Merge pull request #13 from BreakerLab/hotfix_farnam

A couple path changes due to storage relocation on Yale Farnam cluster

Author: kenibrewer

src/shell/cmfinder_source_template.sh

@@ -1,5 +1,5 @@
 # Replace path below with the location of the cmfinder executables on your compute cluster
-export PATH=$PATH:/ysm-gpfs/pi/breaker/software/packages/cmfinder-0.4.1.18/bin
+export PATH=$PATH:/gpfs/gibbs/pi/breaker/software/packages/cmfinder-0.4.1.18/bin
 
 #################################
 # Do not modify below this line

src/shell/infernal_source_template.sh

@@ -2,12 +2,12 @@
 module load Infernal
 
 # Replace with the path to the downloaded microbial igr database
-DATABASE=/gpfs/ysm/pi/breaker/data/refseq98/s50.igr.fasta
+DATABASE=/gpfs/gibbs/pi/breaker/data/refseq98/s50.igr.fasta
 
 #################################
 # Do not modify below this line
 #################################
 SEQDIR=$STEPNAME/$SEQNAME
 CMBUILDCOMMAND="cmbuild -F $NOSS -o $SEQDIR/$SEQNAME.out  $SEQDIR/$SEQNAME.cm  $SEQDIR/$SEQNAME.sto"
 CMCALIBRATECOMMAND="cmcalibrate  $SEQDIR/$SEQNAME.cm"
-CMSEARCHCOMMAND="cmsearch -E 0.01 -o  $SEQDIR/$SEQNAME.cm.out --tblout  $SEQDIR/$SEQNAME.cm.tblout -A  $SEQDIR/$SEQNAME.cm.align.sto  $SEQDIR/$SEQNAME.cm $DATABASE"
+CMSEARCHCOMMAND="cmsearch -E 0.01 -o  $SEQDIR/$SEQNAME.cm.out --tblout  $SEQDIR/$SEQNAME.cm.tblout -A  $SEQDIR/$SEQNAME.cm.align.sto  $SEQDIR/$SEQNAME.cm $DATABASE"