# HG changeset patch
# User mingchen0919
# Date 1527724356 14400
# Node ID 845f4b9d7cf3d602db4469a08891d394c6b25f71
# Parent  8b0ac9578ad47cbc30f706f57553003a8d99bc31
planemo upload commit 602f5b82864867a81c2e4ea2be9b52f4b635bd7b-dirty

diff -r 8b0ac9578ad4 -r 845f4b9d7cf3 rmarkdown_report.Rmd
--- a/rmarkdown_report.Rmd	Tue May 29 09:08:00 2018 -0400
+++ b/rmarkdown_report.Rmd	Wed May 30 19:52:36 2018 -0400
@@ -80,7 +80,7 @@
                  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/test-galaxy/tools/_conda/bin/bdss transfer -u ', url)
     system(bdss_command, intern = TRUE)
     # convert .sra to .fastq/.fasta
     if('FORMAT' == 'fasta') {
@@ -102,7 +102,7 @@
                  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/test-galaxy/tools/_conda/bin/bdss transfer -u ', url)
     system(bdss_command, intern = TRUE)
     # convert .sra to .fastq/.fasta
     if(opt$X_f == 'fasta') {
diff -r 8b0ac9578ad4 -r 845f4b9d7cf3 rmarkdown_report.xml
--- a/rmarkdown_report.xml	Tue May 29 09:08:00 2018 -0400
+++ b/rmarkdown_report.xml	Wed May 30 19:52:36 2018 -0400
@@ -6,6 +6,7 @@
         <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
         <requirement type="package" version="1.20.0">r-getopt</requirement>
         <requirement type="package" version="1.6">r-rmarkdown</requirement>
+        <requirement type="package" version="0.6.2">parallel-fastq-dump</requirement>
     </requirements>
     <command><![CDATA[