recipe viralflye

viralFlye is a pipeline to recover high-quality viral genomes from long-read metagenomic sequencing.

Homepage:

https://github.com/Dmitry-Antipov/viralFlye/

License:

BSD-3-Clause

Recipe:

/viralflye/meta.yaml

package viralflye

versions:

0.2-0

depends bcftools:

depends biopython:

depends blast:

depends bwa:

depends freebayes:

depends minced:

depends minimap2:

depends numpy:

depends prodigal:

depends pysam:

depends python:

>=3.6

depends samtools:

depends scipy:

depends seqtk:

depends tabix:

depends vcflib:

depends viralverify:

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 viralflye

and update with::

   mamba update viralflye

To create a new environment, run:

mamba create --name myenvname viralflye

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/viralflye:<tag>

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

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Link to this page

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