwl Jobs/local-small.ERR034597.test-workflow.yml
: <lots of output>
: INFO Final process status is success
Note that I hard coded two paths which you need to point to your Guix
profile first:
: Tools/trimmomaticPE.cwl: valueFrom: /gnu/store/v2jys382g6j5b7lsxzh8v4vfhd414nhz-profile/lib/share/jar/trimmomatic-0.38.jar
: Tools/trimmomaticPE.cwl: valueFrom: 'ILLUMINACLIP:/gnu/store/v2jys382g6j5b7lsxzh8v4vfhd414nhz-profile/lib/share/jar/adapters/TruSeq2-PE.fa:2:40:15'
This is not typical and I should find a proper way to do this ;)
|
