Usually I don't like to type "java -jar" when calling picard tools so I always wrap them in bash scripts with the script below:
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#!/bin/sh | |
picard_jars='/data_alpha/local/bioinformatic_tools/picard-tools-1.77' | |
bin="$picard_jars/bin" | |
for i in $picard_jars/*.jar | |
do | |
command_name=`echo $i | perl -plane 's/.*\/(\S+).jar/$1/g'` | |
echo $command_name | |
echo '#!/usr/bin/env sh' > $bin/$command_name | |
echo 'java -jar '$i' $@' >> $bin/$command_name | |
chmod +x $bin/$command_name | |
done |