- recipe qorts
QoRTs toolkit for analysis, quality control, and data management of RNA-Seq datasets.
- Homepage:
- License:
Public Domain
- Recipe:
- 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:
on openjdk
on python
on r-qorts
1.3.6
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install qorts
to add into an existing workspace instead, run:
pixi add qorts
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install qorts
Alternatively, to install into a new environment, run:
conda create -n envname qorts
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/qorts:<tag>
(see qorts/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
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
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/qorts/README.html)
