recipe fusioncatcher

Finder of Somatic Fusion Genes in RNA-seq data.

Homepage:

https://github.com/ndaniel/fusioncatcher

License:

GPL / GPL-3.0

Recipe:

/fusioncatcher/meta.yaml

Links:

doi: 10.1101/011650

package fusioncatcher

Versions:

1.33-4,  1.33-3,  1.33-2,  1.33-1,  1.33-0,  1.30-1,  1.30-0,  1.20-2,  1.20-1, 

1.33-4,  1.33-3,  1.33-2,  1.33-1,  1.33-0,  1.30-1,  1.30-0,  1.20-2,  1.20-1,  1.20-0,  1.10-3,  1.10-2,  1.10-0,  1.00-1,  1.00-0

Depends:

• bbmap 38.44.*

• biopython >=1.50

• blat 35.*

• bowtie 1.2.3.*

• bowtie2 2.3.5.*

• bwa 0.7.12.*

• coreutils

• fastqtk

• fusioncatcher-seqtk 1.2.*

• grep

• gzip

• lzo

• lzop

• numpy 1.13.1.*

• oases

• openjdk

• openpyxl 2.5.0a2.*

• parallel 20171222.*

• picard 2.10.6.*

• pigz 2.3.*

• python <3

• samtools 0.1.19.*

• sra-tools 2.9.6.*

• star 2.7.2b.*

• tbb 2020.2.*

• ucsc-fatotwobit

• ucsc-liftover

• velvet 1.2.10.*

• xlrd 1.0.0.*

• zip

Required By:

Installation

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

conda install fusioncatcher

and update with:

conda update fusioncatcher

or use the docker container:

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

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

Notes

download-human-db.sh should be updated when new version of FusionCatcher is released.

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/fusioncatcher/README.html)