- recipe arcas-hla
high-resolution HLA typing from RNA seq
- Homepage:
- License:
GPL-3.0-only
- Recipe:
- Links:
arcasHLA performs high-resolution genotyping for HLA class I and class II genes from RNA sequencing, supporting both paired and single-end samples.
- package arcas-hla¶
- Versions:
0.6.0-2,0.6.0-1,0.6.0-0,0.5.0-3,0.5.0-2,0.5.0-1,0.5.0-0,0.4.0-0,0.3.0-0,0.6.0-2,0.6.0-1,0.6.0-0,0.5.0-3,0.5.0-2,0.5.0-1,0.5.0-0,0.4.0-0,0.3.0-0,0.2.5-0,0.2.0-1,0.2.0-0- Depends:
on bedtools
on biopython
on coreutils
on git
on git-lfs
on kallisto
0.44on numpy
on pandas
on pigz
on pip
on pyarrow
on pytest
on python
on samtools
on scipy
- 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 arcas-hla
to add into an existing workspace instead, run:
pixi add arcas-hla
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 arcas-hla
Alternatively, to install into a new environment, run:
conda create -n envname arcas-hla
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/arcas-hla:<tag>
(see arcas-hla/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.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/arcas-hla/README.html)
