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authorGlenn Johnson <glenn-johnson@uiowa.edu>2020-02-10 04:08:04 -0600
committerGitHub <noreply@github.com>2020-02-10 11:08:04 +0100
commit745a843911aad95f900c806ebc8704132e48fa74 (patch)
treef67b6cf4ef510c41d8070f962c045b89bc2608d9
parentcb3dbea198433641c806a9b1fa9a58d32fefc389 (diff)
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New package: r-biomartr (#14812)
This PR creates the r-biomartr package as well as needed new packages and updates. - new dependency: r-philentropy - update: r-curl
-rw-r--r--var/spack/repos/builtin/packages/r-biomartr/package.py44
-rw-r--r--var/spack/repos/builtin/packages/r-curl/package.py8
-rw-r--r--var/spack/repos/builtin/packages/r-philentropy/package.py28
3 files changed, 77 insertions, 3 deletions
diff --git a/var/spack/repos/builtin/packages/r-biomartr/package.py b/var/spack/repos/builtin/packages/r-biomartr/package.py
new file mode 100644
index 0000000000..6cb63e979c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-biomartr/package.py
@@ -0,0 +1,44 @@
+# 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 RBiomartr(RPackage):
+ """Perform large scale genomic data retrieval and functional annotation
+ retrieval. This package aims to provide users with a standardized way to
+ automate genome, proteome, 'RNA', coding sequence ('CDS'), 'GFF', and
+ metagenome retrieval from 'NCBI RefSeq', 'NCBI Genbank', 'ENSEMBL',
+ 'ENSEMBLGENOMES', and 'UniProt' databases. Furthermore, an interface to the
+ 'BioMart' database (Smedley et al. (2009) <doi:10.1186/1471-2164-10-22>)
+ allows users to retrieve functional annotation for genomic loci. In
+ addition, users can download entire databases such as 'NCBI RefSeq' (Pruitt
+ et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr', 'NCBI nt', 'NCBI
+ Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>), etc. as well as
+ 'ENSEMBL' and 'ENSEMBLGENOMES' with only one command."""
+
+ homepage = "https://docs.ropensci.org/biomartr"
+ url = "https://cloud.r-project.org/src/contrib/biomartr_0.9.2.tar.gz"
+ list_url = "https://cloud.r-project.org/src/contrib/Archive/biomartr"
+
+ version('0.9.2', sha256='d88085696e9c5614828602254c33f2cdd3bbfeebc2f21a705eee3cb961097c89')
+
+ depends_on('r-biomart', type=('build', 'run'))
+ depends_on('r-biostrings', type=('build', 'run'))
+ depends_on('r-curl', type=('build', 'run'))
+ depends_on('r-tibble', type=('build', 'run'))
+ depends_on('r-jsonlite', type=('build', 'run'))
+ depends_on('r-data-table@1.9.4:', type=('build', 'run'))
+ depends_on('r-dplyr@0.3.0:', type=('build', 'run'))
+ depends_on('r-readr@0.2.2:', type=('build', 'run'))
+ depends_on('r-downloader@0.3:', type=('build', 'run'))
+ depends_on('r-rcurl@1.95-4.5:', type=('build', 'run'))
+ depends_on('r-xml@3.98-1.1:', type=('build', 'run'))
+ depends_on('r-httr@0.6.1:', type=('build', 'run'))
+ depends_on('r-stringr@0.6.2:', type=('build', 'run'))
+ depends_on('r-purrr', type=('build', 'run'))
+ depends_on('r-r-utils', type=('build', 'run'))
+ depends_on('r-philentropy', type=('build', 'run'))
+ depends_on('r-fs@1.3.1:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-curl/package.py b/var/spack/repos/builtin/packages/r-curl/package.py
index 25081b86f7..f1a7a2de60 100644
--- a/var/spack/repos/builtin/packages/r-curl/package.py
+++ b/var/spack/repos/builtin/packages/r-curl/package.py
@@ -21,12 +21,14 @@ class RCurl(RPackage):
url = "https://cloud.r-project.org/src/contrib/curl_2.3.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/curl"
+ version('4.3', sha256='7406d485bb50a6190e3ed201e3489063fd249b8b3b1b4f049167ac405a352edb')
version('4.0', sha256='09a99c9c86666449188fbb211cb1e9fbdb5108ab56f0d09322cd0ae50e926171')
version('3.3', sha256='0cb0b9a9280edc42ebed94708541ec86b4f48779e722171e45227eab8a88a5bd')
version('3.0', sha256='7bf8e3ae7cc77802ae300277e85d925d4c0611a9b7dad5c5601e0d2cbe14a506')
- version('2.3', sha256='f901dad6bb70a6875a85da75bcbb42afffdcdf4ef221909733826bcb012d7c3d')
- version('1.0', sha256='f8927228754fdfb21dbf08b9e67c5f97e06764c4adf327a4126eed84b1508f3d')
+ version('2.3', sha256='f901dad6bb70a6875a85da75bcbb42afffdcdf4ef221909733826bcb012d7c3d')
+ version('1.0', sha256='f8927228754fdfb21dbf08b9e67c5f97e06764c4adf327a4126eed84b1508f3d')
version('0.9.7', sha256='46e150998723fd1937da598f47f49fe47e40c1f57ec594436c6ef1e0145b44dc')
depends_on('r@3.0.0:', type=('build', 'run'))
- depends_on('curl')
+ depends_on('curl', when='@4.3:')
+ depends_on('curl@:7.63', when='@:4.0')
diff --git a/var/spack/repos/builtin/packages/r-philentropy/package.py b/var/spack/repos/builtin/packages/r-philentropy/package.py
new file mode 100644
index 0000000000..2814ebc676
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-philentropy/package.py
@@ -0,0 +1,28 @@
+# 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 RPhilentropy(RPackage):
+ """Computes 46 optimized distance and similarity measures for comparing
+ probability functions (Drost (2018) <doi:10.21105/joss.00765>). These
+ comparisons between probability functions have their foundations in a broad
+ range of scientific disciplines from mathematics to ecology. The aim of
+ this package is to provide a core framework for clustering, classification,
+ statistical inference, goodness-of-fit, non-parametric statistics,
+ information theory, and machine learning tasks that are based on comparing
+ univariate or multivariate probability functions."""
+
+ homepage = "https://github.com/HajkD/philentropy"
+ url = "https://cloud.r-project.org/src/contrib/philentropy_0.4.0.tar.gz"
+ list_url = "https://cloud.r-project.org/src/contrib/Archive/philentropy"
+
+ version('0.4.0', sha256='bfd30bf5635aab6a82716299a87d44cf96c7ab7f4ee069843869bcc85c357127')
+
+ depends_on('r@3.1.2:', type=('build', 'run'))
+ depends_on('r-rcpp', type=('build', 'run'))
+ depends_on('r-dplyr', type=('build', 'run'))
+ depends_on('r-kernsmooth', type=('build', 'run'))