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:

1.3.7-0,  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, 

1.3.7-0,  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 _openmp_mutex:

>=4.5

depends bcbio-gff:

depends bifrost:

>=1.2

depends bifrost:

>=1.3.5,<1.4.0a0

depends biopython:

1.80.*

depends boost-cpp:

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,<2.0a0

depends mafft:

depends matplotlib-base:

depends mkl:

>=2022.2.1,<2023.0a0

depends networkx:

depends numpy:

depends pandas:

depends pthread-stubs:

depends python:

>=3.9,<3.10.0a0

depends python-edlib:

depends python-wget:

depends python_abi:

3.9.* *_cp39

depends pytorch:

1.10.*

depends pytorch:

>=1.10.2,<1.11.0a0

depends pytorch-cpu:

1.10.*

depends rapidnj:

depends scipy:

depends seaborn:

depends snp-sites:

depends tbb:

>=2021.12.0

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 myenvname being 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>``)

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