recipe mtbseq

Pipeline for WGS analysis of M. tuberculosis

Homepage:

https://github.com/ngs-fzb/MTBseq_source

License:

GPLv3

Recipe:

/mtbseq/meta.yaml

MTBseq is a semi-automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from Illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates

package mtbseq

versions:

1.1.0-0,  1.0.4-2,  1.0.4-1,  1.0.4-0,  1.0.3-1,  1.0.3-0

depends bwa:

0.7.17

depends gatk:

3.8

depends openjdk:

>=8,<9

depends perl:

>=5.22

depends perl-mce:

>=1.836

depends perl-number-format:

depends perl-statistics-basic:

>=1.6611

depends picard:

>=2.17.0,<3

depends samtools:

1.6

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 mtbseq

and update with::

   mamba update mtbseq

To create a new environment, run:

mamba create --name myenvname mtbseq

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/mtbseq:<tag>

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

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