recipe srnapipe

Pipeline for bioinformatic in-depth exploration of small RNA-seq data



Academic Free License v3.0



package srnapipe

(downloads) docker_srnapipe



depends bedtools:


depends bioconductor-sushi:

depends bwa:


depends fonts-conda-ecosystem:

depends perl:

>=5.32.1,<6.0a0 *_perl5

depends perl-file-copy-recursive:

depends perl-getopt-long:

depends perl-math-cdf:

depends perl-parallel-forkmanager:

depends perl-statistics-r:

depends perl-string-random:

depends r-base:


depends r-ggplot2:

depends r-plotrix:

depends r-rcolorbrewer:

depends samtools:




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 srnapipe

and update with::

   mamba update srnapipe

To create a new environment, run:

mamba create --name myenvname srnapipe

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<tag>

(see `srnapipe/tags`_ for valid values for ``<tag>``)

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