# HG changeset patch # User mingchen0919 # Date 1522678890 14400 # Node ID 52ecc1cfd205a22e0627a441cbe49313924e21b5 # Parent 4f9f1e76f7e6ed7cf02f049264d035edcf744ac1 planemo upload commit 979e0f1c28c74ca7df02ef20c2208e9677bc820a-dirty diff -r 4f9f1e76f7e6 -r 52ecc1cfd205 list_paired.Rmd --- a/list_paired.Rmd Mon Apr 02 09:16:17 2018 -0400 +++ b/list_paired.Rmd Mon Apr 02 10:21:30 2018 -0400 @@ -30,25 +30,18 @@ ``` ```{r, echo=FALSE} -# write('', file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh')) +write('', file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh')) if (nrow(df) > 0) { for (i in 1:nrow(df)) { tool_output_dir = readLines(df[i, 'tool_output_dir'])[1] full_path = paste0(tool_output_dir, '/', df[i, 'relative_path']) + # if it is a directory path, add '/*' to the end. if (dir.exists(full_path)) { - from_files = list.files(full_path, full.names = TRUE) - to_files = list.files(full_path) - to_files = paste0(list_paired_path, to_files) - file.copy(from = from_files, to = to_files) + full_path = paste0(full_path, '/*') } - if (file.exists(full_path)) { - # to_files = list.files(full_path) - to_file = tail(strsplit(full_path, '/')[[1]], 1) - file.copy(from = full_path, to = paste0(list_paired_path, to_file)) - } - # command_line = paste0('cp -r ', full_path, ' paired') - # write(command_line, append = TRUE, - # file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh')) + command_line = paste0('cp -r ', full_path, ' list_paired') + write(command_line, append = TRUE, + file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh')) } } ``` diff -r 4f9f1e76f7e6 -r 52ecc1cfd205 list_paired_render.R --- a/list_paired_render.R Mon Apr 02 09:16:17 2018 -0400 +++ b/list_paired_render.R Mon Apr 02 10:21:30 2018 -0400 @@ -20,9 +20,6 @@ # create three folders within working directory dir.create('list_paired') -job_working_dir = getwd() -list_paired_path = paste0(job_working_dir, '/list_paired/') - #-----------------render Rmd-------------- # copy R markdown file to working directory and render it within the working directory. render(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/list_paired.Rmd'), @@ -33,7 +30,7 @@ # the solution is to render the rmarkdown to a explicitly specified file and then copy the # file to ${REPORT} system(command = 'cp ${REPORT_FILES_PATH}/report.html ${REPORT}') -# system(command = 'sh ${REPORT_FILES_PATH}/script.sh') +system(command = 'sh ${REPORT_FILES_PATH}/script.sh') # rename files so that all files have the name pattern BASENAME_forward.EXT and BASENAME_reverse.EXT from_files = list.files('list_paired', full.names = TRUE)