# HG changeset patch
# User mingchen0919
# Date 1528815535 14400
# Node ID c062782a7534ba1c6211e445a8c4ff65cf27cef6
# Parent  cf17a419986122c5b5dcf528b3c76486c056ddce
planemo upload for repository https://github.com/feltus/BDSS

diff -r cf17a4199861 -r c062782a7534 rmarkdown_report.Rmd
--- a/rmarkdown_report.Rmd	Tue Jun 12 09:49:08 2018 -0400
+++ b/rmarkdown_report.Rmd	Tue Jun 12 10:58:55 2018 -0400
@@ -74,7 +74,7 @@
                  substr(id, 1, 3), '/',
                  substr(id, 1, 6), '/', id, '/', id, '.sra')
     # download sra file with bdss
-    bdss_command = paste0('bdss transfer -u ', url)
+    bdss_command = paste0('bdss transfer -u ', url, '>> ${REPORT_FILES_PATH}/log.txt 2>&1')
     command_stdout = system(bdss_command, intern = TRUE)
     write(command_stdout, file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/bdss-download.log.txt'), append = TRUE)
     # convert .sra to .fastq/.fasta
@@ -98,7 +98,7 @@
                  substr(id, 1, 3), '/',
                  substr(id, 1, 6), '/', id, '/', id, '.sra')
     # download sra file with bdss
-    bdss_command = paste0('bdss transfer -u ', url)
+    bdss_command = paste0('bdss transfer -u ', url, '>> ${REPORT_FILES_PATH}/log.txt 2>&1')
     command_stdout = system(bdss_command, intern = TRUE)
     write(command_stdout, file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/bdss-download.log.txt'), append = TRUE)
     # convert .sra to .fastq/.fasta