Verified Commit 7ee730b6 authored by Bertrand  NÉRON's avatar Bertrand NÉRON

Merge branch 'branch_1.0' of gitlab.pasteur.fr:bneron/craw into branch_1.0

parents d823fd45 fabb0331
Pipeline #17162 passed with stages
in 3 minutes and 40 seconds
......@@ -4,7 +4,7 @@ MAINTAINER Bertrand Neron <bneron@pasteur.fr>
LABEL maintainer="Bertrand Neron <bneron@pasteur.fr>"
LABEL package.name="craw"
LABEL package.version="1.0"
LABEL package.version="1.0.0"
LABEL package.homepage="https://gitlab.pasteur.fr/bneron/craw"
LABEL package.license="GPLv3"
......@@ -14,7 +14,7 @@ RUN apt-get update -y && \
apt-get install -y --no-install-recommends python3 python3-tk &&\
apt-get install -y python3-pip
RUN pip3 install craw==1.0
RUN pip3 install craw==1.0.0
COPY craw.sh /usr/local/bin/craw
......
......@@ -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
==========
......
......@@ -25,9 +25,8 @@
import sys
import logging
import time
__version__ = '1.dev{}'.format(time.strftime('%Y%m%d'))
__version__ = '1.0.0'
def get_version_message():
......
......@@ -32,8 +32,6 @@ from: ubuntu:bionic
apt-get autoremove -y
apt-get clean -y
%test
/usr/bin/python3 /craw/tests/run_tests.py -vv
%environment
# to be reproducible we should nevr search
......@@ -41,6 +39,15 @@ from: ubuntu:bionic
# and is mounted automically
export PYTHONNOUSERSITE=1
%test
mkdir /test_craw
cd /test_craw
pip3 download --no-deps craw==1.0.0
tar -xzf craw-1.0.0.tar.gz
/usr/bin/python3 craw-1.0.0/tests/run_tests.py -vv
cd /
rm -Rf /test_craw
%help
This singularity image contains the Counter RNAseq Window (CRAW) package.
Two commands are available \"coverage\" and \"htmp\.
......
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