recipe rnalyze

A comprehensive pipeline for RNA-Seq data analysis.

Homepage:

https://github.com/MohamedElsisii/rnalyze

Documentation:

https://github.com/MohamedElsisii/rnalyze#readme

License:

MIT

Recipe:

/rnalyze/meta.yaml

rnalyze is a Bash-based pipeline for analyzing RNA-Seq data. It supports both single-end and paired-end data, includes quality control, trimming, alignment, and feature counting, and is highly customizable.

package rnalyze

versions:

1.0.1-1,  1.0.1-0,  1.0.0-0

depends bowtie2:

depends bwa:

depends cutadapt:

5.0.*

depends fastqc:

depends hisat2:

depends multiqc:

depends samtools:

depends sra-tools:

depends subread:

depends trimmomatic:

depends xopen:

1.6.0.*

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 rnalyze

and update with::

   mamba update rnalyze

To create a new environment, run:

mamba create --name myenvname rnalyze

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/rnalyze:<tag>

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

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