recipe ddocent

dDocent is an interactive bash wrapper to QC, assemble, map, and call SNPs from all types of RAD data

Homepage:

http://ddocent.com

License:

The MIT License (MIT)

Recipe:

/ddocent/meta.yaml

package ddocent

versions:

2.9.4-1,  2.9.4-0,  2.8.13-3,  2.8.13-2,  2.8.13-1,  2.8.13-0,  2.8.12-0,  2.7.8-4,  2.7.8-3, 

2.9.4-1,  2.9.4-0,  2.8.13-3,  2.8.13-2,  2.8.13-1,  2.8.13-0,  2.8.12-0,  2.7.8-4,  2.7.8-3,  2.7.8-2,  2.7.8-1,  2.7.8-0,  2.7.7-0,  2.7.6-0,  2.6.0-2,  2.6.0-1,  2.6.0-0,  2.5.6-0,  2.5.5-0,  2.5.2-1,  2.5.2-0,  2.5.1-0,  2.3.8-0,  2.2.25-2,  2.2.25-1,  2.2.25-0,  2.2.20-0,  2.2.19-0,  2.2.16-0,  2.2.15-0,  2.2.13-0,  2.2.8-0,  2.2.7-0,  2.2.4-0,  2.1-0

depends bedops:

depends bedtools:

>=2.26.0

depends bwa:

>=0.7.13

depends cd-hit:

depends coreutils:

>=8.22

depends curl:

depends fastp:

>=0.20.0

depends freebayes:

>=1

depends gnuplot:

depends grep:

depends mawk:

depends parallel:

depends pear:

depends rainbow:

depends samtools:

>=1.6

depends sed:

depends seqtk:

>=1.3

depends unzip:

depends vcflib:

>=0.1.11

depends vcftools:

>=0.1.15

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 ddocent

and update with::

   mamba update ddocent

To create a new environment, run:

mamba create --name myenvname ddocent

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/ddocent:<tag>

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

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