Package Recipe 'ggcaller'

recipe ggcaller

A de Bruijn graph-based gene-caller and pangenome analysis tool

Homepage:: https://github.com/bacpop/ggCaller
License:: MIT / MIT
Recipe:: /ggcaller/meta.yaml

package ggcaller¶

Versions:

1.4.3-0, 1.4.2-0, 1.4.1-0, 1.3.7-0, 1.3.6-0, 1.3.5-0, 1.3.4-0, 1.3.3-1, 1.3.3-0,

1.4.3-0, 1.4.2-0, 1.4.1-0, 1.3.7-0, 1.3.6-0, 1.3.5-0, 1.3.4-0, 1.3.3-1, 1.3.3-0, 1.3.2-0, 1.3.1-0, 1.3.0-1, 1.3.0-0, 1.2.4-2, 1.2.4-1, 1.2.4-0, 1.2.3-0, 1.2.2-0, 1.2.1-0, 1.1.1-0, 1.0.0-0

Depends:

on _openmp_mutex >=4.5
on bcbio-gff
on bifrost >=1.2
on bifrost >=1.3.5,<2.0a0
on biopython 1.80.*
on boost-cpp
on bzip2 >=1.0.8,<2.0a0
on cd-hit
on diamond >=2.0
on gffutils
on hmmer
on intbitset
on joblib
on libgcc >=13
on libstdcxx >=13
on libzlib >=1.3.1,<2.0a0
on mafft
on matplotlib-base
on mkl >=2022.2.1,<2023.0a0
on networkx
on numpy
on pandas
on pthread-stubs
on python >=3.9,<3.10.0a0
on python-edlib
on python-wget
on python_abi 3.9.* *_cp39
on pytorch 1.10.*
on pytorch >=1.10.2,<1.11.0a0
on pytorch-cpu 1.10.*
on rapidnj
on scipy
on seaborn
on snp-sites
on tbb >=2021.13.0
on tqdm
on uncertainties
on xorg-libxaw
on xorg-libxcomposite
on xorg-libxcursor
on xorg-libxdamage
on xorg-libxfixes
on xorg-libxi
on xorg-libxinerama
on xorg-libxpm
on xorg-libxrandr
on zlib

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 ggcaller

to add into an existing workspace instead, run:

pixi add ggcaller

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 ggcaller

Alternatively, to install into a new environment, run:

conda create -n envname ggcaller

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/ggcaller:<tag>

(see ggcaller/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/ggcaller/README.html)