recipe cap-mirseq

A comprehensive analysis pipeline for deep microRNA sequencing

Homepage

http://bioinformaticstools.mayo.edu/research/cap-mirseq/

License

GPL

Recipe

/cap-mirseq/meta.yaml

package cap-mirseq

(downloads) docker_cap-mirseq

Versions

version-0

Depends bedtools

>=2.17.0

Depends bioconductor-edger

>=3.14.0

Depends bowtie

>=1.1.2

Depends fastqc

>=0.11.5

Depends java-jdk

Depends mirdeep2

>=2.0.0.7

Depends perl-threaded

Depends picard

>=1.97

Depends r-base

3.2.2*

Depends r-essentials

Depends samtools

>=0.1.19

Depends vcftools

>=0.1.11

Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install cap-mirseq

and update with:

conda update cap-mirseq

or use the docker container:

docker pull quay.io/biocontainers/cap-mirseq:<tag>

(see cap-mirseq/tags for valid values for <tag>)

Link to this page

Render an install-with-bioconda 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/cap-mirseq/README.html)