recipe parascopy

Calling paralog-specific copy number and sequence variants in duplicated genes using short-read whole-genome sequencing.

Homepage:

https://github.com/tprodanov/parascopy

Documentation:

https://github.com/tprodanov/parascopy/blob/v1.18.0/README.md

License:

MIT / MIT

Recipe:

/parascopy/meta.yaml

Links:

doi: 10.1038/s41467-022-30930-3, doi: 10.1093/bioinformatics/btad268, biotools: parascopyvc

package parascopy

versions:

1.18.0-1,  1.18.0-0,  1.17.4-0,  1.17.2-1,  1.17.2-0,  1.17.1-1,  1.17.1-0,  1.17.0-0,  1.16.3-0, 

1.18.0-1,  1.18.0-0,  1.17.4-0,  1.17.2-1,  1.17.2-0,  1.17.1-1,  1.17.1-0,  1.17.0-0,  1.16.3-0,  1.16.2-0,  1.16.0-0,  1.15.1-2,  1.15.1-1,  1.15.1-0,  1.15.0-0,  1.14.1-0,  1.14.0-0,  1.13.9-0,  1.12.0-0,  1.11.0-2,  1.11.0-1,  1.11.0-0,  1.10.6-0,  1.9.7-1,  1.9.7-0,  1.9.1-0,  1.7.6-0,  1.7.4-0,  1.7.3-0,  1.7.1-0,  1.7.0-0,  1.6.2-0,  1.6.1-0,  1.5.0-0,  1.4.0-0,  1.3.4-0,  1.3.3-0,  1.3.2-0,  1.3.1-0,  1.3.0-0,  1.2.6-0,  1.2.4-0,  1.2.3-0,  1.2.2-0,  1.2.1-0,  1.2.0-0,  1.1.2-0,  1.1.0-0,  1.0.0-0

depends biopython:

>=1.70

depends bwa:

>=0.7

depends bzip2:

>=1.0.8,<2.0a0

depends construct:

>=2.10

depends htslib:

>=1.21,<1.23.0a0

depends intervaltree:

>=3.0

depends libgcc:

>=13

depends liblzma:

>=5.8.1,<6.0a0

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

depends numpy:

>=1.15

depends parasail-python:

>=1.2

depends pysam:

>=0.17

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends samtools:

>=1.11

depends scipy:

>=1.5

depends simpleeval:

>=0.9

depends tabixpp:

>=1.1.2,<1.1.3.0a0

requirements:

additional platforms:

linux-aarch64

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 parascopy

and update with::

   mamba update parascopy

To create a new environment, run:

mamba create --name myenvname parascopy

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/parascopy:<tag>

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

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