recipe advntr

A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data

Homepage:

https://github.com/mehrdadbakhtiari/adVNTR

License:

BSD 3-Clause

Recipe:

/advntr/meta.yaml

package advntr

versions:

1.5.0-0,  1.4.1-2,  1.4.1-1,  1.4.1-0,  1.4.0-2,  1.4.0-1,  1.4.0-0,  1.3.3-2,  1.3.3-1, 

1.5.0-0,  1.4.1-2,  1.4.1-1,  1.4.1-0,  1.4.0-2,  1.4.0-1,  1.4.0-0,  1.3.3-2,  1.3.3-1,  1.3.3-0,  1.3.2-1,  1.3.2-0,  1.3.1-0,  1.3.0-1,  1.2.0-0,  1.1.1-1,  1.1.1-0,  1.1.0-1,  1.1.0-0,  1.0.3-0

depends biopython:

depends cython:

depends htslib:

1.9.*

depends joblib:

depends keras:

2.2.4.*

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends matplotlib-base:

depends muscle:

3.8.1551.*

depends networkx:

1.11.*

depends numpy:

>=1.16.5,<2.0a0

depends pysam:

0.15.1.*

depends python:

>=2.7,<2.8.0a0

depends python_abi:

2.7.* *_cp27mu

depends scikit-learn:

depends scipy:

>=1.2.1,<2.0a0

depends tensorflow:

1.13.1.*

requirements:

additional platforms:

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 advntr

and update with::

   mamba update advntr

To create a new environment, run:

mamba create --name myenvname advntr

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/advntr:<tag>

(see `advntr/tags`_ for valid values for ``<tag>``)

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