recipe pifcosm

PisCoSm is a pipeline to construct supermatrix trees from GenBank data

Homepage:

https://github.com/RybergGroup/PifCoSm

License:

GPL-3.0-only

Recipe:

/pifcosm/meta.yaml

Links:

doi: 10.1073/pnas.1922539117

package pifcosm

versions:

0.1.1-0

depends cd-hit:

depends fasttree:

depends gblocks:

depends hmmer:

depends mafft:

depends muscle:

depends perl:

depends perl-dbd-sqlite:

depends perl-dbi:

depends phylommand:

depends raxml:

depends roguenarok:

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 pifcosm

and update with::

   mamba update pifcosm

To create a new environment, run:

mamba create --name myenvname pifcosm

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/pifcosm:<tag>

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

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