Remove hardcoding of path to java executable
Fix MANIFEST - legacy file left in generating false warning
remove spuriously merged file

functionality of this "classic" is in bcl2bam_phix_deplex_wtsi_stage1_template
use samtools_cmd as subst id for samtools and remove Sanger specific path to samtools-1.1
Fix template name and description

no need to call stage2 as no treatment of existing PhiX alignment.
Merge branch 'dkj-devel' into devel
removed the incorrect "level=0" from the final bamrecompress
removed the superfluous sortorder flag from the final bamrecompress
Merge pull request #44 from dozy/bamreccompress_fix

removed the incorrect "level=0" and sortorder flag from the final bamrecompress
install action should not remove lib directory at target; added compilation test; enabled warnings in scripts
Merge branch 'mgcam-devel' into devel
allow specification of (biobambam) markduplicates executable as a subst_param, with a default of bammarkduplicates2 until questions about bammarkstreamingduplicates are resolved
Merge pull request #46 from dozy/bammarkduplicates_change

allow specification of markduplicates executable as parameter
change default markduplicates to bammarkduplicates2 for vtlib template set
Merge pull request #48 from dozy/bmd_change_vtlib

bammarkduplicates2 for vtlib
Merge pull request #47 from wtsi-npg/devel

release 0.09