From db4e35b6895722fa5d015cfdf35b50f4e3735397 Mon Sep 17 00:00:00 2001 From: Li Jianfeng Date: Fri, 23 Jun 2017 22:11:15 +0800 Subject: [PATCH] Cancel windows install step --- .gitignore | 1 + ChangeLog | 4 +++ DESCRIPTION | 5 ++-- R/install.R | 8 ++--- inst/extdata/github.toml | 60 +------------------------------------ inst/extdata/nongithub.toml | 54 +++------------------------------ 6 files changed, 17 insertions(+), 115 deletions(-) diff --git a/.gitignore b/.gitignore index 7cdbb43..5aa1f35 100644 --- a/.gitignore +++ b/.gitignore @@ -25,3 +25,4 @@ vignettes/*.pdf *.knit.md inst/extdata/softwares_db_demo.yaml .Rproj.user +inst/doc diff --git a/ChangeLog b/ChangeLog index b193364..58ddbec 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,7 @@ +2017-06-23 Li Jianfeng + + * Cancel windows install step (Download still work) + 2017-06-22 Li Jianfeng * Use v0.3.0 configr: glue parse be supported diff --git a/DESCRIPTION b/DESCRIPTION index 9d33ccb..908b9ef 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: BioInstaller Title: Lightweight Biology Software Installer -Version: 0.1.1.5 +Version: 0.1.2 Authors@R: person("Jianfeng", "Li", email = "lee_jianfeng@sjtu.edu.cn", role = c("aut", "cre")) -Description: +Description: Can be used to install and download massive bioinformatics analysis softwares and databases, such as NGS reads mapping tools with its required databases. Depends: R (>= 3.3.0) @@ -25,3 +25,4 @@ RoxygenNote: 6.0.1 Suggests: knitr, rmarkdown, testthat +VignetteBuilder: knitr diff --git a/R/install.R b/R/install.R index f50a515..426dac4 100644 --- a/R/install.R +++ b/R/install.R @@ -217,8 +217,8 @@ install.github <- function(name = "", download.dir = NULL, destdir = NULL, versi args.all <- as.list(match.call()) args.all$version <- version - args.all$destdir <- destdir - args.all$download.dir <- download.dir + args.all$destdir <- normalizePath(destdir, "/", FALSE) + args.all$download.dir <- normalizePath(download.dir, "/", FALSE) args.all$os.version <- get.os() args.all <- args.all[names(args.all) != ""] config <- configr::parse.extra(config = config, extra.list = args.all) @@ -377,8 +377,8 @@ install.nongithub <- function(name = "", download.dir = NULL, destdir = NULL, ve args.all <- as.list(match.call()) args.all$version <- version - args.all$destdir <- destdir - args.all$download.dir <- download.dir + args.all$destdir <- normalizePath(destdir, "/", FALSE) + args.all$download.dir <- normalizePath(download.dir, "/", FALSE) args.all$os.version <- get.os() args.all <- args.all[names(args.all) != ""] args.all <- configr::config.list.merge(args.all, extra.list) diff --git a/inst/extdata/github.toml b/inst/extdata/github.toml index 94f8668..fa53718 100644 --- a/inst/extdata/github.toml +++ b/inst/extdata/github.toml @@ -29,7 +29,6 @@ bin_dir = ["{{destdir}}/bin"] [bwa.install] linux = "make && mkdir -p {{destdir}}/bin; cp {{download.dir}}/bwa {{destdir}}/bin" mac = "make && mkdir -p {{destdir}}/bin; cp {{download.dir}}/bwa {{destdir}}/bin" -windows = "make && md {{destdir}}\bin; cp {{download.dir}}\bwa {{destdir}}\bin" [star] github_url = "https://github.com/alexdobin/STAR" @@ -49,7 +48,6 @@ mac = "{{destdir}}/bin" [star.install] linux = "make && mkdir -p {{destdir}}/bin; cp {{download.dir}}/bin/Linux_x86_64/* {{destdir}}/bin" mac = "make && mkdir -p {{destdir}}/bin; cp {{download.dir}}/bin/MacOSX_x86_64/* {{destdir}}/bin" -windows = "make && mkdir -p {{destdir}}/bin; cp {{download.dir}}/bin/Linux_x86_64/* {{destdir}}/bin" [samtools_old] github_url = "https://github.com/samtools/samtools" @@ -71,7 +69,6 @@ bin_dir = ["{{destdir}}/bin"] [samtools_old.install] linux = "make && mkdir -p {{destdir}}/bin; cp samtools {{destdir}}/bin/samtools_{{version}}" mac = "make && mkdir -p {{destdir}}/bin; cp samtools {{destdir}}/bin/samtools_{{version}}" -windows = "make && mkdir -p {{destdir}}/bin; cp samtools {{destdir}}/bin/samtools_{{version}}" [bcftools] github_url = "https://github.com/samtools/bcftools" @@ -91,7 +88,6 @@ bin_dir = ["{{destdir}}/bin"] [bcftools.install] linux = "sed -i 's;HTSDIR = ../htslib;HTSDIR = {{htslib:source.dir}};' Makefile; make; mkdir -p {{destdir}}/bin; cp bcftools {{destdir}}/bin" mac = "sed -i 's;HTSDIR = ../htslib;HTSDIR = {{htslib:source.dir}};' Makefile; make; mkdir -p {{destdir}}/bin; cp bcftools {{destdir}}/bin" -windows = "sed -i 's;HTSDIR = ../htslib;HTSDIR = {{htslib:source.dir}};' Makefile; make; mkdir -p {{destdir}}/bin; cp bcftools {{destdir}}/bin" [bowtie] github_url = "https://github.com/BenLangmead/bowtie" @@ -107,7 +103,7 @@ bin_dir = ["{{destdir}}/bin"] [bowtie.install] linux = "make && mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'` fn=`echo $fn | tr ' ' '\n' |grep -v '.h' | grep -v '.cpp'|sort -u`;cp $fn {{destdir}}/bin" mac = "make && mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'` fn=`echo $fn | tr ' ' '\n' |grep -v '.h' | grep -v '.cpp'|sort -u`;cp $fn {{destdir}}/bin" -windows = "make && mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'` fn=`echo $fn | tr ' ' '\n' |grep -v '.h' | grep -v '.cpp'|sort -u`;cp $fn {{destdir}}/bin" + [bowtie2] github_url = "https://github.com/BenLangmead/bowtie2" @@ -123,7 +119,6 @@ bin_dir = ["{{destdir}}/bin"] [bowtie2.install] linux = "make && mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'` fn=`echo $fn | tr ' ' '\n' |grep -v '.h' | grep -v '.cpp'|sort -u`;cp $fn {{destdir}}/bin" mac = "make && mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'` fn=`echo $fn | tr ' ' '\n' |grep -v '.h' | grep -v '.cpp'|sort -u`;cp $fn {{destdir}}/bin" -windows = "make && mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'` fn=`echo $fn | tr ' ' '\n' |grep -v '.h' | grep -v '.cpp'|sort -u`;cp $fn {{destdir}}/bin" [tophat2] github_url = "https://github.com/infphilo/tophat" @@ -139,7 +134,6 @@ bin_dir = ["{{destdir}}/bin"] [tophat2.install] linux = "sh autogen.sh && ./configure --prefix={{destdir}} && make && make install" mac = "sh autogen.sh && ./configure --prefix={{destdir}} && make && make install" -windows = "sh autogen.sh && ./configure --prefix={{destdir}} && make && make install" [varscan2] github_url = "https://github.com/Miachol/varscan" @@ -155,7 +149,6 @@ bin_dir = ["{{destdir}}/bin"] [varscan2.install] linux = "mkdir -p {{destdir}}/bin; cp `ls *.jar` {{destdir}}/bin" mac = "mkdir -p {{destdir}}/bin; cp `ls *.jar` {{destdir}}/bin" -windows = "mkdir -p {{destdir}}/bin; cp `ls *.jar` {{destdir}}/bin" [picard] github_url = "https://github.com/broadinstitute/picard" @@ -171,7 +164,6 @@ bin_dir = ["{{destdir}}/bin"] [picard.install] linux = "{{download.dir}}/gradlew shadowJar && mkdir {{destdir}}/bin; cp {{download.dir}}/build/libs/* {{destdir}}/bin" mac = "{{download.dir}}/gradlew shadowJar && mkdir {{destdir}}/bin; cp {{download.dir}}/build/libs/* {{destdir}}/bin" -windows = "{{download.dir}}/gradlew shadowJar && mkdir {{destdir}}/bin; cp {{download.dir}}/build/libs/* {{destdir}}/bin" [vcftools] github_url = "https://github.com/vcftools/vcftools" @@ -187,7 +179,6 @@ bin_dir = ["{{destdir}}/bin"] [vcftools.install] linux = "./autogen.sh && ./configure --prefix={{destdir}} && make && make install" mac = "./autogen.sh && ./configure --prefix={{destdir}} && make && make install" -windows = "./autogen.sh && ./configure --prefix={{destdir}} && make && make install" [pindel] github_url = "https://github.com/genome/pindel" @@ -207,7 +198,6 @@ bin_dir = ["{{destdir}}/bin"] [pindel.install] linux = "./INSTALL {{htslib:source.dir}}; mkdir {{destdir}}/bin; cp `ls -F {{download.dir}} |grep '*' | grep -v 'INSTALL'` {{destdir}}/bin" mac = "./INSTALL {{htslib:source.dir}}; mkdir {{destdir}}/bin; cp `ls -F {{download.dir}} |grep '*' | grep -v 'INSTALL'` {{destdir}}/bin" -windows = "./INSTALL {{htslib:source.dir}}; mkdir {{destdir}}/bin; cp `ls -F {{download.dir}} |grep '*' | grep -v 'INSTALL'` {{destdir}}/bin" [lofreq] github_url = "https://github.com/Miachol/lofreq" @@ -223,7 +213,6 @@ bin_dir = ["{{destdir}}/bin/"] [lofreq.install] linux = "mkdir -p {{destdir}}/bin; bindir={{download.dir}}/lofreq_star-2.1.2_linux-x86-64/bin; files=`ls $bindir/*`; cd $bindir; chmod +x $files; cp $files {{destdir}}/bin" mac = "mkdir -p {{destdir}}/bin; bindir={{download.dir}}/lofreq_star-2.1.2_linux-x86-64/bin; files=`ls $bindir/*`; cd $bindir; chmod +x $files; cp $files {{destdir}}/bin" -windows = "mkdir -p {{destdir}}/bin; bindir={{download.dir}}/lofreq_star-2.1.2_linux-x86-64/bin; files=`ls $bindir/*`; cd $bindir; chmod +x $files; cp $files {{destdir}}/bin" [hisat2] github_url = "https://github.com/infphilo/hisat2" @@ -239,7 +228,6 @@ bin_dir = ["{{download.dir}}"] [hisat2.install] linux = "make && mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'` fn=`echo $fn | tr ' ' '\n' |grep -v '.h' | grep -v '.cpp'|sort -u`;cp $fn {{destdir}}/bin" mac = "make && mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'` fn=`echo $fn | tr ' ' '\n' |grep -v '.h' | grep -v '.cpp'|sort -u`;cp $fn {{destdir}}/bin" -windows = "make && mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'` fn=`echo $fn | tr ' ' '\n' |grep -v '.h' | grep -v '.cpp'|sort -u`;cp $fn {{destdir}}/bin" [freebayes] github_url = "https://github.com/ekg/freebayes" @@ -258,7 +246,6 @@ bin_dir = ["{{destdir}}/bin"] [freebayes.install] linux = ["make", "mkdir -p {{destdir}}/bin; cp {{download.dir}}/bin/* {{destdir}}/bin"] mac = ["make", "mkdir -p {{destdir}}/bin; cp {{download.dir}}/bin/* {{destdir}}/bin"] -windows = ["make", "mkdir -p {{destdir}}/bin; cp {{download.dir}}/bin/* {{destdir}}/bin"] [macs] github_url = "https://github.com/taoliu/MACS/" @@ -274,12 +261,10 @@ bin_dir = ["{{download.dir}}/bin"] [macs.before_install] linux = "pip install cython" mac = "pip install cython" -windows = "pip install cython" [macs.install] linux = "if [ -f setup_w_cython.py ]; then python setup_w_cython.py install; else python setup.py install ;fi" mac = "if [ -f setup_w_cython.py ]; then python setup_w_cython.py install; else python setup.py install ;fi" -windows = "if [ -f setup_w_cython.py ]; then python setup_w_cython.py install; else python setup.py install ;fi" [bedtools] github_url = "https://github.com/arq5x/bedtools2" @@ -295,7 +280,6 @@ bin_dir = ["{{destdir}}/bin"] [bedtools.install] linux = ["make", "mkdir -p {{destdir}}/bin; cp {{download.dir}}/bin/* {{destdir}}/bin"] mac = ["make", "mkdir -p {{destdir}}/bin; cp {{download.dir}}/bin/* {{destdir}}/bin"] -windows = ["make", "mkdir -p {{destdir}}/bin; cp {{download.dir}}/bin/* {{destdir}}/bin"] [sparsehash] github_url = "https://github.com/sparsehash/sparsehash" @@ -311,7 +295,6 @@ bin_dir = ["{{destdir}}/bin"] [sparsehash.install] linux = "sh autogen.sh && ./configure --prefix={{destdir}} && make && make install" mac = "sh autogen.sh && ./configure --prefix={{destdir}} && make && make install" -windows = "sh autogen.sh && ./configure --prefix={{destdir}} && make && make install" [abyss] github_url = "https://github.com/bcgsc/abyss" @@ -331,7 +314,6 @@ bin_dir = ["{{destdir}}/bin"] [abyss.install] linux = "sh autogen.sh && ./configure --enable-maxk=96 --prefix={{destdir}} --with-mpi --with-sqlite={{sqlite:install.dir}} CPPFLAGS=-I{{sparsehash:install.dir}}/include && make" mac = "sh autogen.sh && ./configure --enable-maxk=96 --prefix={{destdir}} --with-mpi --with-sqlite={{sqlite:install.dir}} CPPFLAGS=-I{{sparsehash:install.dir}}/include && make" -windows = "sh autogen.sh && ./configure --enable-maxk=96 --prefix={{destdir}} --with-mpi --with-sqlite={{sqlite:install.dir}} CPPFLAGS=-I{{sparsehash:install.dir}}/include && make" [bamtools] github_url = "https://github.com/pezmaster31/bamtools" @@ -347,12 +329,10 @@ bin_dir = ["{{destdir}}/bin"] [bamtools.before_install] linux = "mkdir build; cd build && cmake .." mac = "mkdir build; cd build && cmake .." -windows = "md build; cd build && cmake .." [bamtools.install] linux = ["cd build && make", "mkdir -p {{destdir}}/bin; cp {{download.dir}}/bin/* {{destdir}}/bin"] mac = ["cd build && make", "mkdir -p {{destdir}}/bin; cp {{download.dir}}/bin/* {{destdir}}/bin"] -windows = ["cd build && make", "mkdir -p {{destdir}}/bin; cp {{download.dir}}/bin/* {{destdir}}/bin"] [breakdancer] github_url = "https://github.com/genome/breakdancer" @@ -369,12 +349,10 @@ bin_dir = ["{{download.dir}}/build/bin"] [breakdancer.before_install] linux = ["mkdir build; cd build && cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local"] mac = ["mkdir build; cd build && cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local"] -windows = ["mkdir build; cd build && cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local"] [breakdancer.install] linux = "cd build && make && make install" mac = "cd build && make && make install" -windows = "cd build && make && make install" [htseq] github_url = "https://github.com/simon-anders/htseq" @@ -390,12 +368,10 @@ bin_dir = ["{{download.dir}}/scripts"] [htseq.before_install] linux = ["pip install numpy", "pip install Cython", "pip install 'matplotlib>=1.4'"] mac = ["pip install numpy", "pip install Cython", "pip install 'matplotlib>=1.4'"] -windows = ["pip install numpy", "pip install Cython", "pip install 'matplotlib>=1.4'"] [htseq.install] linux = "pip install ." mac = "pip install ." -windows = "pip install ." [seqtk] github_url = "https://github.com/ndaniel/seqtk" @@ -411,7 +387,6 @@ bin_dir = ["{{destdir}}/bin"] [seqtk.install] linux = "make && mkdir -p {{destdir}}/bin; cp {{download.dir}}/seqtk {{destdir}}/bin" mac = "make && mkdir -p {{destdir}}/bin; cp {{download.dir}}/seqtk {{destdir}}/bin" -windows = "make && mkdir -p {{destdir}}/bin; cp {{download.dir}}/seqtk {{destdir}}/bin" [delly] github_url = "https://github.com/dellytools/delly" @@ -429,7 +404,6 @@ bin_dir = ["{{destdir}}/bin"] [delly.install] linux = "make all; mkdir -p {{destdir}}/bin; fn=`ls -F src|grep '*' | tr -d '*'` fn=`echo $fn | tr ' ' '\n' |grep -v '.h' | grep -v '.cpp'|sort -u`;cd src; cp $fn {{destdir}}/bin" mac = "make all; mkdir -p {{destdir}}/bin; fn=`ls -F src|grep '*' | tr -d '*'` fn=`echo $fn | tr ' ' '\n' |grep -v '.h' | grep -v '.cpp'|sort -u`;cd src; cp $fn {{destdir}}/bin" -windows = "make all; mkdir -p {{destdir}}/bin; fn=`ls -F src|grep '*' | tr -d '*'` fn=`echo $fn | tr ' ' '\n' |grep -v '.h' | grep -v '.cpp'|sort -u`;cd src; cp $fn {{destdir}}/bin" [tmap] github_url = "git://github.com/iontorrent/TMAP" @@ -446,15 +420,12 @@ bin_dir = ["{{destdir}}/bin"] [tmap.before_install] linux = ["git submodule init", " git submodule update"] mac = ["git submodule init", " git submodule update"] -windows = ["git submodule init", " git submodule update"] [tmap.install] linux = ["git checkout -b {{version}} tmap.{{version}}", "git submodule update", "sh autogen.sh && ./configure --prefix={{destdir}} && make", "make install"] mac = ["git checkout -b {{version}} tmap.{{version}}", "git submodule update", "sh autogen.sh && ./configure --prefix={{destdir}} && make", "make install"] -windows = ["git checkout -b {{version}} tmap.{{version}}", "git submodule update", - "sh autogen.sh && ./configure --prefix={{destdir}} && make", "make install"] [somaticsniper] github_url = "https://github.com/genome/somatic-sniper" @@ -470,7 +441,6 @@ bin_dir = ["{{destdir}}/bin"] [somaticsniper.install] linux = "mkdir build; cd build && cmake ../ && make deps && make -j && make test; mkdir -p {{destdir}}/bin; cp {{download.dir}}/build/bin/* {{destdir}}/bin" mac = "mkdir build; cd build && cmake ../ && make deps && make -j && make test; mkdir -p {{destdir}}/bin; cp {{download.dir}}/build/bin/* {{destdir}}/bin" -windows = "mkdir build; cd build && cmake ../ && make deps && make -j && make test; mkdir -p {{destdir}}/bin; cp {{download.dir}}/build/bin/* {{destdir}}/bin" [bamutil] github_url = "https://github.com/statgen/bamUtil" @@ -486,7 +456,6 @@ bin_dir = ["{{destdir}}/bin"] [bamutil.install] linux = "make cloneLib && make && make install INSTALLDIR={{destdir}}" mac = "make cloneLib && make && make install INSTALLDIR={{destdir}}" -windows = "make cloneLib && make && make install INSTALLDIR={{destdir}}" [vcflib] github_url = "https://github.com/vcflib/vcflib" @@ -504,7 +473,6 @@ bin_dir = ["{{destdir}}/bin"] [vcflib.install] linux = ["make", "mkdir -p {{destdir}}/bin; cp {{download.dir}}/bin/* {{destdir}}/bin"] mac = ["make", "mkdir -p {{destdir}}/bin; cp {{download.dir}}/bin/* {{destdir}}/bin"] -windows = ["make", "mkdir -p {{destdir}}/bin; cp {{download.dir}}/bin/* {{destdir}}/bin"] [jvarkit] github_url = "https://github.com/lindenb/jvarkit/" @@ -520,7 +488,6 @@ bin_dir = ["{{download.dir}}/dist"] [jvarkit.install] linux = ["make all", "mkdir -p {{destdir}}/bin; cp {{download.dir}}/dist/* {{destdir}}/bin"] mac = ["make all", "mkdir -p {{destdir}}/bin; cp {{download.dir}}/dist/* {{destdir}}/bin"] -windows = ["make all", "mkdir -p {{destdir}}/bin; cp {{download.dir}}/dist/* {{destdir}}/bin"] [fastx_toolkit] github_url = "https://github.com/agordon/fastx_toolkit" @@ -540,7 +507,6 @@ bin_dir = ["{{destdir}}/bin"] [fastx_toolkit.install] linux = "export PKG_CONFIG_PATH=PKG_CONFIG_PATH:{{libgtextutils:source.dir}}; ./reconf && ./configure --prefix={{destdir}} && make && make install" mac = "export PKG_CONFIG_PATH=PKG_CONFIG_PATH:{{libgtextutils:source.dir}}; ./reconf && ./configure --prefix={{destdir}} && make && make install" -windows = "export PKG_CONFIG_PATH=PKG_CONFIG_PATH:{{libgtextutils:source.dir}}; ./reconf && ./configure --prefix={{destdir}} && make && make install" [libgtextutils] github_url = "https://github.com/agordon/libgtextutils" @@ -556,7 +522,6 @@ bin_dir = ["{{destdir}}/lib"] [libgtextutils.install] linux = "./reconf && ./configure --prefix={{destdir}} && make && make install" mac = "./reconf && ./configure --prefix={{destdir}} && make && make install" -windows = "./reconf && ./configure --prefix={{destdir}} && make && mak install" [trinityrnaseq] github_url = "https://github.com/trinityrnaseq/trinityrnaseq" @@ -572,7 +537,6 @@ bin_dir = ["{{destdir}}/bin"] [trinityrnaseq.install] linux = "make && mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'` fn=`echo $fn | tr ' ' '\n' |grep -v '.h' | grep -v '.cpp'|sort -u`;cp $fn {{destdir}}/bin" mac = "make && mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'` fn=`echo $fn | tr ' ' '\n' |grep -v '.h' | grep -v '.cpp'|sort -u`;cp $fn {{destdir}}/bin" -windows = "make && mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'` fn=`echo $fn | tr ' ' '\n' |grep -v '.h' | grep -v '.cpp'|sort -u`;cp $fn {{destdir}}/bin" [oases] github_url = "https://github.com/dzerbino/oases" @@ -590,7 +554,6 @@ bin_dir = ["{{destdir}}/bin"] [oases.install] linux = "make && mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'` fn=`echo $fn | tr ' ' '\n' |grep -v '.h' | grep -v '.cpp'|sort -u`;cp $fn {{destdir}}/bin" mac = "make && mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'` fn=`echo $fn | tr ' ' '\n' |grep -v '.h' | grep -v '.cpp'|sort -u`;cp $fn {{destdir}}/bin" -windows = "make && mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'` fn=`echo $fn | tr ' ' '\n' |grep -v '.h' | grep -v '.cpp'|sort -u`;cp $fn {{destdir}}/bin" [rum] github_url = "https://github.com/itmat/rum" @@ -606,7 +569,6 @@ bin_dir = ["{{destdir}}/bin"] [rum.install] linux = ["cpan -i autodie", "cpan -i Log::Log4perl", "perl Makefile.PL INSTALL_BASE={{destdir}} && make", "make install"] mac = ["cpan -i autodie", "cpan -i Log::Log4perl", "perl Makefile.PL INSTALL_BASE={{destdir}} && make", "make install"] -windows = ["cpan -i autodie", "cpan -i Log::Log4perl", "perl Makefile.PL INSTALL_BASE={{destdir}} && make", "make install"] [igraph] github_url = "https://github.com/igraph/igraph" @@ -622,7 +584,6 @@ bin_dir = ["{{destdir}}/lib"] [igraph.install] linux = "sh bootstrap.sh;./configure --prefix={{destdir}} && make && make install" mac = "sh bootstrap.sh;./configure --prefix={{destdir}} && make && make install" -windows = "sh bootstrap.sh;./configure --prefix={{destdir}} && make && make install" [pxz] github_url = "https://github.com/jnovy/pxz" @@ -638,7 +599,6 @@ bin_dir = ["{{destdir}}/bin"] [pxz.install] linux = "make && mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'` fn=`echo $fn | tr ' ' '\n' |grep -v '.h' | grep -v '.cpp'|sort -u`;cp $fn {{destdir}}/bin" mac = "make && mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'` fn=`echo $fn | tr ' ' '\n' |grep -v '.h' | grep -v '.cpp'|sort -u`;cp $fn {{destdir}}/bin" -windows = "make && mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'` fn=`echo $fn | tr ' ' '\n' |grep -v '.h' | grep -v '.cpp'|sort -u`;cp $fn {{destdir}}/bin" [cnvkit] github_url = "https://github.com/etal/cnvkit" @@ -654,7 +614,6 @@ bin_dir = ["{{download.dir}}"] [cnvkit.install] linux = "pip install ." mac = "pip install ." -windows = "pip install ." [speedseq] github_url = "https://github.com/hall-lab/speedseq" @@ -675,7 +634,6 @@ bin_dir = ["{{destdir}}/bin/speedseq"] [speedseq.install] linux = "source ~/.bashrc; make; mkdir {{destdir}}/bin/speedseq; fn=`ls -F bin|grep '*' | tr -d '*'` fn=`echo $fn | tr ' ' '\n' |grep -v '.h' | grep -v '.cpp'|sort -u`;cd bin; cp $fn {{destdir}}/bin/speedseq" mac = "source ~/.bashrc; make; mkdir {{destdir}}/bin/speedseq; fn=`ls -F bin|grep '*' | tr -d '*'` fn=`echo $fn | tr ' ' '\n' |grep -v '.h' | grep -v '.cpp'|sort -u`;cd bin; cp $fn {{destdir}}/bin/speedseq" -windows = "source ~/.bashrc; make; mkdir {{destdir}}/bin/speedseq; fn=`ls -F bin|grep '*' | tr -d '*'` fn=`echo $fn | tr ' ' '\n' |grep -v '.h' | grep -v '.cpp'|sort -u`;cd bin; cp $fn {{destdir}}/bin/speedseq" [cnvnator] @@ -696,7 +654,6 @@ bin_dir = ["{{destdir}}/bin"] [cnvnator.install] linux = "source ~/.bashrc; ln -s {{cnvnator_samtools:source.dir}} ./samtools; make; mkdir -p {{destdir}}/bin; cp cnvnator cnvnator2VCF.pl {{destdir}}/bin" mac = "source ~/.bashrc; ln -s {{cnvnator_samtools:source.dir}} ./samtools; make; mkdir -p {{destdir}}/bin; cp cnvnator cnvnator2VCF.pl {{destdir}}/bin" -windows = "source ~/.bashrc; ln -s {{cnvnator_samtools:source.dir}} ./samtools; make; mkdir -p {{destdir}}/bin; cp cnvnator cnvnator2VCF.pl {{destdir}}/bin" [asap] github_url = "https://github.com/DeplanckeLab/ASAP" @@ -709,7 +666,6 @@ no.need.download = true linux = """#R#source('http://bioconductor.org/biocLite.R'); biocLite(c('edgeR', 'cqn')); library(devtools);install_github('zjdaye/MDSeq', ref = '{{version}}')#R#""" mac = "#R#library(devtools);install_github('zjdaye/MDSeq', ref = '{{version}}')#R#" -windows = "#R#library(devtools);install_github('zjdaye/MDSeq', ref = '{{version}}')#R#" [sclvm] github_url = "https://github.com/PMBio/scLVM" @@ -719,7 +675,6 @@ version_newest_fixed = "master" [sclvm.install] linux = 'pip install .' mac = 'pip install .' -windows = 'pip install .' [fsclvm] github_url = "https://github.com/PMBio/f-scLVM" @@ -727,7 +682,6 @@ github_url = "https://github.com/PMBio/f-scLVM" [fsclvm.install] linux = 'pip install .' mac = 'pip install .' -windows = 'pip install .' [bearscc] github_url = "https://github.com/Miachol/bearscc" @@ -737,7 +691,6 @@ make_dir = ["./package"] [bearscc.install] linux = "#R#install.packages('./', repos=NULL, type='source')#R#" mac = "#R#install.packages('./', repos=NULL, type='source')#R#" -windows = "#R#install.packages('./', repos=NULL, type='source')#R#" [singlesplice] github_url = "https://github.com/jw156605/SingleSplice" @@ -747,7 +700,6 @@ bin_dir = "./diffsplice/bin" [singlesplice.install] linux = 'make' mac = 'make' -windows = 'make' [isop] github_url = "https://github.com/nghiavtr/ISOP" @@ -756,7 +708,6 @@ no.need.download = true [isop.install] linux = "#R#library(devtools);install_github('nghiavtr/ISOP', ref='{{version}}')#R#" mac = "#R#library(devtools);install_github('nghiavtr/ISOP', ref='{{version}}')#R#" -windows = "#R#library(devtools);install_github('nghiavtr/ISOP', ref='{{version}}')#R#" [brie] github_url = "https://github.com/huangyh09/brie" @@ -764,7 +715,6 @@ github_url = "https://github.com/huangyh09/brie" [brie.install] linux = 'pip install .' mac = 'pip install .' -windows = 'pip install .' [outrigger] github_url = "https://github.com/YeoLab/outrigger" @@ -772,7 +722,6 @@ github_url = "https://github.com/YeoLab/outrigger" [outrigger.install] linux = 'pip install .' mac = 'pip install .' -windows = 'pip install .' [raceid] github_url = "https://github.com/dgrun/RaceID" @@ -785,7 +734,6 @@ version_newest_fixed = "master" [backspin.install] linux = 'pip install .' mac = 'pip install .' -windows = 'pip install .' [zifa] github_url = "https://github.com/epierson9/ZIFA" @@ -793,7 +741,6 @@ github_url = "https://github.com/epierson9/ZIFA" [zifa.install] linux = 'pip install .' mac = 'pip install .' -windows = 'pip install .' [seurat] github_url = "https://github.com/satijalab/seurat" @@ -802,7 +749,6 @@ no.need.download = true [seurat.install] linux = "#R#library(devtools);install_github('satijalab/seurat')#R#" mac = "#R#library(devtools);install_github('satijalab/seurat')#R#" -windows = "#R#library(devtools);install_github('satijalab/seurat')#R#" [rca] github_url = "https://github.com/GIS-SP-Group/RCA" @@ -811,7 +757,6 @@ no.need.download = true [rca.install] linux = "#R#library(devtools);install_github('GIS-SP-Group/RCA', ref = '{{version}}')#R#" mac = "#R#library(devtools);install_github('GIS-SP-Group/RCA', ref = '{{version}}')#R#" -windows = "#R#library(devtools);install_github('GIS-SP-Group/RCA', ref = '{{version}}')#R#" [mimosca] github_url = "https://github.com/asncd/MIMOSCA" @@ -822,7 +767,6 @@ github_url = "https://github.com/teichlab/tracer" [tracer.install] linux = 'pip install .' mac = 'pip install .' -windows = 'pip install .' [scnorm] github_url = "https://github.com/rhondabacher/SCnorm" @@ -831,7 +775,6 @@ no.need.download = true [scnorm.install] linux = "#R#library(devtools);install_github('rhondabacher/SCnorm', ref = '{{version}}')#R#" mac = "#R#library(devtools);install_github('rhondabacher/SCnorm', ref = '{{version}}')#R#" -windows = "#R#library(devtools);install_github('rhondabacher/SCnorm', ref = '{{version}}')#R#" [sleuth] github_url = "https://github.com/pachterlab/sleuth" @@ -840,4 +783,3 @@ no.need.download = true [sleuth.install] linux = "#R#source('http://bioconductor.org/biocLite.R'); biocLite('rhdf5'); library(devtools); devtools::install_github('pachterlab/sleuth', ref = '{{version}}')#R#" mac = "#R#source('http://bioconductor.org/biocLite.R'); biocLite('rhdf5'); library(devtools); devtools::install_github('pachterlab/sleuth', ref = '{{version}}')#R#" -windows = "#R#source('http://bioconductor.org/biocLite.R'); biocLite('rhdf5'); library(devtools); devtools::install_github('pachterlab/sleuth', ref = '{{version}}')#R#" diff --git a/inst/extdata/nongithub.toml b/inst/extdata/nongithub.toml index 01998f3..15b57a7 100644 --- a/inst/extdata/nongithub.toml +++ b/inst/extdata/nongithub.toml @@ -35,7 +35,6 @@ bin_dir = ["{{destdir}}/bin"] [gmap.install] linux = ["./configure --prefix={{destdir}} && make", "make install"] mac = ["sed -i s/\"## CFLAGS='-O3 -m64' .*\"/\"CFLAGS='-O3 -m64'\"/ config.site && ./configure --prefix={{destdir}} && make", "make install"] -windows = ["./configure --prefix={{destdir}} && make", "make install"] [annovar] source_url = "http://www.openbioinformatics.org/annovar/download/0wgxR2rIVP/annovar.{{version}}.tar.gz" @@ -128,6 +127,7 @@ url_all_download = false version_newest = "EdenaV3.131028" version_available = ["EdenaV3.131028", "EdenaV3.130110", "EdenaV3.121122", "Edena3dev120926_linux64", "Edena3Dev120626_linux64", "Edena3Dev120626_linux32", "Edena3Dev120615_linux64", "Edena3Dev120615_linux32", "Edena3Dev110920_linux64", "Edena3Dev110920_linux32", "Edena3Dev110815_linux64", "Edena3Dev110815_linux32", "Edena3Dev110814_linux64", "Edena3Dev110814_linux32", "Edena3Dev110705_linux64", "Edena3Dev110705_linux32", "edena2.1.1_linux32", "edena2.1.1_linux64", "edena2.1.1_windows"] + version_order_fixed = true after_failure = "echo 'fail!'" @@ -141,7 +141,6 @@ bin_dir = ["{{destdir}}/bin"] [edena.install] linux = ["make", "mkdir -p {{destdir}}/bin; cp {{download.dir}}/bin/* {{destdir}}/bin"] mac = ["make", "mkdir -p {{destdir}}/bin; cp {{download.dir}}/bin/* {{destdir}}/bin"] -windows = ["make", "mkdir -p {{destdir}}/bin; cp {{download.dir}}/bin/* {{destdir}}/bin"] [ucsc_utils] source_url = "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.{{version}}.src.tgz" @@ -161,7 +160,6 @@ bin_dir = ["{{destdir}}/bin"] [ucsc_utils.install] linux = ["make", "mkdir -p {{destdir}}/bin; cp {{download.dir}}/bin/* {{destdir}}/bin"] mac = ["make", "mkdir -p {{destdir}}/bin; cp {{download.dir}}/bin/* {{destdir}}/bin"] -windows = ["make", "mkdir -p {{destdir}}/bin; cp {{download.dir}}/bin/* {{destdir}}/bin"] [fastqc] source_url = ["http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v{{version}}.zip"] @@ -202,13 +200,10 @@ bin_dir = ["{{destdir}}/bin"] [sqlite.before_install] linux = "autoreconf -ivf" mac = "autoreconf -ivf" -windows = "autoreconf -ivf" [sqlite.install] linux = ["./configure --prefix={{destdir}} && make", "make install"] mac = ["./configure --prefix={{destdir}} && make ", "make install"] -windows = ["./configure --prefix={{destdir}} && make", "make install"] - [cesa] source_url = ["http://liulab.dfci.harvard.edu/CEAS/src/CEAS-Package-{{version}}.tar.gz"] @@ -228,7 +223,6 @@ bin_dir = ["{{download.dir}}/bin"] [cesa.install] linux = "python setup.py install" mac = "python setup.py install" -windows = "python setup.py install" [novoalign] source_url = ["http://bioinfo.rjh.com.cn/download/novocraft/download.php?filename=novocraft{{version}}.tar.gz"] @@ -249,7 +243,6 @@ bin_dir = ["{{destdir}}/bin"] [novoalign.install] linux = "mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'`;cp $fn {{destdir}}/bin" mac = "mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'`;cp $fn {{destdir}}/bin" -windows = "mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'`;cp $fn {{destdir}}/bin" [ssaha2] source_url = ["ftp://ftp.sanger.ac.uk/pub/resources/software/ssaha2/ssaha2_{{version}}.tgz"] @@ -269,7 +262,6 @@ bin_dir = ["{{destdir}}/bin"] [ssaha2.install] linux = "mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'`;cp $fn {{destdir}}/bin" mac = "mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'`;cp $fn {{destdir}}/bin" -windows = "mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'`;cp $fn {{destdir}}/bin" [gatk] source_url = ["http://bioinfo.rjh.com.cn/download/gatk/download.php?filename=gatk{{version}}.zip"] @@ -289,7 +281,6 @@ bin_dir = ["{{destdir}}/bin"] [gatk.install] linux = "mkdir -p {{destdir}}/bin; cp *.jar {{destdir}}/bin" mac = "mkdir -p {{destdir}}/bin; cp *.jar {{destdir}}/bin" -windows = "mkdir -p {{destdir}}/bin; cp *.jar {{destdir}}/bin" [mutect] source_url = ["http://bioinfo.rjh.com.cn/download/gatk/download.php?filename=mutect{{version}}.zip"] @@ -309,8 +300,6 @@ bin_dir = ["{{download.dir}}"] [mutect.install] linux = "mkdir -p {{destdir}}/bin; cp *.jar {{destdir}}/bin" mac = "mkdir -p {{destdir}}/bin; cp *.jar {{destdir}}/bin" -windows = "mkdir -p {{destdir}}/bin; cp *.jar {{destdir}}/bin" - [sratools] version_newest = "2.8.2-1" @@ -327,13 +316,12 @@ bin_dir = ["{{download.dir}}/bin"] [sratools.source_url] linux = "https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/{{version}}/sratoolkit.@>@if('{{os.version}}' == 'centos') {'{{version}}-centos_linux64'} else if ('{{os.version}}' == 'ubuntu') {'{{version}}-ubuntu64'}@<@.tar.gz" -windows = "https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/{{version}}/sratoolkit.{{version}}-win64.zip" + mac = "https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/{{version}}/sratoolkit.{{version}}-mac64.zip" [sratools.install] linux = ["mkdir -p {{destdir}}/bin; fn=`ls -F bin|grep '*' | tr -d '*'` ;cd bin;", " cp $fn {{destdir}}/bin"] mac = ["mkdir -p {{destdir}}/bin; fn=`ls -F bin|grep '*' | tr -d '*'` ;cd bin;", " cp $fn {{destdir}}/bin"] -windows = ["mkdir -p {{destdir}}/bin; fn=`ls -F bin|grep '*' | tr -d '*'` ;cd bin;", " cp $fn {{destdir}}/bin"] [fusioncatcher] source_url = ["https://sourceforge.net/projects/fusioncatcher/files/fusioncatcher_{{version}}.zip", @@ -358,7 +346,6 @@ bin_dir = ["{{destdir}}/bin/fusioncatcher"] [fusioncatcher.install] linux = ["mkdir {{destdir}}/bin/fusioncatcher; chmod +x bin/*; ", "cp bin/* {{destdir}}/bin/fusioncatcher"] mac = ["mkdir {{destdir}}/bin/fusioncatcher; chmod +x bin/*; ", "cp bin/* {{destdir}}/bin/fusioncatcher"] -windows = ["mkdir {{destdir}}/bin/fusioncatcher; chmod +x bin/*; ", "cp bin/* {{destdir}}/bin/fusioncatcher"] [pigz] source_url = "http://cdn-fastly.deb.debian.org/debian/pool/main/p/pigz/pigz_{{version}}.orig.tar.gz" @@ -378,7 +365,6 @@ bin_dir = ["{{download.dir}}"] [pigz.install] linux = "make; mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'`;cp $fn {{destdir}}/bin" mac = "make; mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'`;cp $fn {{destdir}}/bin" -windows = "make; mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'`;cp $fn {{destdir}}/bin" [velvet] source_url = "http://www.ebi.ac.uk/~zerbino/velvet/velvet_{{version}}.tgz" @@ -398,7 +384,6 @@ bin_dir = ["{{destdir}}/bin"] [velvet.install] linux = "make && mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'` ;cp $fn {{destdir}}/bin" mac = "make && mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'` ;cp $fn {{destdir}}/bin" -windows = "make && mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'` ;cp $fn {{destdir}}/bin" [lzo] source_url = "http://www.oberhumer.com/opensource/lzo/download/lzo-{{version}}.tar.gz" @@ -418,7 +403,6 @@ bin_dir = ["{{destdir}}/lib"] [lzo.install] linux = ["./configure --prefix={{destdir}} --enable-shared && make", " make install"] mac = ["./configure --prefix={{destdir}} --enable-shared && make", " make install"] -windows = ["./configure --prefix={{destdir}} --enable-shared && make", " make install"] [lzop] source_url = "http://www.lzop.org/download/lzop-{{version}}.tar.gz" @@ -442,7 +426,6 @@ bin_dir = ["{{destdir}}/lib"] [lzop.install] linux = ["export CPPFLAGS='-I{{lzo:install.dir}}/include';export LDFLAGS='-L{{lzo:install.dir}}/lib'; ./configure --prefix={{destdir}}&& make", "make install"] mac = ["export CPPFLAGS='-I{{lzo:install.dir}}/include';export LDFLAGS='-L{{lzo:install.dir}}/lib'; ./configure --prefix={{destdir}}&& make", "make install"] -windows = ["export CPPFLAGS='-I{{lzo:install.dir}}/include';export LDFLAGS='-L{{lzo:install.dir}}/lib'; ./configure --prefix={{destdir}}&& make", "make install"] [fusioncatcher_reffa] source_url = ["https://sourceforge.net/projects/fusioncatcher/files/data/ensembl_v{{version}}.tar.gz.aa", @@ -494,7 +477,6 @@ bin_dir = ["./bin"] [tvc.install] linux = ["#R#fn.sh <- system.file('extdata', 'scripts/install_tvc.sh', package = 'BioInstaller'); system(sprintf('sh %s {{destdir}} {{version}}', fn.sh));#R#", 'mkdir {{destdir}}/bin; cp bin/* {{destdir}}/bin'] mac = ["#R#fn.sh <- system.file('extdata', 'scripts/install_tvc.sh', package = 'BioInstaller'); system(sprintf('sh %s {{destdir}} {{version}}', fn.sh));#R#", 'mkdir {{destdir}}/bin; cp bin/* {{destdir}}/bin'] -windows = ["#R#fn.sh <- system.file('extdata', 'scripts/install_tvc.sh', package = 'BioInstaller'); system(sprintf('sh %s {{destdir}} {{version}}', fn.sh));#R#", 'mkdir {{destdir}}/bin; cp bin/* {{destdir}}/bin'] [imagej] version_newest = "150" @@ -512,7 +494,6 @@ bin_dir = ["{{download.dir}}"] [imagej.source_url] linux = "http://wsr.imagej.net/distros/linux/ij{{version}}-linux64-java8.zip" mac = "http://wsr.imagej.net/distros/osx/ij{{version}}-osx-java8.zip" -windows = "http://wsr.imagej.net/distros/win/ij{{version}}-win-java8.zip" [zlib] version_newest = "1.2.11" @@ -530,12 +511,10 @@ bin_dir = ["{{destdir}}/lib"] [zlib.source_url] linux = ["https://sourceforge.net/projects/libpng/files/zlib/{{version}}/zlib-{{version}}.tar.gz"] mac = ["https://sourceforge.net/projects/libpng/files/zlib/{{version}}/zlib-{{version}}.tar.gz"] -windows = ["https://sourceforge.net/projects/libpng/files/zlib/{{version}}/zlib@>@str_replace_all('{{version}}', fixed('.'), '')@<@.zip"] [zlib.install] linux = ["./configure --prefix={{destdir}} && make", "make install"] mac = ["./configure --prefix={{destdir}} && make", "make install"] -windows = "" [bzip2] source_url = "http://www.bzip.org/{{version}}/bzip2-{{version}}.tar.gz" @@ -554,7 +533,6 @@ bin_dir = ["{{destdir}}/bin"] [bzip2.install] linux = ["sed -i 's;CC=gcc;CC=gcc -fPIC;' Makefile; make -f Makefile-libbz2_so && make clean && make","make install PREFIX={{destdir}}"] mac = ["sed -i 's;CC=gcc;CC=gcc -fPIC;' Makefile; make -f Makefile-libbz2_so && make clean && make", "make install PREFIX={{destdir}}"] -windows = ["sed -i 's;CC=gcc;CC=gcc -fPIC;' Makefile; make -f Makefile-libbz2_so && make clean && make", "make install PREFIX={{destdir}}"] [armadillo] source_url = ["@>@ if('{{version}}' != '4.600.1') {'https://sourceforge.net/projects/arma/files/armadillo-{{version}}.tar.xz'} else {'http://updates.iontorrent.com/updates/software/external/armadillo-{{version}}.tar.gz'}@<@"] @@ -574,7 +552,6 @@ bin_dir = ["{{destdir}}/lib"] [armadillo.install] linux = ["@>@if('{{version}}' != '4.600.1'){' cmake .; make; make install DESTDIR={{destdir}}'} else {%'%sed -i 's:^// #define ARMA_USE_LAPACK$:#define ARMA_USE_LAPACK:g' include/armadillo_bits/config.hpp; sed -i 's:^// #define ARMA_USE_BLAS$:#define ARMA_USE_BLAS:g' include/armadillo_bits/config.hpp && cmake . && make -j4; make install DESTDIR={{destdir}}%'%}@<@"] mac = ["@>@if('{{version}}' != '4.600.1'){' cmake .; make; make install DESTDIR={{destdir}}'} else {%'%sed -i 's:^// #define ARMA_USE_LAPACK$:#define ARMA_USE_LAPACK:g' include/armadillo_bits/config.hpp; sed -i 's:^// #define ARMA_USE_BLAS$:#define ARMA_USE_BLAS:g' include/armadillo_bits/config.hpp && cmake . && make -j4; make install DESTDIR={{destdir}}%'%}@<@"] -windows = ["@>@if('{{version}}' != '4.600.1'){' cmake .; make; make install DESTDIR={{destdir}}'} else {%'%sed -i 's:^// #define ARMA_USE_LAPACK$:#define ARMA_USE_LAPACK:g' include/armadillo_bits/config.hpp; sed -i 's:^// #define ARMA_USE_BLAS$:#define ARMA_USE_BLAS:g' include/armadillo_bits/config.hpp && cmake . && make -j4; make install DESTDIR={{destdir}}%'%}@<@"] [samstat] source_url = "https://sourceforge.net/projects/samstat/files/samstat-{{version}}.tar.gz" @@ -594,12 +571,10 @@ bin_dir = ["{{destdir}}/bin"] [samstat.before_install] linux = "autoreconf -ivf" mac = "autoreconf -ivf" -windows = "autoreconf -ivf" [samstat.install] linux = ["./configure --prefix={{destdir}} && make", "make install"] mac = ["./configure --prefix={{destdir}} && make", "make install"] -windows = ["./configure --prefix={{destdir}} && make", "make install"] [prinseq] source_url = "https://sourceforge.net/projects/prinseq/files/standalone/prinseq-lite-{{version}}.tar.gz" @@ -619,7 +594,6 @@ bin_dir = ["{{destdir}}/bin"] [prinseq.install] linux = "chmod +x *.pl && mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'` ;cp $fn {{destdir}}/bin" mac = "chmod +x *.pl && mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'` ;cp $fn {{destdir}}/bin" -windows = "chmod +x *.pl && mkdir -p {{destdir}}/bin; fn=`ls -F |grep '*' | tr -d '*'` ;cp $fn {{destdir}}/bin" [solexaqa] source_url = ["https://sourceforge.net/projects/solexaqa/files/src/SolexaQA++_v{{version}}.zip", @@ -641,7 +615,6 @@ bin_dir = ["{{destdir}}/bin"] [solexaqa.install] linux = "chmod -R +x {{download.dir}}/Linux_x64/*; mkdir -p {{destdir}}/bin; cp {{download.dir}}/Linux_x64/* {{destdir}}/bin" mac = "chmod -R +x {{download.dir}}/MacOs_10.7+/*; mkdir -p {{destdir}}/bin; cp {{download.dir}}/MacOs_10.7+/* {{destdir}}/bin" -windows = "chmod -R +x {{download.dir}}/SolexaQA++.exe/*; mkdir -p {{destdir}}/bin; cp {{download.dir}}/SolexaQA++.exe/* {{destdir}}/bin" [mapsplice2] source_url = "http://protocols.netlab.uky.edu/~zeng/MapSplice-v{{version}}.zip" @@ -658,11 +631,9 @@ make_dir = ["./"] bin_dir = ["{{destdir}}/bin"] - [mapsplice2.install] linux = ["make", "mkdir -p {{destdir}}/bin; cp {{download.dir}}/bin/* {{destdir}}/bin"] mac = ["make", "mkdir -p {{destdir}}/bin; cp {{download.dir}}/bin/* {{destdir}}/bin"] -windows = ["make", "mkdir -p {{destdir}}/bin; cp {{download.dir}}/bin/* {{destdir}}/bin"] [bcl2fastq2] source_url = "https://support.illumina.com/content/dam/illumina-support/documents/downloads/software/bcl2fastq/bcl2fastq2-v{{version}}.tar.gz" @@ -682,7 +653,6 @@ bin_dir = ["{{destdir}}/bin"] [bcl2fastq2.install] linux = ["mkdir build; cd build; ../src/configure --prefix={{destdir}} && make", "make install"] mac = ["mkdir build; cd build; ../src/configure --prefix={{destdir}} && make", "make install"] -windows = ["mkdir build; cd build; ../src/configure --prefix={{destdir}} && make","make install"] [blat] decompress = false @@ -701,12 +671,10 @@ bin_dir = ["{{destdir}}/bin"] [blat.source_url] linux = "http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/blat" mac = "http://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/blat/blat" -windows = "http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/blat" [blat.install] linux = "chmod +x blat; mkdir -p {{destidr}}/bin; cp blat {{destdir}}/bin" mac = "chmod +x blat; mkdir -p {{destidr}}/bin; cp blat {{destdir}}/bin" -windows = "chmod +x blat; mkdir -p {{destidr}}/bin; cp blat {{destdir}}/bin" [fatotwobit] decompress = false @@ -725,12 +693,10 @@ bin_dir = ["{{destdir}}/bin"] [fatotwobit.source_url] linux = "http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit" mac = "http://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/faToTwoBit" -windows = "http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit" [fatotwobit.install] linux = "chmod +x faToTwoBit; mkdir -p {{destidr}}/bin; cp faToTwoBit {{destdir}}/bin" mac = "chmod +x faToTwoBit; mkdir -p {{destidr}}/bin; cp faToTwoBit {{destdir}}/bin" -windows = "chmod +x faToTwoBit; mkdir -p {{destidr}}/bin; cp faToTwoBit {{destdir}}/bin" [liftover] decompress = false @@ -749,12 +715,10 @@ bin_dir = ["{{destdir}}/bin"] [liftover.source_url] linux = "http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/liftOver" mac = "http://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/liftOver" -windows = "http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/liftOver" [liftover.install] linux = "chmod +x liftOver; mkdir -p {{destdir}}/bin; cp liftOver {{destdir}}/bin" mac = "chmod +x liftOver; mkdir -p {{destidr}}/bin; cp liftOver {{destdir}}/bin" -windows = "chmod +x liftOver; mkdir -p {{destidr}}/bin; cp liftOver {{destdir}}/bin" [svtoolkit] source_url = "http://bioinfo.rjh.com.cn/download/svtoolkit/download.php?filename=svtoolkit_{{version}}.tar.gz" @@ -774,7 +738,6 @@ bin_dir = ["{{download.dir}}/lib"] [svtoolkit.install] linux = "" mac = "" -windows = "" [root] source_url = "https://root.cern.ch/download/root_v{{version}}.source.tar.gz" @@ -794,7 +757,6 @@ bin_dir = ["{{download.dir}}/build/bin"] [root.install] linux = ["mkdir build; cd build && cmake .. && make -j8"] mac = ["mkdir build; cd build && cmake .. && make -j8"] -windows = ["md build; cd build && cmake .. && make -j8"] [cnvnator_samtools] source_url = "http://bioinfo.rjh.com.cn/download/svtoolkit/download.php?filename=cnvnator_samtools_{{version}}.tar.gz" @@ -814,7 +776,6 @@ bin_dir = ["{{download.dir}}"] [cnvnator_samtools.install] linux = "make" mac = "make" -windows = "make" [htslib] source_url = "https://github.com/samtools/htslib/archive/{{version}}.tar.gz" @@ -829,7 +790,7 @@ bin_dir = ["{{destdir}}/bin"] [htslib.install] linux = ["autoheader; autoconf; ./configure --prefix={{destdir}}; make;", " make install"] -windows = ["autoheader; autoconf; ./configure --prefix={{destdir}}; make;", " make install"] + mac = ["autoheader; autoconf; ./configure --prefix={{destdir}}; make;", " make install"] [samtools] @@ -850,7 +811,6 @@ bin_dir = ["{{destdir}}/bin"] [samtools.install] linux = ["autoconf -Wno-syntax; sed -i 's;HTSDIR = ../htslib;HTSDIR = {{htslib:source.dir}};' config.mk; ./configure --prefix={{destdir}}; make ", "make install prefix={{destdir}}"] mac = ["autoconf -Wno-syntax; sed -i 's;HTSDIR = ../htslib;HTSDIR = {{htslib:source.dir}};' config.mk; ./configure --prefix={{destdir}}; make ", "make install prefix={{destdir}}"] -windows = ["autoconf -Wno-syntax; sed -i 's;HTSDIR = ../htslib;HTSDIR = {{htslib:source.dir}};' config.mk; ./configure --prefix={{destdir}}; make", "make install prefix={{destdir}}"] [pcre] source_url = "https://ftp.pcre.org/pub/pcre/pcre-{{version}}.tar.gz" @@ -870,7 +830,6 @@ bin_dir = ["{{destdir}}/bin"] [pcre.install] linux = ["autoreconf -ivf && ./configure --enable-utf8 --prefix={{destdir}} && make -j3", "make install"] mac = ["./configure --enable-utf8 --prefix={{destdir}} && make -j3", "make install"] -windows = ["./configure --enable-utf8 --prefix={{destdir}} && make -j3", "make install"] [xz] source_url = "http://tukaani.org/xz/xz-{{version}}.tar.gz" @@ -891,7 +850,6 @@ bin_dir = ["{{destdir}}/bin"] [xz.install] linux = ["tar -xzvf xz-{{version}}.tar.gz && cd xz-{{version}} && ./configure --prefix={{destdir}} && make -j3", "make install"] mac = ["tar -xzvf xz-{{version}}.tar.gz && cd xz-{{version}} && ./configure --prefix={{destdir}} && make -j3", "make install"] -windows = ["tar -xzvf xz-{{version}}.tar.gz && cd xz-{{version}} && ./configure --prefix={{destdir}} && make -j3", "make install"] [curl] source_url = "https://curl.haxx.se/download/curl-{{version}}.tar.gz" @@ -911,7 +869,6 @@ bin_dir = ["{{destdir}}/bin"] [curl.install] linux = ["./configure --prefix={{destdir}} --with-ssl && make -j3", "make install"] mac = ["./configure --prefix={{destdir}} --with-ssl && make -j3", "make install"] -windows = ["./configure --prefix={{destdir}} --with-ssl && make -j3", "make install"] [r] version_newest = "3.4.0" @@ -937,8 +894,6 @@ linux = ["https://cran.r-project.org/src/base/R-3/R-{{version}}.tar.gz", "https://cran.r-project.org/src/base/R-0/R-{{version}}.tgz"] mac = ["https://cran.r-project.org/bin/macosx/R-{{version}}.pkg", "https://cran.r-project.org/bin/macosx/old/R-{{version}}.pkg"] -windows = ["https://cran.r-project.org/bin/windows/base/R-{{version}}-win.exe", - "https://cran.r-project.org/bin/windows/base/old/{{version}}/R-{{version}}-win.exe"] [r.install] linux = ["""./configure --enable-R-shlib --prefix={{destdir}} CFLAGS='\ @@ -969,7 +924,6 @@ lib.flag <- lib.flag[!str_detect(lib.flag, ':')] paste(lib.flag, collapse=' ') @<@' \ && make""", "make install"] -windows="" [reditools] source_url = "https://nchc.dl.sourceforge.net/project/reditools/REDItools-{{version}}.tar.gz" @@ -977,4 +931,4 @@ source_url = "https://nchc.dl.sourceforge.net/project/reditools/REDItools-{{vers [reditools.install] linux = "pip install ." mac = "pip install ." -windows = "pip install ." +