recipe polap

POLAP: plant organelle long-read assembly pipeline

Homepage:

https://github.com/goshng/polap

Documentation:

https://goshng.github.io/polap/polap.html

License:

GPL / GPL-3.0-or-later

Recipe:

/polap/meta.yaml

package polap

versions:

0.2.6-0,  0.2.4-0

depends assembly-stats:

depends bedtools:

depends bioawk:

depends bioconductor-ggtree:

depends blast:

depends clustalw:

depends csvtk:

depends entrez-direct:

depends flye:

>=2.9.2

depends gfastats:

depends icu:

depends kmer-jellyfish:

depends libxml2:

depends minimap2:

>=2.24

depends orthofinder:

depends parallel:

depends perl:

depends perl-xml-libxml:

depends python:

depends r-base:

depends r-dplyr:

depends r-optparse:

depends r-readr:

depends r-stringr:

depends r-tidyr:

depends samtools:

depends seqkit:

depends seqtk:

depends sra-tools:

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 polap

and update with::

   mamba update polap

To create a new environment, run:

mamba create --name myenvname polap

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/polap:<tag>

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

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/polap/README.html)