# HG changeset patch
# User mingchen0919
# Date 1508211273 14400
# Node ID 3764ba86f0da0548992f01b1d49e3ca54d800c70
# Parent  6efe73e1f06d8510f1b83f36a175d10798dd0631
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 7c282211dbff8125b5aeef6e0172d5eb2f3a2ddb-dirty

diff -r 6efe73e1f06d -r 3764ba86f0da bdss_client.Rmd
--- a/bdss_client.Rmd	Mon Oct 16 23:32:45 2017 -0400
+++ b/bdss_client.Rmd	Mon Oct 16 23:34:33 2017 -0400
@@ -41,7 +41,7 @@
 # loop through SRA accessions to download and extract reads.
 for(url in urls) {
     print(url)
-    bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer --destination read_files_directory -u ', url)
+    bdss_command = paste0('/main/sites/galaxy/galaxy/tools/_conda/bin/bdss transfer --destination read_files_directory -u ', url)
     print(bdss_command)
     print(system(bdss_command, intern = TRUE))
 }
diff -r 6efe73e1f06d -r 3764ba86f0da bdss_client_sra.Rmd
--- a/bdss_client_sra.Rmd	Mon Oct 16 23:32:45 2017 -0400
+++ b/bdss_client_sra.Rmd	Mon Oct 16 23:34:33 2017 -0400
@@ -46,7 +46,7 @@
                  substr(id, 1, 3), '/',
                  substr(id, 1, 6), '/', id, '/', id, '.sra')
     # download sra file with bdss
-    bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer -u ', url)
+    bdss_command = paste0('/main/sites/galaxy/galaxy/tools/_conda/bin/bdss transfer -u ', url)
     system(bdss_command, intern = TRUE)
     # convert .sra to .fastq/.fasta
     if('FORMAT' == 'fasta') {
@@ -68,7 +68,7 @@
                  substr(id, 1, 3), '/',
                  substr(id, 1, 6), '/', id, '/', id, '.sra')
     # download sra file with bdss
-    bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer -u ', url)
+    bdss_command = paste0('/main/sites/galaxy/galaxy/tools/_conda/bin/bdss transfer -u ', url)
     system(bdss_command, intern = TRUE)
     # convert .sra to .fastq/.fasta
     if('FORMAT' == 'fasta') {