Package Recipe 'spechla'

recipe spechla

Full-resolution HLA typing from sequencing data

Homepage:: https://github.com/deepomicslab/SpecHLA
License:: MIT / MIT
Recipe:: /spechla/meta.yaml

SpecHLA enables full-resolution HLA typing from various sequencing data types including WGS, WES, RNA-seq, and long-read sequencing.

package spechla¶

Versions:

1.0.10-0

Depends:

on arpack >=3.9.1,<3.10.0a0 nompi_*
on bamutil
on bcftools
on bedtools
on biopython
on blast
on blat
on bowtie2 >=2.5.5,<3.0a0
on bwa
on fermikit
on freebayes
on htslib >=1.23,<2.0a0
on k8
on libgcc >=14
on libstdcxx >=14
on libzlib >=1.3.1,<2.0a0
on longshot
on minimap2
on numpy
on pandas
on parallel
on pbmm2
on pbsv
on perl
on perl-findbin
on perl-getopt-long
on pulp
on pysam
on python >=3.12,<3.13.0a0
on python-edlib
on python_abi 3.12.* *_cp312
on pyvcf3
on samtools >=1.13
on scipy
on trinity

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 spechla

to add into an existing workspace instead, run:

pixi add spechla

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 spechla

Alternatively, to install into a new environment, run:

conda create -n envname spechla

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/spechla:<tag>

(see spechla/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:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/spechla/README.html)