recipe microhapulator

Tools for empirical microhaplotype calling, forensic interpretation, and simulation.

Homepage:

https://github.com/bioforensics/MicroHapulator/

License:

BSD / BSD-3-Clause

Recipe:

/microhapulator/meta.yaml

package microhapulator

(downloads) docker_microhapulator

versions:
0.8.4-0,  0.8.3-0,  0.8.2-0,  0.8.1-0,  0.8-0,  0.7.2-0,  0.7.1-0,  0.6.1-0,  0.5-1, 

0.8.4-0,  0.8.3-0,  0.8.2-0,  0.8.1-0,  0.8-0,  0.7.2-0,  0.7.1-0,  0.6.1-0,  0.5-1,  0.5-0,  0.4.1-0,  0.3-0,  0.2-0,  0.1.3-0

depends biopython:

depends fastqc:

>=0.11.9

depends flash:

>=1.2

depends happer:

>=0.1

depends insilicoseq:

>=1.5.4,<2.0

depends jsonschema:

>=4.0

depends matplotlib-base:

>=3.0

depends microhapdb:

>=0.10.1

depends minimap2:

>=2.25

depends multiqc:

>=1.14

depends nbformat:

>=5.0,<5.6

depends numpy:

>=1.19

depends pandas:

>1.0

depends pulp:

2.3.1

depends pysam:

>=0.15.2

depends python:

<3.12

depends samtools:

>=1.12

depends scipy:

>=1.7

depends seaborn-base:

>=0.13.2

depends snakemake-minimal:

>=7.15.2,<8.0

depends termgraph:

>=0.5

depends tqdm:

>=4.0

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 microhapulator

and update with::

   mamba update microhapulator

To create a new environment, run:

mamba create --name myenvname microhapulator

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/microhapulator:<tag>

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

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Link to this page

Render an install-with-bioconda 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/microhapulator/README.html)