comparison bdss_client.Rmd @ 13:03893b1ee3ef draft

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

12:bfc6133f3a2b

# 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 -u ', url)
    system(bdss_command)
}
move_files_command = 'find . -type f -print0 | xargs -0 mv -t ./read_files_directory'
system(move_files_command)
```

* `fastq-dump` command
```{r}
print(command)

13:03893b1ee3ef

# 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)
    system(bdss_command)
}
```

* `fastq-dump` command
```{r}
print(command)