Package Recipe 'pgcgap'

recipe pgcgap

A prokaryotic genomics and comparative genomics analysis pipeline

Homepage:: https://github.com/liaochenlanruo/pgcgap/blob/master/README.md
Documentation:: https://liaochenlanruo.fun/pgcgap/
Developer docs:: https://github.com/liaochenlanruo/pgcgap/tree/master
License:: GPL / GPLv3
Recipe:: /pgcgap/meta.yaml
Links:: biotools: pgcgap

PGCGAP is a pipeline for prokaryotic comparative genomics analysis. It can take the pair-end reads, ONT reads or PacBio reads as input. In addition to genome assembly, gene prediction and annotation, it can also get common comparative genomics analysis results such as phylogenetic trees of single-core proteins and core SNPs, pan-genome, whole-genome Average Nucleotide Identity (ANI), orthogroups and orthologs, COG annotations, substitutions (SNPs) and insertions/deletions (indels), and antimicrobial and virulence genes mining with only one line of commands.

package pgcgap¶

Versions:

1.0.35-1, 1.0.35-0, 1.0.34-0, 1.0.33-0, 1.0.32-0, 1.0.31-0, 1.0.30-0, 1.0.29-0, 1.0.28-0,

1.0.35-1, 1.0.35-0, 1.0.34-0, 1.0.33-0, 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:

on abricate 1.0.1.*
on abyss 2.3.5.*
on canu 2.1.1.*
on coreutils 9.1.*
on fastani 1.33.*
on fastp 0.23.2.*
on htslib 1.16.*
on mamba 0.22.1.*
on mash 2.3.*
on matplotlib-base 3.5.3.*
on muscle 5.1.*
on numpy 1.21.6.*
on openjdk 17.0.3.*
on orthofinder 2.5.4.*
on pal2nal 14.1.*
on panaroo 1.1.2.*
on pandas 1.3.5.*
on perl 5.32.1.*
on perl >=5.32.1,<6.0a0 *_perl5
on perl-data-dumper 2.183.*
on perl-file-copy-recursive 0.45.*
on perl-file-tee 0.07.*
on perl-parallel-forkmanager 2.02.*
on perl-pod-usage 2.03.*
on perl-posix 1.38_03.*
on prokka 1.14.6.*
on r-base 4.2.1.*
on r-corrplot 0.92.*
on r-ggplot2 3.3.6.*
on r-gplots 3.1.3.*
on r-pheatmap 1.0.12.*
on r-plotrix 3.8_2.*
on seaborn 0.12.0.*
on sickle-trim 1.33.*
on snippy 4.6.0.*
on snpeff 5.0.*
on trimal 1.4.1.*
on unicycler 0.4.8.*
on wget 1.20.3.*

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install pgcgap

to add into an existing workspace instead, run:

pixi add pgcgap

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install pgcgap

Alternatively, to install into a new environment, run:

conda create -n envname pgcgap

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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)