Package Recipe 'bioconductor-snplocs.hsapiens.dbsnp144.grch37'

recipe bioconductor-snplocs.hsapiens.dbsnp144.grch37

SNP locations for Homo sapiens (dbSNP Build 144)

Homepage:: https://bioconductor.org/packages/3.20/data/annotation/html/SNPlocs.Hsapiens.dbSNP144.GRCh37.html
License:: Artistic-2.0
Recipe:: /bioconductor-snplocs.hsapiens.dbsnp144.grch37/meta.yaml

SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped to reference genome GRCh37.p13. WARNING: Note that the GRCh37.p13 genome is a patched version of GRCh37. However the patch doesn't alter chromosomes 1-22, X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for the mitochondrion chromosome. Therefore, the SNPs in this package can be "injected" in BSgenome.Hsapiens.UCSC.hg19 and they will land at the correct position but this injection will exclude chrM (i.e. nothing will be injected in that sequence).

package bioconductor-snplocs.hsapiens.dbsnp144.grch37¶

Versions:

0.99.20-14, 0.99.20-13, 0.99.20-12, 0.99.20-11, 0.99.20-10, 0.99.20-9, 0.99.20-8, 0.99.20-7, 0.99.20-6,

0.99.20-14, 0.99.20-13, 0.99.20-12, 0.99.20-11, 0.99.20-10, 0.99.20-9, 0.99.20-8, 0.99.20-7, 0.99.20-6, 0.99.20-5, 0.99.20-4, 0.99.20-3, 0.99.20-2, 0.99.20-0

Depends:

on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-bsgenome >=1.78.0,<1.79.0
on bioconductor-data-packages >=20260207
on bioconductor-genomeinfodb >=1.46.0,<1.47.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on curl
on r-base >=4.5,<4.6.0a0

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-snplocs.hsapiens.dbsnp144.grch37

to add into an existing workspace instead, run:

pixi add bioconductor-snplocs.hsapiens.dbsnp144.grch37

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-snplocs.hsapiens.dbsnp144.grch37

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-snplocs.hsapiens.dbsnp144.grch37

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-snplocs.hsapiens.dbsnp144.grch37:<tag>

(see bioconductor-snplocs.hsapiens.dbsnp144.grch37/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/README.html)