- recipe bioconductor-rsamtools
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
- Homepage:
https://bioconductor.org/packages/3.20/bioc/html/Rsamtools.html
- License:
Artistic-2.0 | file LICENSE
- Recipe:
- Links:
biotools: rsamtools, doi: 10.1038/nmeth.3252
This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.
- package bioconductor-rsamtools¶
- versions:
2.22.0-1,2.22.0-0,2.18.0-2,2.18.0-1,2.18.0-0,2.16.0-0,2.14.0-1,2.14.0-0,2.10.0-2,2.22.0-1,2.22.0-0,2.18.0-2,2.18.0-1,2.18.0-0,2.16.0-0,2.14.0-1,2.14.0-0,2.10.0-2,2.10.0-1,2.10.0-0,2.8.0-0,2.6.0-1,2.6.0-0,2.4.0-0,2.2.0-0,2.0.0-1,1.34.0-0,1.32.3-0,1.30.0-0,1.28.0-0,1.26.1-0,1.24.0-0,1.22.0-1,1.22.0-0- depends bioconductor-biocgenerics:
>=0.52.0,<0.53.0- depends bioconductor-biocgenerics:
>=0.52.0,<0.53.0a0- depends bioconductor-biocparallel:
>=1.40.0,<1.41.0- depends bioconductor-biocparallel:
>=1.40.0,<1.41.0a0- depends bioconductor-biostrings:
>=2.74.0,<2.75.0- depends bioconductor-biostrings:
>=2.74.0,<2.75.0a0- depends bioconductor-genomeinfodb:
>=1.42.0,<1.43.0- depends bioconductor-genomeinfodb:
>=1.42.0,<1.43.0a0- depends bioconductor-genomicranges:
>=1.58.0,<1.59.0- depends bioconductor-genomicranges:
>=1.58.0,<1.59.0a0- depends bioconductor-iranges:
>=2.40.0,<2.41.0- depends bioconductor-iranges:
>=2.40.0,<2.41.0a0- depends bioconductor-rhtslib:
>=3.2.0,<3.3.0- depends bioconductor-rhtslib:
>=3.2.0,<3.3.0a0- depends bioconductor-s4vectors:
>=0.44.0,<0.45.0- depends bioconductor-s4vectors:
>=0.44.0,<0.45.0a0- depends bioconductor-xvector:
>=0.46.0,<0.47.0- depends bioconductor-xvector:
>=0.46.0,<0.47.0a0- depends bioconductor-zlibbioc:
>=1.52.0,<1.53.0- depends bioconductor-zlibbioc:
>=1.52.0,<1.53.0a0- depends libblas:
>=3.9.0,<4.0a0- depends libgcc:
>=13- depends liblapack:
>=3.9.0,<4.0a0- depends liblzma:
>=5.8.1,<6.0a0- depends libstdcxx:
>=13- depends libzlib:
>=1.3.1,<2.0a0- depends r-base:
>=4.4,<4.5.0a0- depends r-bitops:
- 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 bioconductor-rsamtools and update with:: mamba update bioconductor-rsamtools
To create a new environment, run:
mamba create --name myenvname bioconductor-rsamtools
with
myenvnamebeing 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/bioconductor-rsamtools:<tag> (see `bioconductor-rsamtools/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-rsamtools/README.html)
