# HG changeset patch
# User mingchen0919
# Date 1507736959 14400
# Node ID 415ebc9016daa9b2c48101d615e06036fa5017ce
# Parent  04100e773314276203598dc2c787b56e8bec5ba3
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty

diff -r 04100e773314 -r 415ebc9016da bdss_client_sra_pe.Rmd
--- a/bdss_client_sra_pe.Rmd	Wed Oct 11 11:43:39 2017 -0400
+++ b/bdss_client_sra_pe.Rmd	Wed Oct 11 11:49:19 2017 -0400
@@ -64,11 +64,11 @@
       print(paste0('Two fastq files found for this SRA accession: ', id))
       url_1 = paste0(url_base, '/', all_fastq_files[1])
       bdss_command_1 = paste0('/tool_deps/_conda/bin/bdss transfer -u ', url_1)
-      run_bdss_1 = system(bdss_command, intern = TRUE)
+      run_bdss_1 = system(bdss_command_1, intern = TRUE)
       print(run_bdss_1)
       url_2 = paste0(url_base, '/', all_fastq_files[1])
       bdss_command_2 = paste0('/tool_deps/_conda/bin/bdss transfer -u ', url_2)
-      run_bdss_2 = system(bdss_command, intern = TRUE)
+      run_bdss_2 = system(bdss_command_2, intern = TRUE)
       print(run_bdss_2)
     }
   }