Merge branch 'readhandling'
Pair library files required to be different to qualify for paired runs
Merge branch 'readhandling'
changes to the JAVA_OPTION
Jobnames tagged with NGs
bugfix recal
Java unset in all scripts
bugfix reCalAln
java issues resolved
reCalAln hardcode -Xmx200m for initial version query
bugfix reCalAln2 nt
merge with upstream (allpower)
Update trigger.sh

Added basic trinity execution lines.
Merge branch 'master' into homer_chipseq

Conflicts:
	mods/bowtie.sh
	mods/bowtie2.sh
Revert "homer chipseq summary added"

This reverts commit 254eb2fa05cf1627b779de46b0d012994520c338.