Mercurial > repos > mingchen0919 > rmarkdown_bdss_client

diff bdss_client.Rmd @ 29:69d51de74c0f draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 7c282211dbff8125b5aeef6e0172d5eb2f3a2ddb-dirty
author mingchen0919
date Mon, 16 Oct 2017 23:55:36 -0400
parents 3764ba86f0da
children
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--- a/bdss_client.Rmd	Mon Oct 16 23:34:33 2017 -0400
+++ b/bdss_client.Rmd	Mon Oct 16 23:55:36 2017 -0400
@@ -41,7 +41,7 @@
 # loop through SRA accessions to download and extract reads.
 for(url in urls) {
     print(url)
-    bdss_command = paste0('/main/sites/galaxy/galaxy/tools/_conda/bin/bdss transfer --destination read_files_directory -u ', 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))
 }