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.*

depends bedtools:

2.17.0.*

depends bwa:

0.7.12.*

depends fastqc:

0.11.5.*

depends fqtools:

2.0.*

depends gatk:

3.6.*

depends kraken:

0.10.5.*

depends openjdk:

8.*

depends perl-vcftools-vcf:

0.1.16.*

depends picard:

1.141.*

depends pigz:

2.3.4.*

depends prinseq:

0.20.4.*

depends python:

depends pyyaml:

5.1.*

depends qualimap:

2.1.3.*

depends samtools:

1.2.*

depends snpeff:

4.1.*

depends vcftools:

0.1.16.*

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 uvp

and update with::

   mamba update uvp

To create a new environment, run:

mamba create --name myenvname uvp

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/uvp:<tag>

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

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