comparison bdss_client.Rmd @ 26:fb8f1d1ceeae draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit b212086a85c4d1e62e0d0c0e77b6f3fcabea04ef

25:821832531529

urls = strsplit(gsub(',', ' ', 'URLS'), ' ')[[1]]
urls = urls[urls != '']
# loop through SRA accessions to download and extract reads.
for(url in urls) {
    print(url)
    bdss_command = paste0('/main/sites/galaxy/galaxy/tools/_conda/bin/bdss transfer --destination read_files_directory -u ', url)
    print(bdss_command)
    print(system(bdss_command, intern = TRUE))
}
# all files that need to be saved should be moved to REPORT_DIR directory
# print(system('mv read_files_directory REPORT_DIR', intern = TRUE))

26:fb8f1d1ceeae

urls = strsplit(gsub(',', ' ', 'URLS'), ' ')[[1]]
urls = urls[urls != '']
# loop through SRA accessions to download and extract reads.
for(url in urls) {
    print(url)
    bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer --destination read_files_directory -u ', url)
    print(bdss_command)
    print(system(bdss_command, intern = TRUE))
}
# all files that need to be saved should be moved to REPORT_DIR directory
# print(system('mv read_files_directory REPORT_DIR', intern = TRUE))