From 13f1781beafbd5989d855568eea2bca8e163d23d Mon Sep 17 00:00:00 2001 From: lingnanyuan <1297162327@qq.com> Date: Thu, 2 Nov 2017 15:21:32 -0500 Subject: Add package r-reportingtools and update url for its dependencies. (#6071) * r-reportingtools: Create new package. * r-go-db: Update url. * r-gseabase: Update url. * r-pfam-db: Update url. --- .../repos/builtin/packages/r-go-db/package.py | 3 +- .../repos/builtin/packages/r-gseabase/package.py | 4 +- .../repos/builtin/packages/r-pfam-db/package.py | 2 +- .../builtin/packages/r-reportingtools/package.py | 67 ++++++++++++++++++++++ 4 files changed, 71 insertions(+), 5 deletions(-) create mode 100644 var/spack/repos/builtin/packages/r-reportingtools/package.py diff --git a/var/spack/repos/builtin/packages/r-go-db/package.py b/var/spack/repos/builtin/packages/r-go-db/package.py index 62ecc68a48..895f675c03 100644 --- a/var/spack/repos/builtin/packages/r-go-db/package.py +++ b/var/spack/repos/builtin/packages/r-go-db/package.py @@ -30,8 +30,7 @@ class RGoDb(RPackage): Ontology assembled using data from GO.""" homepage = "https://www.bioconductor.org/packages/GO.db/" - url = "https://www.bioconductor.org/packages/release/data/annotation/src/contrib/GO.db_3.4.1.tar.gz" - list_url = homepage + url = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/GO.db_3.4.1.tar.gz" version('3.4.1', 'e16ee8921d8adc1ed3cbac2a3e35e386') depends_on('r-annotationdbi', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gseabase/package.py b/var/spack/repos/builtin/packages/r-gseabase/package.py index 6f8c7d8a91..45587d39d3 100644 --- a/var/spack/repos/builtin/packages/r-gseabase/package.py +++ b/var/spack/repos/builtin/packages/r-gseabase/package.py @@ -30,9 +30,9 @@ class RGseabase(RPackage): Set Enrichment Analysis (GSEA).""" homepage = "https://www.bioconductor.org/packages/GSEABase/" - url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/GSEABase_1.38.2.tar.gz" + url = "https://git.bioconductor.org/packages/GSEABase" - version('1.38.2', '027bdf1c9811f4991f3d11075ca40226') + version('1.38.2', git='https://git.bioconductor.org/packages/GSEABase', commit='84c9f10c316163118ca990900a7a67555b96e75b') depends_on('r@3.4.0:3.4.9', when='@1.38.2') depends_on('r-biocgenerics', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pfam-db/package.py b/var/spack/repos/builtin/packages/r-pfam-db/package.py index dd413e5632..5b9c443b54 100644 --- a/var/spack/repos/builtin/packages/r-pfam-db/package.py +++ b/var/spack/repos/builtin/packages/r-pfam-db/package.py @@ -30,7 +30,7 @@ class RPfamDb(RPackage): public repositories.""" homepage = "https://www.bioconductor.org/packages/PFAM.db/" - url = "https://www.bioconductor.org/packages/release/data/annotation/src/contrib/PFAM.db_3.4.1.tar.gz" + url = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/PFAM.db_3.4.1.tar.gz" version('3.4.1', '65ed35887ecc44f5ac9f9c8563e03f44') diff --git a/var/spack/repos/builtin/packages/r-reportingtools/package.py b/var/spack/repos/builtin/packages/r-reportingtools/package.py new file mode 100644 index 0000000000..3a1b5484d8 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-reportingtools/package.py @@ -0,0 +1,67 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RReportingtools(RPackage): + """The ReportingTools software package enables users to easily + display reports of analysis results generated from sources such + as microarray and sequencing data. The package allows users to + create HTML pages that may be viewed on a web browser such as + Safari, or in other formats readable by programs such as Excel. + Users can generate tables with sortable and filterable columns, + make and display plots, and link table entries to other data + sources such as NCBI or larger plots within the HTML page. Using + the package, users can also produce a table of contents page to + link various reports together for a particular project that can + be viewed in a web browser. For more examples, please visit our + site: http:// research-pub.gene.com/ReportingTools.""" + + homepage = "https://bioconductor.org/packages/ReportingTools/" + url = "https://git.bioconductor.org/packages/ReportingTools" + + version('2.16.0', git='https://git.bioconductor.org/packages/ReportingTools', commit='b1aa0ea302da7f2993ce8087b1d09c11ddf03663') + + depends_on('r@3.4.0:3.4.9', when='@2.16.0') + depends_on('r-knitr', type=('build', 'run')) + depends_on('r-biobase', type=('build', 'run')) + depends_on('r-hwriter', type=('build', 'run')) + depends_on('r-category', type=('build', 'run')) + depends_on('r-gostats', type=('build', 'run')) + depends_on('r-limma', type=('build', 'run')) + depends_on('r-limma', type=('build', 'run')) + depends_on('r-lattice', type=('build', 'run')) + depends_on('r-annotationdbi', type=('build', 'run')) + depends_on('r-edger', type=('build', 'run')) + depends_on('r-annotate', type=('build', 'run')) + depends_on('r-pfam-db', type=('build', 'run')) + depends_on('r-gseabase', type=('build', 'run')) + depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-xml', type=('build', 'run')) + depends_on('r-utils', type=('build', 'run')) + depends_on('r-deseq2', type=('build', 'run')) + depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-ggbio', type=('build', 'run')) + depends_on('r-iranges', type=('build', 'run')) -- cgit v1.2.3-70-g09d2