recipe trace-crispr

TRACE: Triple-aligner Read Analysis for CRISPR Editing

Homepage:

https://github.com/k-roy/TRACE

License:

MIT / MIT

Recipe:

/trace-crispr/meta.yaml

TRACE provides robust quantification of CRISPR editing outcomes including HDR, NHEJ, and large deletions using a triple-aligner consensus approach (BWA-MEM, BBMap, minimap2).

package trace-crispr

versions:

0.4.0-0

depends bbmap:

>=39

depends bwa:

>=0.7

depends click:

>=8.0

depends minimap2:

>=2.24

depends numpy:

>=1.20

depends pandas:

>=1.5

depends pysam:

>=0.20

depends python:

>=3.9

depends pyyaml:

>=6.0

depends rapidfuzz:

>=3.0

depends samtools:

>=1.16

depends tqdm:

>=4.60

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 trace-crispr

and update with::

   mamba update trace-crispr

To create a new environment, run:

mamba create --name myenvname trace-crispr

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/trace-crispr:<tag>

(see `trace-crispr/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

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