recipe pairtools

CLI tools to process mapped Hi-C data.

Homepage:

https://github.com/open2c/pairtools

Documentation:

https://pairtools.readthedocs.io

License:

MIT / MIT

Recipe:

/pairtools/meta.yaml

Links:

doi: 10.1101/2023.02.13.528389, usegalaxy-eu: pairtools_dedup, usegalaxy-eu: pairtools_parse, usegalaxy-eu: pairtools_split, usegalaxy-eu: pairtools_sort, usegalaxy-eu: pairtools_stats

package pairtools

versions:

1.1.3-0,  1.1.2-0,  1.1.0-3,  1.1.0-2,  1.1.0-1,  1.1.0-0,  1.0.3-0,  1.0.2-1,  1.0.2-0, 

1.1.3-0,  1.1.2-0,  1.1.0-3,  1.1.0-2,  1.1.0-1,  1.1.0-0,  1.0.3-0,  1.0.2-1,  1.0.2-0,  1.0.1-0,  0.3.0-6,  0.3.0-5,  0.3.0-4,  0.3.0-3,  0.3.0-2,  0.3.0-1,  0.3.0-0,  0.2.2-0,  0.2.1-0,  0.2.0-0,  0.1.1-0

depends bioframe:

>=0.3.3

depends click:

depends coreutils:

depends htslib:

depends libgcc:

>=13

depends libstdcxx:

>=13

depends lz4-c:

depends numpy:

>=1.22.4,<2.0a0

depends pandas:

depends pbgzip:

depends pysam:

>=0.19

depends pysam:

>=0.23.0,<0.24.0a0

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends pyyaml:

depends samtools:

depends scipy:

>=1.7

requirements:

additional platforms:

linux-aarch64,  osx-arm64

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 pairtools

and update with::

   mamba update pairtools

To create a new environment, run:

mamba create --name myenvname pairtools

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/pairtools:<tag>

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

Download stats

Link to this page

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