recipe amalgkit

Tools for transcriptome amalgamation

Homepage:

https://github.com/kfuku52/amalgkit

License:

BSD-3-Clause

Recipe:

/amalgkit/meta.yaml

package amalgkit

versions:

0.12.16-0,  0.12.15-0

depends bioconductor-edger:

depends bioconductor-pcamethods:

depends bioconductor-ruvseq:

depends bioconductor-sva:

depends biopython:

depends fastp:

depends kallisto:

depends lxml:

depends numpy:

depends pandas:

depends parallel-fastq-dump:

depends python:

>=3.9

depends r-amap:

depends r-base:

depends r-colorspace:

depends r-dendextend:

depends r-ggplot2:

depends r-mass:

depends r-nmf:

depends r-patchwork:

depends r-pvclust:

depends r-rcolorbrewer:

depends r-rtsne:

depends seqkit:

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 amalgkit

and update with::

   mamba update amalgkit

To create a new environment, run:

mamba create --name myenvname amalgkit

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/amalgkit:<tag>

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

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