From ddce89e4cea06463f91d3a75b840841e5bf400c1 Mon Sep 17 00:00:00 2001 From: Desmond Orton Date: Fri, 26 Mar 2021 20:26:01 -0600 Subject: New R package vcfr (#22495) --- var/spack/repos/builtin/packages/r-vcfr/package.py | 39 ++++++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 var/spack/repos/builtin/packages/r-vcfr/package.py diff --git a/var/spack/repos/builtin/packages/r-vcfr/package.py b/var/spack/repos/builtin/packages/r-vcfr/package.py new file mode 100644 index 0000000000..9d1c10694d --- /dev/null +++ b/var/spack/repos/builtin/packages/r-vcfr/package.py @@ -0,0 +1,39 @@ +# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RVcfr(RPackage): + """Manipulate and Visualize VCF Data + + Facilitates easy manipulation of variant call format (VCF) data. Functions + are provided to rapidly read from and write to VCF files. Once VCF data is + read into R a parser function extracts matrices of data. This information + can then be used for quality control or other purposes. Additional + functions provide visualization of genomic data. Once processing is + complete data may be written to a VCF file (*.vcf.gz). It also may be + converted into other popular R objects (e.g., genlight, DNAbin). VcfR + provides a link between VCF data and familiar R software.""" + + homepage = "https://github.com/knausb/vcfR" + cran = "vcfR" + + maintainers = ['dorton21'] + + version('1.12.0', sha256='dd87ff010365de363864a44ca49887c0fdad0dd18d0d9c66e44e39c2d4581d52') + + depends_on('r@3.0.1:', type=('build', 'run')) + depends_on('r-ape', type=('build', 'run')) + depends_on('r-dplyr', type=('build', 'run')) + depends_on('r-magrittr', type=('build', 'run')) + depends_on('r-memuse', type=('build', 'run')) + depends_on('r-pinfsc50', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-stringr', type=('build', 'run')) + depends_on('r-tibble', type=('build', 'run')) + depends_on('r-vegan', type=('build', 'run')) + depends_on('r-viridislite', type=('build', 'run')) + depends_on('zlib') -- cgit v1.2.3-70-g09d2