recipe fermikit

FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.

Homepage:

https://github.com/lh3/fermikit

License:

Unknown

Recipe:

/fermikit/meta.yaml

package fermikit

versions:

0.14.dev1-1,  0.14.dev1-0

depends bfc:

==r181

depends bwa:

==0.7.15

depends fermi2:

==r193

depends htsbox:

==r327

depends perl:

5.22.0*

depends ropebwt2:

==r187

depends seqtk:

==r82

depends trimadap:

==r10

depends zlib:

1.2.11*

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 fermikit

and update with::

   mamba update fermikit

To create a new environment, run:

mamba create --name myenvname fermikit

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/fermikit:<tag>

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

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