comparison bdss_client.Rmd @ 14:c0b8476fbc85 draft

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

13:03893b1ee3ef

```{r}
system('echo "[metadata_repository]" > bdss.cfg')
system('echo url=http://bdss.bioinfo.wsu.edu/ >> bdss.cfg')
```

# Download and extract reads

```{r 'download and extract reads'}
# create a directory to store read files
dir.create('read_files_directory')
# 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)
```

* `command line stdout`

```{r}
system(command = command, intern = TRUE)
```

14:c0b8476fbc85

```{r}
system('echo "[metadata_repository]" > bdss.cfg')
system('echo url=http://bdss.bioinfo.wsu.edu/ >> bdss.cfg')
```

# Download data

```{r 'download and extract reads'}
# create a directory to store read files
dir.create('read_files_directory')
# 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)
    print(system(bdss_command, intern = TRUE))
}
```