Mercurial > repos > mingchen0919 > rmarkdown_bdss_client

changeset 14:c0b8476fbc85 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
author mingchen0919
date Wed, 11 Oct 2017 14:36:19 -0400
parents 03893b1ee3ef
children fe5f30584308
files bdss_client.Rmd
diffstat 1 files changed, 2 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/bdss_client.Rmd	Wed Oct 11 14:04:57 2017 -0400
+++ b/bdss_client.Rmd	Wed Oct 11 14:36:19 2017 -0400
@@ -29,7 +29,7 @@
 system('echo url=http://bdss.bioinfo.wsu.edu/ >> bdss.cfg')
 ```
 
-# Download and extract reads
+# Download data
 
 ```{r 'download and extract reads'}
 # create a directory to store read files
@@ -40,18 +40,8 @@
 # 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)
+    print(system(bdss_command, intern = TRUE))
 }
 ```
 
-* `fastq-dump` command
-```{r}
-print(command)
-```
 
-* `command line stdout`
-
-```{r}
-system(command = command, intern = TRUE)
-```
-