Package Recipe 'egap'

recipe egap

EGAP pipeline for genome assembly and QC analysis

Homepage:: https://github.com/iPsychonaut/EGAP
License:: BSD-3-Clause
Recipe:: /egap/meta.yaml

EGAP (Entheome Genome Assembly Pipeline) is a versatile bioinformatics pipeline for hybrid genome assembly from Oxford Nanopore, Illumina, and PacBio data. It supports multiple input modes and assembly methods and determines the best based on multiple metrics: BUSCO Completeness (Single + Duplicated), Assembly Contig Count, Assembly N50, Assembly L50, and Assembly GC-content.

package egap¶

Versions:

3.3.9-0, 3.3.8-0, 3.3.7-0, 3.3.6-0, 3.3.5-0, 3.3.4-0, 3.3c-0, 3.2c-0, 3.1-0,

3.3.9-0, 3.3.8-0, 3.3.7-0, 3.3.6-0, 3.3.5-0, 3.3.4-0, 3.3c-0, 3.2c-0, 3.1-0, 3.1b-0, 3.0.0f-0, 3.0.0b-0, 2.6.6-0, 2.6.5-0, 2.6.4-0, 2.6.2-0, 2.5.4-0, 2.5.3-0

Depends:

on abyss >=2.0.2
on bamtools >=2.5.2
on bbmap >=39.15
on beautifulsoup4 >=4.12.3
on bifrost >=1.3.5
on biopython >=1.81
on busco >=5.8.2
on bwa-mem2 >=2.2.1
on compleasm >=0.2.7
on fastqc >=0.12.1
on filtlong >=0.2.1
on flye >=2.9.5
on geopy >=2.4.1
on gfatools >=0.5
on hifiasm >=0.21.0
on jinja2 >=3.1.4
on kmc >=3.2.4
on masurca >=4.1.2
on matplotlib-base >=3.7.3
on minimap2 >=2.28
on nanoplot >=1.43.0
on ncbi-datasets-cli >=18.3.1
on numpy >=1.24.3
on openpyxl >=3.1.5
on pandas >=2.0.3
on pbccs >=6.4.0
on pilon >=1.22
on psutil >=6.0.0
on purge_dups >=1.2.6
on pyinaturalist >=0.20
on python >=3.8,<3.9
on quast >=5.2.0
on racon >=1.5.0
on ragtag >=2.1.0
on ratatosk >=0.9.0
on requests >=2.32.3
on rich >=13.3.3
on samtools >=1.21
on sepp >=4.5.1
on spades >=4.0.0
on sra-tools >=3.2.0
on tabulate >=0.9.0
on termcolor >=2.3.0
on textual >=0.4.2
on tgsgapcloser >=1.2.1
on trimmomatic >=0.39

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 egap

to add into an existing workspace instead, run:

pixi add egap

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 egap

Alternatively, to install into a new environment, run:

conda create -n envname egap

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/egap:<tag>

(see egap/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.

Notes¶

This package installs a custom executable named "EGAP" in $PREFIX/bin. Please refer to the upstream GitHub page for usage instructions.

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/egap/README.html)