Mercurial > repos > mingchen0919 > aurora_bdss_sra

changeset 4:c062782a7534 draft

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planemo upload for repository https://github.com/feltus/BDSS
author mingchen0919
date Tue, 12 Jun 2018 10:58:55 -0400
parents cf17a4199861
children a1dfadeb3b59
files rmarkdown_report.Rmd
diffstat 1 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- 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