Mercurial > repos > mingchen0919 > rmarkdown_bdss_client

diff bdss_client.Rmd @ 13:03893b1ee3ef draft

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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 14:04:57 -0400
parents bfc6133f3a2b
children c0b8476fbc85
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line diff
--- a/bdss_client.Rmd	Wed Oct 11 13:48:03 2017 -0400
+++ b/bdss_client.Rmd	Wed Oct 11 14:04:57 2017 -0400
@@ -39,11 +39,9 @@
 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)
+    bdss_command = paste0('cd ./read_files_directory && /tool_deps/_conda/bin/bdss transfer -u ', url)
     system(bdss_command)
 }
-move_files_command = 'find . -type f -print0 | xargs -0 mv -t ./read_files_directory'
-system(move_files_command)
 ```
 
 * `fastq-dump` command