recipe bam2fasta

bam2fasta: cli tool to convert bam to fastas

Homepage:

https://github.com/czbiohub/bam2fasta

License:

MIT / MIT

Recipe:

/bam2fasta/meta.yaml

Links:

biotools: bam2fasta

package bam2fasta

versions:

1.0.8-0,  1.0.7-0,  1.0.6-0,  1.0.5-0,  1.0.4-0,  1.0.3-0,  1.0.1-0

depends numpy:

depends pandas:

>=0.24.1

depends pathos:

>=0.2.5

depends pysam:

>=0.15.3

depends python:

depends screed:

>=0.9

depends tqdm:

>=4.36.1

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 bam2fasta

and update with::

   mamba update bam2fasta

To create a new environment, run:

mamba create --name myenvname bam2fasta

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/bam2fasta:<tag>

(see `bam2fasta/tags`_ for valid values for ``<tag>``)

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