diff --git a/README.md b/README.md index 21ff9656087988613965b6639f1040f09cda9aee..6a8ffff9b309123543da204b6cff62152295155b 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,10 @@ Counter RnAseq Window [](http://bneron.pages.pasteur.fr/craw/) [](https://opensource.org/licenses/GPL-3.0) [](https://pypi.python.org/pypi/craw) +[](https://singularity-hub.org/collections/2703) +[](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 ==========