recipe itsxpress

ITSxpress: Software to rapidly trim the Internally Transcribed Spacer (ITS) region from FASTQ files.

Homepage:

http://github.com/usda-ars-gbru/itsxpress

License:

PUBLIC-DOMAIN / CC0-1.0

Recipe:

/itsxpress/meta.yaml

Links:

biotools: ITSxpress, doi: 10.5281/zenodo.1304349, doi: 10.12688/f1000research.15704.1

package itsxpress

versions:

2.1.4-0,  2.1.3-2,  2.1.3-1,  2.1.3-0,  2.1.2-0,  2.1.1-0,  2.1.0-0,  2.0.2-0,  2.0.1-0, 

2.1.4-0,  2.1.3-2,  2.1.3-1,  2.1.3-0,  2.1.2-0,  2.1.1-0,  2.1.0-0,  2.0.2-0,  2.0.1-0,  2.0.0-0,  1.8.1-0,  1.8.0-2,  1.8.0-1,  1.8.0-0,  1.7.2-1,  1.7.2-0,  1.7.1-0,  1.6.4-0,  1.6.3-0,  1.6.1-1,  1.6.1-0,  1.5.6-0

depends biopython:

>=1.79

depends hmmer:

>=3.1b2

depends pandas:

depends python:

>=3.7

depends pyzstd:

depends vsearch:

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 itsxpress

and update with::

   mamba update itsxpress

To create a new environment, run:

mamba create --name myenvname itsxpress

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/itsxpress:<tag>

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

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Link to this page

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