comparison bdss_client.Rmd @ 10:b7171118a078 draft

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

9:072568c2c96a

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)
    print(system(bdss_command, intern = TRUE))
}
move_files_command = 'find . -type f -print0 | xargs -0 mv -t ./read_files_directory'
print(system(move_files_command, intern = TRUE))
```

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

10:b7171118a078

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, intern = TRUE)
}
move_files_command = 'find . -type f -print0 | xargs -0 mv -t ./read_files_directory'
system(move_files_command, intern = TRUE)
```

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