recipe pgcgap

A prokaryotic genomics and comparative genomics analysis pipeline

Homepage

https://github.com/liaochenlanruo/pgcgap/blob/master/README.md

Developer docs

https://github.com/liaochenlanruo/pgcgap/tree/master

License

GPL / GPLv3

Recipe

/pgcgap/meta.yaml

Links

biotools: pgcgap

package pgcgap

Versions

1.0.10-0, 1.0.9-2, 1.0.9-1, 1.0.9-0, 1.0.8-0, 1.0.7-0, 1.0.6-0, 1.0.5-0, 1.0.4-0, 1.0.3-0, 1.0.2-4, 1.0.2-3, 1.0.2-2, 1.0.2-1, 1.0.1-1, 1.0.1-0, 1.0.0-0

Depends

• abricate

• abyss >=2.1.5

• biopython

• canu

• cd-hit >=4.8.1

• coreutils

• diamond >=0.9.24

• fastani >=1.1

• fastme >=2.1.5

• fasttree >=2.1.10

• gubbins

• htslib >=1.9

• mafft >=7.402

• mash

• matplotlib

• minced 0.3.*

• mmseqs2 >=7-4e23d

• numpy

• openjdk 8.*

• orthofinder >=2.3.8

• pal2nal

• pandas

• perl-data-dumper >=2.173

• perl-file-tee

• perl-getopt-long >=2.50

• perl-parallel-forkmanager

• perl-pod-usage >=1.69

• prokka >=1.13.4

• r-corrplot

• r-ggplot2

• r-gplots

• r-pheatmap

• r-plotrix

• roary >=3.12.0

• seaborn

• sickle-trim >=1.33

• snippy >=4.3.6

• wget

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install pgcgap

and update with:

conda update pgcgap

or use the docker container:

docker pull quay.io/biocontainers/pgcgap:<tag>

(see pgcgap/tags for valid values for <tag>)

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/pgcgap/README.html)