Mercurial > repos > greg > ideas_preprocessor

changeset 25:f7563bb242fc draft

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Uploaded
author greg
date Thu, 01 Feb 2018 11:22:27 -0500
parents 71345e154c66
children 06e63b5cb025
files ideas_preprocessor.R
diffstat 1 files changed, 6 insertions(+), 16 deletions(-) [+]
line wrap: on
line diff
--- a/ideas_preprocessor.R	Thu Feb 01 11:22:19 2018 -0500
+++ b/ideas_preprocessor.R	Thu Feb 01 11:22:27 2018 -0500
@@ -33,18 +33,6 @@
 args <- parse_args(parser, positional_arguments=TRUE)
 opt <- args$options
 
-create_primary_html = function(output, output_files_path) {
-    files = list.files(path=output_files_path);
-    s <- paste('<html><head></head><body>', sep="\n");
-    s <- paste(s, '<h3>Files prepared for IDEAS</h3>\n', sep="");
-    s <- paste(s, '<ul>\n', sep="");
-    for (i in 1:length(files)) {
-        s <- paste(s, '<li><a href="', files[i], '">', files[i], '</a></li>\n', sep="");
-    }
-    s <- paste(s, '</ul></body></html>', sep="");
-    cat(s, file=output);
-}
-
 tmp_dir = "tmp";
 
 # Read the ideaspre_input_config text file which has this format:
@@ -99,9 +87,12 @@
 # Archive the tmp directory.
 cmd = "tar -cvf tmp.tar tmp";
 system(cmd);
+# Compress the archive.
+cmd = "gzip tmp.tar";
+system(cmd);
 # Move the tmp archive to the output directory.
-to_path = paste(opt$output_files_path, "tmp.tar", sep="/");
-file.rename("tmp.tar", to_path);
+to_path = paste(opt$output_files_path, "tmp.tar.gz", sep="/");
+file.rename("tmp.tar.gz", to_path);
 
 if (!is.null(opt$chrom_bed_input) && !is.null(opt$chromosome_windows)) {
     # Renane opt$chrom_bed_input to be chromosomes.bed
@@ -112,5 +103,4 @@
     to_path = paste(opt$output_files_path, opt$chromosome_windows, sep="/");
     file.rename(opt$chromosome_windows, to_path);
 }
-# Create the primary HTML dataset.
-create_primary_html(opt$output, opt$output_files_path);
+