downloadDir<-"BioToolsInstall" #download 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","rdp_classifier_2.5.zip",mode='wb') unzip("rdp_classifier_2.5.zip") Sys.setenv(RDP_JAR_PATH="rdp_classifier_2.5/rdp_classifier-2.5.jar") # download clustal for windows download.file("http://www.clustal.org/download/current/clustalw-2.1-win.msi","clustalw-2.1.msi",mode='wb') system("msiexec /i clustalw-2.1.msi") # download blast for windows download.file("ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.2.28+-win64.exe","ncbi-blast-2.28+-win64.exe",mode='wb' ) System("ncbi-blast-2.28+-win64.exe") #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"))