Skip to content
Snippets Groups Projects
Verified Commit fabb0331 authored by Bertrand  NÉRON's avatar Bertrand NÉRON
Browse files

🐛 fix singularity url

parent 46fd82f3
No related branches found
No related tags found
No related merge requests found
Pipeline #10988 passed
......@@ -6,7 +6,10 @@ Counter RnAseq Window
[![docs](https://img.shields.io/badge/doc-master-blue.svg)](http://bneron.pages.pasteur.fr/craw/)
[![license](https://img.shields.io/badge/license-GPLv3-blue.svg)](https://opensource.org/licenses/GPL-3.0)
[![pypi](https://img.shields.io/badge/pypy-releases-blue.svg)](https://pypi.python.org/pypi/craw)
[![https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg](https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg)](https://singularity-hub.org/collections/2703)
[![hosted](https://img.shields.io/badge/hosted-docker--hub-orange.svg)](https://cloud.docker.com/u/c3bi/repository/docker/c3bi/craw/general)
**C**ounter **R**N**A** seq **W**indow (CRAW) compute and visualize the coverage of RNA seq experiment.
There are 3 ways to use craw:
* by install the standalone python scripts
......@@ -82,29 +85,41 @@ Using Docker Image
==================
Docker images are available. The two scripts are accessible through the sub-command `coverage` or `htmp`.
For instance to use the latest version of craw_htmp::
For instance to use the latest version of craw_htmp
docker pull c3bi/craw
docker run -v$PWD:/root -it c3bi/craw coverage --bam foo.bam --annot foo.annot --ref-col 'Position' --before 3 --after 5 --out foo.cov
docker run -v$PWD:/root -it c3bi/craw htmp --size raw --out foo.png foo.cov
.. note::
In docker the interactive htmp output is not available.
So you must specify the --out option
>**note:**
>
> In docker the interactive htmp output is not available.
> So you must specify the --out option
Using Singularity Image
=======================
Singularity images are available. The two scripts are accessible through the sub-command `coverage` or `htmp`.
For instance to use the latest version of craw_htmp::
For instance to use the latest version of craw_htmp
Pull the image locally
singularity pull --name craw shub://C3BI-pasteur-fr/craw
Then run it
singularity pull --name craw shub://c3bi/craw
./craw coverage --bam foo.bam --annot foo.annot --ref-col 'Position' --before 3 --after 5 --out foo.cov
./craw htmp --size raw --out foo.png foo.cov
.. note::
instead of Docker images, in Singularity images the interactive output is available.
or
singularity run craw htmp --size raw --out foo.png foo.cov
>**note:**
> Instead of Docker images, in Singularity images the interactive output is available.
Quickstart
==========
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment