recipe localhgt

An ultrafast horizontal gene transfer detection method from large microbial communities

Homepage:

https://github.com/deepomicslab/LocalHGT

License:

MIT

Recipe:

/localhgt/meta.yaml

Links:

biotools: localhgt

package localhgt

versions:

1.0.1-3,  1.0.1-2,  1.0.1-1,  1.0.1-0

depends biopython:

depends bwa:

>=0.7.17

depends fastp:

>=0.23.2

depends libgcc:

>=13

depends libstdcxx:

>=13

depends networkx:

>=2.6.3

depends numpy:

<=1.24

depends pandas:

depends pyfaidx:

depends pysam:

depends python:

>=3.7.12

depends samtools:

>=1.11

depends scikit-bio:

>=0.5.6

depends scikit-learn:

depends scipy:

depends seqkit:

>=2.6.1

depends typing-extensions:

>=4.11.0

requirements:

additional platforms:

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 localhgt

and update with::

   mamba update localhgt

To create a new environment, run:

mamba create --name myenvname localhgt

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/localhgt:<tag>

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

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