| SSDSPIPELINEPATH | location of run_SSDS_pipeline binary |
| SSDSPICARDPATH | picard location (recommend: $SSPIPELINEPATH/picard-tools-2.3.0) |
| SSDSFASTXPATH | path to fastx_trimmer binary (recommend: $SSPIPELINEPATH) |
| SSDSSAMTOOLSPATH | path to samtools binary (recommend: $SSPIPELINEPATH) |
| SSDSGENOMESPATH | genomes top level folder |
| SSDSTMPPATH | temporary folder location |
| PERL5LIB | $SSDSPIPELINEPATH must be added to the perl path |
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