recipe rearr

Chimeric alignment of CRISPR-seq

Homepage:

https://github.com/ljw20180420/sx_lcy

Documentation:

https://ljw20180420.github.io/sx_lcy

License:

MIT / MIT

Recipe:

/rearr/meta.yaml

rearr is a package to demultiplex and align CRISPR-seq data.

package rearr

versions:

1.0.0-0

depends bedtools:

depends bowtie2:

depends cutadapt:

depends gawk:

depends libgcc:

>=13

depends libstdcxx:

>=13

depends make:

depends numpy:

depends perl:

depends python:

depends samtools:

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 rearr

and update with::

   mamba update rearr

To create a new environment, run:

mamba create --name myenvname rearr

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/rearr:<tag>

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

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Link to this page

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