recipe pipits

PIPITS: An automated pipeline for analyses of fungal internal transcribed spacer (ITS) sequences from the Illumina sequencing platform.

Homepage:

https://github.com/hsgweon/pipits

Documentation:

https://github.com/hsgweon/pipits/blob/4.0/README.md

License:

GPL3 / GPL-3.0-or-later

Recipe:

/pipits/meta.yaml

Links:

doi: 10.1111/2041-210X.12399

package pipits

(downloads) docker_pipits

versions:
4.0-1,  4.0-0,  3.1-0,  3.0-0,  2.8-0,  2.7-0,  2.6-0,  2.5-0,  2.4-0, 

4.0-1,  4.0-0,  3.1-0,  3.0-0,  2.8-0,  2.7-0,  2.6-0,  2.5-0,  2.4-0,  2.3-4,  2.3-3,  2.3-2,  2.3-1,  2.3-0,  2.2-2,  2.2-1,  2.1-5,  2.1-3,  2.1-2,  2.1-1,  2.0-1,  2.0-0

depends biom-format:

depends fastx_toolkit:

depends hmmer:

depends itsx:

depends numpy:

depends progressbar2:

depends python:

>=3.10

depends rdptools:

depends requests:

depends seqkit:

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 pipits

and update with::

   mamba update pipits

To create a new environment, run:

mamba create --name myenvname pipits

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/pipits:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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