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

1.0.32-0,  1.0.31-0,  1.0.30-0,  1.0.29-0,  1.0.28-0,  1.0.27-0,  1.0.26-0,  1.0.25-0,  1.0.24-0, 

1.0.32-0,  1.0.31-0,  1.0.30-0,  1.0.29-0,  1.0.28-0,  1.0.27-0,  1.0.26-0,  1.0.25-0,  1.0.24-0,  1.0.23-0,  1.0.22-0,  1.0.21-0,  1.0.20-0,  1.0.19-2,  1.0.19-1,  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 1.0.1.*

• abyss 2.2.5.*

• biopython 1.78.*

• canu 2.0.*

• coreutils 8.31.*

• fastani 1.32.*

• fastp 0.20.1.*

• gubbins 2.4.1.*

• htslib 1.10.2.*

• mamba

• mash 2.2.2.*

• matplotlib-base 3.4.1.*

• numpy 1.20.2.*

• openjdk 8.0.152.*

• orthofinder 2.3.8.*

• pal2nal 14.1.*

• pandas 1.2.3.*

• perl >=5.26.2,<5.26.3.0a0

• perl-data-dumper 2.173.*

• perl-file-copy-recursive 0.45.*

• perl-file-tee 0.07.*

• perl-parallel-forkmanager 2.02.*

• perl-pod-usage 1.69.*

• perl-posix 1.38.*

• prokka 1.14.6.*

• python 3.7.8.*

• r-base 3.6.3.*

• r-corrplot 0.88.*

• r-ggplot2 3.3.3.*

• r-gplots 3.1.1.*

• r-pheatmap 1.0.12.*

• r-plotrix 3.8_1.*

• roary 3.13.0.*

• seaborn 0.11.1.*

• sickle-trim >=1.33

• snippy 4.6.0.*

• trimal 1.4.1.*

• unicycler 0.4.7.*

• wget 1.20.1.*

Required By

• bttcmp

• bttoxin_scanner

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>)

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/pgcgap/README.html)