Mercurial > repos > mingchen0919 > aurora_curl
diff rmarkdown_report_render.R @ 2:350afb9412fc draft default tip
planemo upload
| author | mingchen0919 |
|---|---|
| date | Mon, 14 May 2018 16:58:24 -0400 |
| parents | 7a3bb304fe1d |
| children |
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--- a/rmarkdown_report_render.R Mon May 14 16:17:19 2018 -0400 +++ b/rmarkdown_report_render.R Mon May 14 16:58:24 2018 -0400 @@ -16,6 +16,11 @@ #------------------------------------------------------------------ options(stringsAsFactors = FALSE) +#------------------------------------------------ +# create a folder within working directory +dir.create('output_dir') +job_working_dir = getwd() +Sys.setenv(JOB_WORKING_DIR=paste0(job_working_dir, '/output_dir/')) # define two helper functions #-----: helper function 1 @@ -149,6 +154,7 @@ #============== expose outputs to galaxy history =============== system(command = 'sh ${TOOL_INSTALL_DIR}/expose-outputs-to-galaxy-history.sh') +file.copy() #===============================================================