Update all Perl modules via CPAN

This is a quick tip to update all installed modules, just type:

perl -MCPAN -e 'CPAN::Shell->install(CPAN::Shell->r)'

Creating unix command for Picard JAR files

Picard (http://picard.sourceforge.net/) is a nice Java-based toolkit to work with BAM and SAM files.
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:

	#!/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

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