recipe strainflye

Pipeline for analyzing rare mutations in metagenomes assembled using long and accurate reads

Homepage:

https://github.com/fedarko/strainFlye

License:

BSD / BSD-3-Clause

Recipe:

/strainflye/meta.yaml

package strainflye

versions:

0.2.0-0

depends bcftools:

>=1.7,<1.10

depends click:

>=8.0

depends htslib:

>=1.9,<1.10.0a0

depends minimap2:

>=2.10

depends networkx:

depends numpy:

depends pandas:

>=1.0

depends prodigal:

depends pysam:

<0.16

depends pysamstats:

depends python:

>=3.6,<3.8

depends samtools:

>=1.7,<1.10

depends scikit-bio:

depends scipy:

>=1.0

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 strainflye

and update with::

   mamba update strainflye

To create a new environment, run:

mamba create --name myenvname strainflye

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/strainflye:<tag>

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

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