Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
C
craw
Manage
Activity
Members
Labels
Code
Merge requests
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Snippets
Build
Pipelines
Jobs
Pipeline schedules
Artifacts
Deploy
Releases
Container Registry
Model registry
Operate
Environments
Analyze
Value stream analytics
Contributor analytics
CI/CD analytics
Repository analytics
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
Community forum
Contribute to GitLab
Provide feedback
Keyboard shortcuts
?
Snippets
Groups
Projects
Show more breadcrumbs
Bertrand NÉRON
craw
Commits
fabb0331
Verified
Commit
fabb0331
authored
6 years ago
by
Bertrand NÉRON
Browse files
Options
Downloads
Patches
Plain Diff
🐛
fix singularity url
parent
46fd82f3
No related branches found
No related tags found
No related merge requests found
Pipeline
#10988
passed
6 years ago
Stage: test
Stage: coverage
Changes
1
Pipelines
1
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
README.md
+24
-9
24 additions, 9 deletions
README.md
with
24 additions
and
9 deletions
README.md
+
24
−
9
View file @
fabb0331
...
...
@@ -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
==========
...
...
This diff is collapsed.
Click to expand it.
Preview
0%
Loading
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Save comment
Cancel
Please
register
or
sign in
to comment