recipe panpasco

Pipeline for pangenome mapping and pairwise SNP distance

Homepage:

https://gitlab.com/rki_bioinformatics/panpasco

License:

MIT

Recipe:

/panpasco/meta.yaml

PANPASCO uses linear computational pan-genomes and pairwise SNP distance calculation to improve distance matrix analyses

package panpasco

versions:

1.0.1-0,  1.0.0-0

depends bedtools:

2.27.*

depends bioconductor-genomicranges:

depends bwa:

0.7.17.*

depends flash:

1.2.11.*

depends gatk:

3.8.*

depends picard:

2.18.*

depends python:

>3

depends r-argparse:

depends r-base:

>=4.0,<4.1.0a0

depends samtools:

depends seqtk:

depends snakemake:

depends tabix:

depends trimmomatic:

0.36.*

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 panpasco

and update with::

   mamba update panpasco

To create a new environment, run:

mamba create --name myenvname panpasco

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/panpasco:<tag>

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

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