Use gunzip -c instead of zcat on gzipped genomes

On OSX zcat appends ".Z" to all filenames so just using zcat won't work.
aaydenn · Oct 27, 2017 · 283c1a7 · 283c1a7
1 parent 2132b5d
commit 283c1a7
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/scripts/rsync_from_ncbi.pl b/scripts/rsync_from_ncbi.pl
@@ -82,7 +82,7 @@
 my $max_out_chars = 0;
 for my $in_filename (keys %manifest) {
   my $taxid = $manifest{$in_filename};
-  open IN, "zcat $in_filename |" or die "$PROG: can't read $in_filename: $!\n";
+  open IN, "gunzip -c $in_filename |" or die "$PROG: can't read $in_filename: $!\n";
   while (<IN>) {
     if (/^>/) {
       s/^>/>kraken:taxid|$taxid|/;