diff options
8 files changed, 185 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg19/package.py b/var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg19/package.py new file mode 100644 index 0000000000..ae6749434a --- /dev/null +++ b/var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg19/package.py @@ -0,0 +1,23 @@ +# 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')) diff --git a/var/spack/repos/builtin/packages/r-illuminahumanmethylation450kanno-ilmn12-hg19/package.py b/var/spack/repos/builtin/packages/r-illuminahumanmethylation450kanno-ilmn12-hg19/package.py new file mode 100644 index 0000000000..3442430964 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-illuminahumanmethylation450kanno-ilmn12-hg19/package.py @@ -0,0 +1,20 @@ +# 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')) diff --git a/var/spack/repos/builtin/packages/r-lumi/package.py b/var/spack/repos/builtin/packages/r-lumi/package.py new file mode 100644 index 0000000000..d79de8d662 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-lumi/package.py @@ -0,0 +1,37 @@ +# 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')) diff --git a/var/spack/repos/builtin/packages/r-matrixstats/package.py b/var/spack/repos/builtin/packages/r-matrixstats/package.py index 9446add318..9bebc7ad9d 100644 --- a/var/spack/repos/builtin/packages/r-matrixstats/package.py +++ b/var/spack/repos/builtin/packages/r-matrixstats/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/r-methylumi/package.py b/var/spack/repos/builtin/packages/r-methylumi/package.py new file mode 100644 index 0000000000..55f9f42a96 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-methylumi/package.py @@ -0,0 +1,41 @@ +# 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')) diff --git a/var/spack/repos/builtin/packages/r-roc/package.py b/var/spack/repos/builtin/packages/r-roc/package.py new file mode 100644 index 0000000000..90cb6bfb0d --- /dev/null +++ b/var/spack/repos/builtin/packages/r-roc/package.py @@ -0,0 +1,18 @@ +# 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')) diff --git a/var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg19-knowngene/package.py b/var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg19-knowngene/package.py new file mode 100644 index 0000000000..a0d5b6ccde --- /dev/null +++ b/var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg19-knowngene/package.py @@ -0,0 +1,20 @@ +# 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')) diff --git a/var/spack/repos/builtin/packages/r-watermelon/package.py b/var/spack/repos/builtin/packages/r-watermelon/package.py new file mode 100644 index 0000000000..a1d827870c --- /dev/null +++ b/var/spack/repos/builtin/packages/r-watermelon/package.py @@ -0,0 +1,25 @@ +# 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')) |