comparison bdss_client.Rmd @ 21:a709a705ce09 draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty

20:531c00a2acbf

      highlight: tango
---

```{r setup, include=FALSE, warning=FALSE, message=FALSE}
knitr::opts_chunk$set(
  echo = ECHO
)
```

# Command line arguments

# 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))
}
```

21:a709a705ce09

      highlight: tango
---

```{r setup, include=FALSE, warning=FALSE, message=FALSE}
knitr::opts_chunk$set(
  echo = ECHO,
  error=TRUE
)
```

# Command line arguments

# 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) {
    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))
```