recipe discasm

DISCASM aims to extract reads that map to reference genomes in a discordant fashion and optionally include reads that do not map to the genome at all, and perform a de novo transcriptome assembly of these reads. DISCASM relies on the output from STAR (as run via STAR-Fusion), and supports de novo transcriptome assembly using Trinity or Oases. - https://github.com/DISCASM/DISCASM/wiki

Homepage:

https://github.com/DISCASM/DISCASM

License:

BSD-3-Clause

Recipe:

/discasm/meta.yaml

package discasm

versions:

0.1.3-1,  0.1.3-0,  0.1.2-2,  0.1.2-1,  0.1.2-0

depends oases:

>=0.2

depends perl:

depends pysam:

>=0.10.0

depends python:

<3

depends star:

>=2.4

depends trinity:

>=2.4

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 discasm

and update with::

   mamba update discasm

To create a new environment, run:

mamba create --name myenvname discasm

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/discasm:<tag>

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

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