recipe cutesv-ol

cuteSV-OL: real-time structural variation detection for nanopore sequencing

Homepage:

https://github.com/120L022331/cuteSV-OL

License:

MIT

Recipe:

/cutesv-ol/meta.yaml

package cutesv-ol

versions:

1.0.1-0,  1.0.0-0

depends biopython:

depends cigar:

depends libgcc:

>=13

depends minimap2:

depends numpy:

>=1.24.4,<2.0

depends pysam:

>=0.23.0,<0.24.0a0

depends python:

>=3.12,<3.13.0a0

depends python_abi:

3.12.* *_cp312

depends pyvcf3:

depends samtools:

depends scikit-learn:

depends scipy:

depends watchdog:

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 cutesv-ol

and update with::

   mamba update cutesv-ol

To create a new environment, run:

mamba create --name myenvname cutesv-ol

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/cutesv-ol:<tag>

(see `cutesv-ol/tags`_ for valid values for ``<tag>``)

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