recipe chira

An integrated framework for annotation and visualization of chimeric reads.

Homepage:

https://github.com/pavanvidem/chira/

License:

GNU GENERAL PUBLIC LICENSE Version 3

Recipe:

/chira/meta.yaml

Links:

usegalaxy-eu: chira_quantify

package chira

versions:

1.4.3-2,  1.4.3-1,  1.4.3-0,  1.4.2-0,  1.4.0-0,  1.3.7-1,  1.3.7-0,  1.3.6-0,  1.3.5-0, 

1.4.3-2,  1.4.3-1,  1.4.3-0,  1.4.2-0,  1.4.0-0,  1.3.7-1,  1.3.7-0,  1.3.6-0,  1.3.5-0,  1.3.4-0,  1.3.3-0,  1.3.1-1,  1.3.1-0,  1.2.0-0,  1.1.5-0,  1.1.4-0,  1.1.2-0,  1.1.1-0,  1.0.4-0,  1.0.3-0,  1.0.2-2,  1.0.2-1,  1.0.2-0,  1.0.1-0,  1.0.0-0

depends bcbio-gff:

>=0.6.6

depends bedtools:

>=2.29.2

depends biopython:

>=1.76

depends blockbuster:

>=0.0.1.1

depends bwa:

>=0.7.17

depends clan:

>=0.05

depends coreutils:

>=8.31

depends intarna:

>=3.2.0

depends pysam:

>=0.15.3

depends python:

>3

depends samtools:

>=1.9

requirements:

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 chira

and update with::

   mamba update chira

To create a new environment, run:

mamba create --name myenvname chira

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/chira:<tag>

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

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