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author | Glenn Johnson <glenn-johnson@uiowa.edu> | 2020-02-13 19:52:43 -0600 |
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committer | GitHub <noreply@github.com> | 2020-02-13 19:52:43 -0600 |
commit | 7996bc809a085ceb215e2e8012194cd18b347ee9 (patch) | |
tree | b6f128fdd4885bbb7e1edfd81ecec1ebedd61eee | |
parent | 580c8f5b7eacb0a05f4b68fc4d86b14b7750a507 (diff) | |
download | spack-7996bc809a085ceb215e2e8012194cd18b347ee9.tar.gz spack-7996bc809a085ceb215e2e8012194cd18b347ee9.tar.bz2 spack-7996bc809a085ceb215e2e8012194cd18b347ee9.tar.xz spack-7996bc809a085ceb215e2e8012194cd18b347ee9.zip |
New package: r-exomedepth (#14884)
This PR adds the r-exomedepth package and r-aod as a dependency.
-rw-r--r-- | var/spack/repos/builtin/packages/r-aod/package.py | 23 | ||||
-rw-r--r-- | var/spack/repos/builtin/packages/r-exomedepth/package.py | 29 |
2 files changed, 52 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/r-aod/package.py b/var/spack/repos/builtin/packages/r-aod/package.py new file mode 100644 index 0000000000..f221cf661d --- /dev/null +++ b/var/spack/repos/builtin/packages/r-aod/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 RAod(RPackage): + """Provides a set of functions to analyse overdispersed counts or + proportions. Most of the methods are already available elsewhere but are + scattered in different packages. The proposed functions should be + considered as complements to more sophisticated methods such as generalized + estimating equations (GEE) or generalized linear mixed effect models + (GLMM).""" + + homepage = "https://cloud.r-project.org/package=aod" + url = "https://cloud.r-project.org/src/contrib/aod_1.3.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/aod" + + version('1.3.1', sha256='052d8802500fcfdb3b37a8e3e6f3fbd5c3a54e48c3f68122402d2ea3a15403bc') + + depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-exomedepth/package.py b/var/spack/repos/builtin/packages/r-exomedepth/package.py new file mode 100644 index 0000000000..972c92c0b4 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-exomedepth/package.py @@ -0,0 +1,29 @@ +# 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 RExomedepth(RPackage): + """Calls copy number variants (CNVs) from targeted sequence data, typically + exome sequencing experiments designed to identify the genetic basis of + Mendelian disorders.""" + + homepage = "https://cloud.r-project.org/package=ExomeDepth" + url = "https://cloud.r-project.org/src/contrib/ExomeDepth_1.1.15.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ExomeDepth" + + version('1.1.15', sha256='112bcb536f5766d9d0b55e064feedd6727ccab14cb1edfdba1f0d7b890e55ad2') + + depends_on('r@3.4.0:', type=('build', 'run')) + depends_on('r-biostrings', type=('build', 'run')) + depends_on('r-iranges', type=('build', 'run')) + depends_on('r-rsamtools', type=('build', 'run')) + depends_on('r-genomicranges@1.23.0:', type=('build', 'run')) + depends_on('r-aod', type=('build', 'run')) + depends_on('r-vgam@0.8.4:', type=('build', 'run')) + depends_on('r-genomicalignments', type=('build', 'run')) + depends_on('r-dplyr', type=('build', 'run')) + depends_on('r-magrittr', type=('build', 'run')) |