Mercurial > repos > mingchen0919 > rmarkdown_bdss_client

diff bdss_client.Rmd @ 16:c2150a0f9c7c 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 15:06:20 -0400
parents fe5f30584308
children a709a705ce09
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line diff
--- a/bdss_client.Rmd	Wed Oct 11 14:50:19 2017 -0400
+++ b/bdss_client.Rmd	Wed Oct 11 15:06:20 2017 -0400
@@ -39,8 +39,7 @@
 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)
-    bdss_command = paste0('cd ./read_files_directory && /main/sites/galaxy/galaxy/tools/_conda/bin/bdss transfer -u ', url)
+    bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer --destination read_files_directory -u ', url)
     print(system(bdss_command, intern = TRUE))
 }
 ```