recipe hisat2-pipeline

A pipeline to automatically run an RNA-seq analysis using HISAT2/Stringtie using default settings

Homepage:

https://github.com/mcamagna/HISAT2-pipeline

License:

GPL / GPL-3.0-or-later

Recipe:

/hisat2-pipeline/meta.yaml

Links:

https: :https:`//doi.org/10.5281/zenodo.10389729`

package hisat2-pipeline

versions:

1.0.7-0,  1.0.6-0

depends hisat2:

depends openpyxl:

depends pandas:

depends python:

>=3

depends samtools:

>=1.9

depends stringtie:

requirements:

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 hisat2-pipeline

and update with::

   mamba update hisat2-pipeline

To create a new environment, run:

mamba create --name myenvname hisat2-pipeline

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/hisat2-pipeline:<tag>

(see `hisat2-pipeline/tags`_ for valid values for ``<tag>``)

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