From 1edcfa898ef401689361a025abc58920c6e43a40 Mon Sep 17 00:00:00 2001 From: Glenn Gaffield Date: Wed, 16 Sep 2020 12:20:02 -0400 Subject: [PATCH] A couple path changes due to storage relocation on Yale Farnam cluster --- src/shell/cmfinder_source_template.sh | 2 +- src/shell/infernal_source_template.sh | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/shell/cmfinder_source_template.sh b/src/shell/cmfinder_source_template.sh index 2273389..cb1f241 100644 --- a/src/shell/cmfinder_source_template.sh +++ b/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 diff --git a/src/shell/infernal_source_template.sh b/src/shell/infernal_source_template.sh index c66974b..01aef9f 100644 --- a/src/shell/infernal_source_template.sh +++ b/src/shell/infernal_source_template.sh @@ -2,7 +2,7 @@ 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 @@ -10,4 +10,4 @@ DATABASE=/gpfs/ysm/pi/breaker/data/refseq98/s50.igr.fasta 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" \ No newline at end of file +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"