recipe qorts

QoRTs toolkit for analysis, quality control, and data management of RNA-Seq datasets.

Homepage:

http://hartleys.github.io/QoRTs/

License:

Public Domain

Recipe:

/qorts/meta.yaml

package qorts

versions:

1.3.6-1,  1.3.6-0,  1.3.0-2,  1.3.0-1,  1.3.0-0,  1.1.8-0

depends openjdk:

depends python:

depends r-qorts:

1.3.6

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 qorts

and update with::

   mamba update qorts

To create a new environment, run:

mamba create --name myenvname qorts

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/qorts:<tag>

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

Notes

Based on the Picard equivalent, found in the BioConda recipies repo. Simplifies the call to the QoRTs JAVA utility so that you can just go :-

qorts [Java Options] QC [QoRTs options] input.bam annotation.gtf outputDir

which is equivalent to :-

java [Java Options] -jar /path/to/jar/QoRTs.jar QC [QoRTs options] input.bam annotation.gtf outputDir

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