1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
|
# Copyright 2013-2018 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 RShortread(RPackage):
"""This package implements sampling, iteration, and input of FASTQ
files. The package includes functions for filtering and trimming
reads, and for generating a quality assessment report. Data are
represented as DNAStringSet-derived objects, and easily manipulated
for a diversity of purposes. The package also contains legacy support
for early single-end, ungapped alignment formats."""
homepage = "https://www.bioconductor.org/packages/ShortRead/"
git = "https://git.bioconductor.org/packages/ShortRead.git"
version('1.34.2', commit='25daac63b301df66a8ef6e98cc2977522c6786cd')
depends_on('r@3.4.0:3.4.9', when='@1.34.2')
depends_on('r-latticeextra', type=('build', 'run'))
depends_on('r-lattice', type=('build', 'run'))
depends_on('r-zlibbioc', type=('build', 'run'))
depends_on('r-hwriter', type=('build', 'run'))
depends_on('r-genomicranges', type=('build', 'run'))
depends_on('r-genomeinfodb', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-genomicalignments', type=('build', 'run'))
depends_on('r-rsamtools', type=('build', 'run'))
depends_on('r-biostrings', type=('build', 'run'))
depends_on('r-biocparallel', type=('build', 'run'))
depends_on('r-biocgenerics', type=('build', 'run'))
|
