downloadDir<-"~/BioToolsInstall" download.file("http://www.clustal.org/download/current/clustalw-2.1-macosx.dmg",file.path(dowloadDir,"clustalw-2.1-macosx.dmg"),mode='wb') #system("hdiutil mount clustalw-2.1-macosx.dmg") #system("sudo cp -R /Volumes/clustalw-2.1-macosx /Applications") #system("hdiutil unmount clustalw-2.1-macosx") #install kalign download.file("http://msa.sbc.su.se/downloads/kalign/current.tar.gz",file.path(downloadDir,"kalign.tar.gz"),mode='wb') untar(file.path(downloadDir,"kalign.tar.gz"),exdir=file.path(downloadDir,"kalign")) system(file.path(downloadDir,"kalign/configure")) system(file.path(downloadDir,"kalign/make")) system(paste("sudo make",file.path(downloadDir,"install"))) #install blast exec download.file("ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.2.28+.dmg",file.path(downloadDir,"ncbi-blast-2.2.28+.dmg"),mode='wb') #system("hdiutil mount ncbi-blast-2.2.28+.dmg") #system("sudo cp -R /Volumes/ncbi-blast-2.2.28+/ /Applications") #system("hdiutil unmount ncbi-blast-2.2.28+") #install blast db download.file("ftp://ftp.ncbi.nlm.nih.gov/blast/db/16SMicrobial.tar.gz",file.path(downloadDir,"16SMicrobial.tar.gz"),mode='wb') untar(file.path(downloadDir,"16SMicrobial.tar.gz"),exdir=file.path(downloadDir,"16SMicrobialDB")) #install rdp download.file("http://downloads.sourceforge.net/project/rdp-classifier/rdp-classifier/rdp_classifier_2.5.zip?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Frdp-classifier%2Ffiles%2Frdp-classifier%2F&use_mirror=iweb",file.path(downloadDir,"rdp_claassifier_2.5.zip"),mode='wb') unzip(file.path(downloadDir,"rdp_claassifier_2.5.zip")) Sys.setenv(RDP_JAR_PATH=file.path(downloadDir,"rdp_claassifier_2.5.zip"))