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New package: r-watermelon (#14864)

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This PR creates the r-watermelon package, along with dependencies.

- new package: r-fdb-infiniummethylation-hg19
- new package: r-illuminahumanmethylation450kanno-ilmn12-hg19
- new package: r-lumi
- new package: r-methylumi
- new package: r-roc
- new package: r-txdb-hsapiens-ucsc-hg19-knowngene
- updated package: r-matrixstats, new version needed as a dependency
This commit is contained in:
Glenn Johnson 2020-02-10 03:49:34 -06:00 committed by GitHub
parent 1ed0efec7d
commit 8aa1eba2e0
8 changed files with 185 additions and 0 deletions
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# Copyright 2013-2020 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 RFdbInfiniummethylationHg19(RPackage):
"""Compiled HumanMethylation27 and HumanMethylation450 annotations."""
# No available git repository
homepage = "https://bioconductor.org/packages/release/data/annotation/html/FDb.InfiniumMethylation.hg19.html"
url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz"
version('2.2.0', sha256='605aa3643588a2f40a942fa760b92662060a0dfedb26b4e4cd6f1a78b703093f')
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-genomicfeatures@1.7.22:', type=('build', 'run'))
depends_on('r-txdb-hsapiens-ucsc-hg19-knowngene', type=('build', 'run'))
depends_on('r-org-hs-eg-db', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-biostrings', type=('build', 'run'))

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# Copyright 2013-2020 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 RIlluminahumanmethylation450kannoIlmn12Hg19(RPackage):
"""Manifests and annotation for Illumina's 450k array data."""
# This package is available via bioconductor but there is no available git
# repository.
homepage = "https://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylation450kanno.ilmn12.hg19.html"
url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0.tar.gz"
version('0.6.0', sha256='249b8fd62add3c95b5047b597cff0868d26a98862a47cebd656edcd175a73b15')
depends_on('r@3.3.0:', type=('build', 'run'))
depends_on('r-minfi@1.19.15:', type=('build', 'run'))

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# Copyright 2013-2020 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 RLumi(RPackage):
"""The lumi package provides an integrated solution for the Illumina
microarray data analysis. It includes functions of Illumina BeadStudio
(GenomeStudio) data input, quality control, BeadArray-specific variance
stabilization, normalization and gene annotation at the probe level. It
also includes the functions of processing Illumina methylation microarrays,
especially Illumina Infinium methylation microarrays."""
homepage = "https://bioconductor.org/packages/release/bioc/html/lumi.html"
git = "https://git.bioconductor.org/packages/lumi"
version('2.38.0', commit='321d480d44ce9a0c02ce5af1bddc1f549abdea59')
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-biobase@2.5.5:', type=('build', 'run'))
depends_on('r-affy@1.23.4:', type=('build', 'run'))
depends_on('r-methylumi@2.3.2:', type=('build', 'run'))
depends_on('r-genomicfeatures', type=('build', 'run'))
depends_on('r-genomicranges', type=('build', 'run'))
depends_on('r-annotate', type=('build', 'run'))
depends_on('r-lattice', type=('build', 'run'))
depends_on('r-mgcv@1.4-0:', type=('build', 'run'))
depends_on('r-nleqslv', type=('build', 'run'))
depends_on('r-kernsmooth', type=('build', 'run'))
depends_on('r-preprocesscore', type=('build', 'run'))
depends_on('r-rsqlite', type=('build', 'run'))
depends_on('r-dbi', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-mass', type=('build', 'run'))

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@ -18,6 +18,7 @@ class RMatrixstats(RPackage):
url = "https://cloud.r-project.org/src/contrib/matrixStats_0.52.2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/matrixStats"
version('0.55.0', sha256='16d6bd90eee4cee8df4c15687de0f9b72730c03e56603c2998007d4533e8db19')
version('0.54.0', sha256='8f0db4e181300a208b9aedbebfdf522a2626e6675d2662656efb8ba71b05a06f')
version('0.52.2', sha256='39da6aa6b109f89a141dab8913d981abc4fbd3f8be9e206f92e382cc5270d2a5')

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# Copyright 2013-2020 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 RMethylumi(RPackage):
"""This package provides classes for holding and manipulating Illumina
methylation data. Based on eSet, it can contain MIAME information, sample
information, feature information, and multiple matrices of data. An
"intelligent" import function, methylumiR can read the Illumina text files
and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files
from HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
background correction, and quality control features for GoldenGate,
Infinium, and Infinium HD arrays are also included."""
homepage = "https://bioconductor.org/packages/release/bioc/html/methylumi.html"
git = "https://git.bioconductor.org/packages/methylumi"
version('2.32.0', commit='e2a29c1b214c0d43c7325d176f9ce41dcf8e2f9d')
depends_on('r@2.13:', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-scales', type=('build', 'run'))
depends_on('r-reshape2', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-matrixstats', type=('build', 'run'))
depends_on('r-fdb-infiniummethylation-hg19@2.2.0:', type=('build', 'run'))
depends_on('r-minfi', type=('build', 'run'))
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-genomeinfodb', type=('build', 'run'))
depends_on('r-genomicranges', type=('build', 'run'))
depends_on('r-summarizedexperiment', type=('build', 'run'))
depends_on('r-lattice', type=('build', 'run'))
depends_on('r-annotate', type=('build', 'run'))
depends_on('r-genefilter', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-illuminaio', type=('build', 'run'))

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# Copyright 2013-2020 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 RRoc(RPackage):
"""Provide utilities for ROC, with microarray focus."""
homepage = "https://bioconductor.org/packages/release/bioc/html/ROC.html"
git = "https://git.bioconductor.org/packages/ROC"
version('1.62.0', commit='60250fdb091f6a938709b8a2cffe6442ee22a9a2')
depends_on('r@1.9.0:', type=('build', 'run'))
depends_on('r-knitr', type=('build', 'run'))

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# Copyright 2013-2020 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 RTxdbHsapiensUcscHg19Knowngene(RPackage):
"""Exposes an annotation databases generated from UCSC by exposing these as
TxDb objects."""
# This is a bioconductor package but there is no available git repo.
homepage = "https://bioconductor.org/packages/release/data/annotation/html/TxDb.Hsapiens.UCSC.hg19.knownGene.html"
url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz"
version('3.2.2', sha256='063de2b1174782a0b2b8ab7f04a0bdf3c43252cb67c685a9f8ef2b8e318352e9')
depends_on('r-genomicfeatures@1.21.30:', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))

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# Copyright 2013-2020 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 RWatermelon(RPackage):
"""Illumina 450 methylation array normalization and metrics."""
homepage = "https://bioconductor.org/packages/release/bioc/html/wateRmelon.html"
git = "https://git.bioconductor.org/packages/wateRmelon"
version('1.30.0', commit='66d7579fe49206d965832288df7937c3d43ed578')
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-limma', type=('build', 'run'))
depends_on('r-matrixstats', type=('build', 'run'))
depends_on('r-methylumi', type=('build', 'run'))
depends_on('r-lumi', type=('build', 'run'))
depends_on('r-roc', type=('build', 'run'))
depends_on('r-illuminahumanmethylation450kanno-ilmn12-hg19', type=('build', 'run'))
depends_on('r-illuminaio', type=('build', 'run'))