diff bdss_client.Rmd @ 7:efb1938c3020 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bdss_client.Rmd	Wed Oct 11 13:21:54 2017 -0400
@@ -0,0 +1,59 @@
+---
+title: 'Download with BDSS client'
+output:
+    html_document:
+      number_sections: true
+      toc: true
+      theme: cosmo
+      highlight: tango
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(
+  echo = ECHO
+)
+```
+
+# Command line arguments
+
+```{r 'command line arguments'}
+str(opt)
+```
+
+# BDSS configuration file
+
+First, we create a bdss configuration file `bdss.cfg` in the current directory.
+
+```{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('/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)
+```
+
+* `command line stdout`
+
+```{r}
+system(command = command, intern = TRUE)
+```
+