- recipe ggcaller
A de Bruijn graph-based gene-caller and pangenome analysis tool
- Homepage:
- License:
MIT / MIT
- Recipe:
- package ggcaller¶
- versions:
1.3.4-0,1.3.3-1,1.3.3-0,1.3.2-0,1.3.1-0,1.3.0-1,1.3.0-0,1.2.4-2,1.2.4-1,1.3.4-0,1.3.3-1,1.3.3-0,1.3.2-0,1.3.1-0,1.3.0-1,1.3.0-0,1.2.4-2,1.2.4-1,1.2.4-0,1.2.3-0,1.2.2-0,1.2.1-0,1.1.1-0,1.0.0-0- depends _openmp_mutex:
>=4.5- depends bcbio-gff:
- depends bifrost:
- depends biopython:
>=1.8.0- depends boost-cpp:
>=1.78.0,<1.78.1.0a0- depends bzip2:
>=1.0.8,<2.0a0- depends cd-hit:
- depends diamond:
>=2.0- depends gffutils:
- depends hmmer:
- depends intbitset:
- depends joblib:
- depends libgcc-ng:
>=12- depends libstdcxx-ng:
>=12- depends libzlib:
>=1.2.13,<1.3.0a0- depends mafft:
- depends matplotlib-base:
- depends mkl:
>=2022.2.1,<2023.0a0- depends networkx:
- depends numpy:
- depends pandas:
- depends pthread-stubs:
- depends python:
>=3.10,<3.11.0a0- depends python-edlib:
- depends python-wget:
- depends python_abi:
3.10.* *_cp310- depends pytorch:
>=1.13.1,<1.14.0a0- depends rapidnj:
- depends scipy:
- depends seaborn:
- depends snp-sites:
- depends tbb:
>=2021.9.0- depends tqdm:
- depends uncertainties:
- depends xorg-libxaw:
- depends xorg-libxcomposite:
- depends xorg-libxcursor:
- depends xorg-libxdamage:
- depends xorg-libxfixes:
- depends xorg-libxi:
- depends xorg-libxinerama:
- depends xorg-libxpm:
- depends xorg-libxrandr:
- depends zlib:
- requirements:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install ggcaller and update with:: mamba update ggcaller
To create a new environment, run:
mamba create --name myenvname ggcaller
with
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, use the docker container:
docker pull quay.io/biocontainers/ggcaller:<tag> (see `ggcaller/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/ggcaller/README.html)
