recipe clinker

Clinker is a bioinformatics pipeline that generates a superTranscriptome from popular fusion finder outputs (JAFFA, tophatFusion, SOAP, deFUSE, Pizzly, etc), that can be then be either viewed in genome viewers such as IGV or through the included plotting feature developed with GViz.

Homepage:

https://github.com/Oshlack/Clinker

License:

MIT

Recipe:

/clinker/meta.yaml

package clinker

Versions:

1.32-2,  1.32-1,  1.32-0

Depends:

• bioconductor-biomart

• bioconductor-gviz

• bpipe

• python 2.7.*

• samtools

• star >=2.5.3a

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install clinker

and update with:

conda update clinker

or use the docker container:

docker pull quay.io/biocontainers/clinker:<tag>

(see clinker/tags for valid values for <tag>)

Notes

Wrapper script provided to indicate clinker is a bpipe pipeline, provide example command from wiki, and also a passthrough option.

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/clinker/README.html)