recipe pysam

Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.

Homepage:

https://github.com/pysam-developers/pysam

License:

MIT

Recipe:

/pysam/meta.yaml

Links:

biotools: pysam, doi: 10.1093/bioinformatics/btp352

package pysam

(downloads) docker_pysam

versions:
0.23.3-0,  0.23.2-0,  0.23.1-0,  0.23.0-0,  0.22.1-3,  0.22.1-2,  0.22.1-1,  0.22.1-0,  0.22.0-1, 

0.23.3-0,  0.23.2-0,  0.23.1-0,  0.23.0-0,  0.22.1-3,  0.22.1-2,  0.22.1-1,  0.22.1-0,  0.22.0-1,  0.22.0-0,  0.21.0-1,  0.21.0-0,  0.20.0-0,  0.19.1-1,  0.19.1-0,  0.19.0-0,  0.18.0-2,  0.18.0-1,  0.18.0-0,  0.17.0-1,  0.17.0-0,  0.16.0.1-3,  0.16.0.1-2,  0.16.0.1-1,  0.16.0.1-0,  0.16.0-1,  0.16.0-0,  0.15.4-1,  0.15.4-0,  0.15.3-3,  0.15.3-1,  0.15.3-0,  0.15.2-11,  0.15.2-10,  0.15.2-9,  0.15.2-8,  0.15.2-7,  0.15.2-6,  0.15.2-5,  0.15.2-4,  0.15.2-3,  0.15.2-2,  0.15.2-1,  0.15.2-0,  0.15.1-0,  0.15.0.1-1,  0.15.0.1-0,  0.15.0-0,  0.14.1-1,  0.14.1-0,  0.14.0-2,  0.14.0-1,  0.14.0-0,  0.13.0-0,  0.12.0.1-2,  0.12.0.1-1,  0.12.0.1-0,  0.11.2.2-2,  0.11.2.2-1,  0.11.2.2-0,  0.11.2.1-0,  0.11.1-0,  0.11.0-0,  0.10.0-13,  0.10.0-12,  0.10.0-11,  0.10.0-10,  0.10.0-9,  0.10.0-8,  0.10.0-7,  0.10.0-6,  0.10.0-5,  0.10.0-4,  0.10.0-3,  0.10.0-1,  0.9.1.4-1,  0.9.1.4-0,  0.9.1-12,  0.9.1-11,  0.9.1-10,  0.9.1-9,  0.9.1-8,  0.9.1-7,  0.9.1-6,  0.9.1-5,  0.9.1-4,  0.9.1-3,  0.9.1-2,  0.9.1-1,  0.9.1-0,  0.9.0-2,  0.9.0-1,  0.9.0-0,  0.8.4-0,  0.8.4pre0-0,  0.8.3-9,  0.8.3-8,  0.8.3-7,  0.8.3-6,  0.8.3-5,  0.8.3-4,  0.8.3-3,  0.8.3-2,  0.8.3-1,  0.8.3-0,  0.7.7-6,  0.7.7-5,  0.7.7-4,  0.7.7-3,  0.7.7-2,  0.7.7-1,  0.7.7-0

depends bzip2:

>=1.0.8,<2.0a0

depends libcurl:

>=8.14.1,<9.0a0

depends libdeflate:

>=1.22,<1.23.0a0

depends libgcc:

>=13

depends liblzma:

>=5.8.1,<6.0a0

depends libzlib:

>=1.3.1,<2.0a0

depends openssl:

>=3.5.0,<4.0a0

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

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 pysam

and update with::

   mamba update pysam

To create a new environment, run:

mamba create --name myenvname pysam

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/pysam:<tag>

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

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