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

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:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install cap-mirseq

and update with::

   mamba update cap-mirseq

To create a new environment, run:

mamba create --name myenvname cap-mirseq

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

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

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