comparison bdss_client.Rmd @ 16:c2150a0f9c7c draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty

15:fe5f30584308

# download and extract reads
urls = strsplit(gsub(',', ' ', 'URLS'), ' ')[[1]]
urls = urls[urls != '']
# loop through SRA accessions to download and extract reads.
for(url in urls) {
    # bdss_command = paste0('cd ./read_files_directory && /tool_deps/_conda/bin/bdss transfer -u ', url)
    bdss_command = paste0('cd ./read_files_directory && /main/sites/galaxy/galaxy/tools/_conda/bin/bdss transfer -u ', url)
    print(system(bdss_command, intern = TRUE))
}
```

16:c2150a0f9c7c

# download and extract reads
urls = strsplit(gsub(',', ' ', 'URLS'), ' ')[[1]]
urls = urls[urls != '']
# loop through SRA accessions to download and extract reads.
for(url in urls) {
    bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer --destination read_files_directory -u ', url)
    print(system(bdss_command, intern = TRUE))
}
```