recipe micall-lite

A bioinformatic pipeline for mapping of FASTQ data to a set of reference sequences to generate consensus sequences, variant calls and coverage maps.

Homepage:

https://github.com/PoonLab/MiCall-Lite

License:

GNU Affero General Public License v3.0

Recipe:

/micall-lite/meta.yaml

package micall-lite

versions:

0.1rc5-4,  0.1rc5-3,  0.1rc5-2,  0.1rc5-1,  0.1rc5-0,  0.1rc4-0,  0.1rc3-0,  0.1rc2-0,  0.1rc-0

depends bowtie2:

depends libgcc-ng:

>=12

depends python:

>=3.10,<3.11.0a0

depends python-levenshtein:

depends python_abi:

3.10.* *_cp310

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 micall-lite

and update with::

   mamba update micall-lite

To create a new environment, run:

mamba create --name myenvname micall-lite

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/micall-lite:<tag>

(see `micall-lite/tags`_ for valid values for ``<tag>``)

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Link to this page

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