Commit be0b317a authored by Adam Caprez's avatar Adam Caprez
Browse files

Add workaround for -savn filename argument ending in .gz

Workaround for passing run_spp_nodups.R a filename ending in .gz
for -savn argument.  The script calls gzip internally, which bails
out since the file already has a gz extension.  Instead, rename
file without gz extension and then run gzip.
parent 7a703c93
......@@ -6,3 +6,10 @@ module load R spp
# to make r_spp_nodups happy.
args=`echo $@ | sed -e 's/= /=/g'`
Rscript ${SPP_NODUPS} $args
# Workaround for passing run_spp_nodups.R a filename ending in .gz
# for -savn argument. The script calls gzip internally, which bails
# out since the file already has a gz extension. Instead, rename
# file without gz extension and then run gzip.
rename .narrowPeak.gz .narrowPeak *.gz
gzip -v *.narrowPeak
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment