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

1.0.19-0,  1.0.18-1,  1.0.18-0,  1.0.17-0,  1.0.16-0,  1.0.15-0,  1.0.14-0,  1.0.13-1,  1.0.13-0, 

1.0.19-0,  1.0.18-1,  1.0.18-0,  1.0.17-0,  1.0.16-0,  1.0.15-0,  1.0.14-0,  1.0.13-1,  1.0.13-0,  1.0.12-1,  1.0.12-0,  1.0.11-1,  1.0.11-0,  1.0.10-2,  1.0.10-1,  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 >=1.8

• coreutils

• fastani >=1.1

• fastme >=2.1.5

• fastp

• gblocks

• gubbins

• htslib >=1.9

• iqtree

• mash

• matplotlib-base

• minced 0.3.*

• modeltest-ng

• numpy

• openjdk 8.*

• orthofinder >=2.3.8

• pal2nal

• pandas

• perl >=5.26.2,<5.26.3.0a0

• perl-data-dumper >=2.173

• perl-file-tee

• perl-getopt-long >=2.50

• perl-parallel-forkmanager

• perl-pod-usage >=1.69

• perl-posix

• perl-sys-info

• prokka >=1.13.4

• python

• r-base

• r-corrplot

• r-ggplot2 >=3.1.1

• r-gplots

• r-pheatmap

• r-plotrix

• raxml-ng

• roary >=3.12.0

• seaborn

• sickle-trim >=1.33

• snippy >=4.3.6

• unicycler 0.4.7.*

• wget

Required By

• bttcmp

• bttoxin_scanner

• bttoxin_digger

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)