recipe uvp

A Unified Variant Pipeline to identify variants and assign lineage from MTBC sequence data.

Homepage:

https://github.com/CPTR-ReSeqTB/UVP

License:

MIT

Recipe:

/uvp/meta.yaml

package uvp

Versions:

2.7.0-0,  2.6.0-0

Depends:

• bcftools 1.2.*

• bedtools 2.17.0.*

• bwa 0.7.12.*

• fastqc 0.11.5.*

• fqtools 2.0.*

• gatk 3.6.*

• kraken 0.10.5.*

• openjdk 8.*

• perl-vcftools-vcf 0.1.16.*

• picard 1.141.*

• pigz 2.3.4.*

• prinseq 0.20.4.*

• python

• pyyaml 5.1.*

• qualimap 2.1.3.*

• samtools 1.2.*

• snpeff 4.1.*

• vcftools 0.1.16.*

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install uvp

and update with:

conda update uvp

or use the docker container:

docker pull quay.io/biocontainers/uvp:<tag>

(see uvp/tags for valid values for <tag>)

Download stats

Link to this page

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