recipe megapath

MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data; MegaPath-Amplicon: filtering module for metagenomic amplicon data

Homepage:

https://github.com/HKU-BAL/MegaPath

License:

BSD-3-Clause

Recipe:

/megapath/meta.yaml

package megapath

versions:

2-3,  2-2,  2-1,  2-0,  1.0-0

depends bedtools:

depends bwa:

0.7.12.*

depends gatk4:

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends libzlib:

>=1.2.13,<1.3.0a0

depends megahit:

1.1.*

depends minimap2:

depends pandas:

depends parallel:

20191122.*

depends pypy3.6:

depends pysam:

0.16.0.1.*

depends python:

3.6.*

depends samtools:

1.10.*

depends seqtk:

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 megapath

and update with::

   mamba update megapath

To create a new environment, run:

mamba create --name myenvname megapath

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/megapath:<tag>

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

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