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| author | Glenn Johnson <glenn-johnson@uiowa.edu> | 2020-02-13 19:49:24 -0600 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2020-02-13 19:49:24 -0600 |
| commit | 46ae3f0570f3ad19fc559d6fa464e701c29bd2f5 (patch) | |
| tree | e9642d0a98edce06b43bdcc7dfb0a1f68353528f | |
| parent | 725336ee48422be487747c08e0dff58f23a3b7ad (diff) | |
| download | spack-46ae3f0570f3ad19fc559d6fa464e701c29bd2f5.tar.gz spack-46ae3f0570f3ad19fc559d6fa464e701c29bd2f5.tar.bz2 spack-46ae3f0570f3ad19fc559d6fa464e701c29bd2f5.tar.xz spack-46ae3f0570f3ad19fc559d6fa464e701c29bd2f5.zip | |
New package: r-fdb-infiniummethylation-hg18 (#14890)
This PR adds the r-fdb-infiniummethylation-hg18 package and the needed
dependency of r-txdb-hsapiens-ucsc-hg18-knowngene.
| -rw-r--r-- | var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg18/package.py | 23 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg18-knowngene/package.py | 20 |
2 files changed, 43 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg18/package.py b/var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg18/package.py new file mode 100644 index 0000000000..98b09d0353 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg18/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 RFdbInfiniummethylationHg18(RPackage): + """Compiled HumanMethylation27 and HumanMethylation450 annotations""" + + # This is a bioconductor package but there is no available git repository + homepage = "http://bioconductor.org/packages/release/data/annotation/html/FDb.InfiniumMethylation.hg18.html" + url = "http://bioconductor.org/packages/release/data/annotation/src/contrib/FDb.InfiniumMethylation.hg18_2.2.0.tar.gz" + + version('2.2.0', sha256='4a9028ac03c11fffbab731ea750bc7f9b0884fc43c6a8dac6eb2c644e4c79f6f') + + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-genomicfeatures@1.7.22:', type=('build', 'run')) + depends_on('r-txdb-hsapiens-ucsc-hg18-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-txdb-hsapiens-ucsc-hg18-knowngene/package.py b/var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg18-knowngene/package.py new file mode 100644 index 0000000000..fc1500a232 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg18-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 RTxdbHsapiensUcscHg18Knowngene(RPackage): + """Exposes an annotation databases generated from UCSC by exposing these as + TxDb objects""" + + # This is a bioconductor package but ther is no available git repo + homepage = "http://bioconductor.org/packages/release/data/annotation/html/TxDb.Hsapiens.UCSC.hg18.knownGene.html" + url = "http://bioconductor.org/packages/release/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2.tar.gz" + + version('3.2.2', sha256='bc9ca40b4eab87f5ca64a4b876d42502b9b8e9f5983d745bfe0ee349d97b69fa') + + depends_on('r-genomicfeatures@1.21.30:', type=('build', 'run')) + depends_on('r-annotationdbi', type=('build', 'run')) |