pandora.config.hpc.txt

[Step1]
refstar=/ifs/scratch/c2b2/rr_lab/shares/ref/STAR 
refbowtie=/ifs/scratch/c2b2/rr_lab/shares/ref/hg19/faidx/hg19.fa 
gtf=/ifs/scratch/c2b2/rr_lab/shares/ref/pandora_resources/hg19.refFlat.gtf
qparam=-N hsep -V -cwd -o log.out -e log.err -l mem=64G,time=12:: -pe smp 4 -R y

[Step2]
qparam=-N asm -V -cwd -o log.out -e log.err -l mem=80G,time=6:: -pe smp 8 -R y
# qparam=-N asm -V -cwd -o log.out -e log.err -l mem=4G,time=4::

[Step3]
blastdb=/ifs/scratch/c2b2/rr_lab/shares/ref/blastdb/nt-current/nt 
qparam=-N blst -V -cwd -o log.out -e log.err -l mem=6G,time=8::
bmem=8
btime=4

[Step4]
pblastdb=/ifs/scratch/c2b2/rr_lab/shares/ref/blastdb/nr-current/nr
qparam=-N orf -V -cwd -o log.out -e log.err -l mem=2G,time=2::

[Step5]
qparam=-N rep -V -cwd -o log.out -e log.err -l mem=4G,time=1::
taxid2names=/ifs/scratch/c2b2/rr_lab/shares/ref/taxdump/names.dmp
blacklist=/ifs/scratch/c2b2/rr_lab/shares/ref/pandora_resources/blacklist.txt

[StepA1]
taxid2names=/ifs/scratch/c2b2/rr_lab/shares/ref/taxdump/names.dmp
taxid2nodes=/ifs/scratch/c2b2/rr_lab/shares/ref/taxdump/nodes.dmp
accblacklist=/ifs/scratch/c2b2/rr_lab/shares/ref/pandora_resources/accession_ID_blacklist.txt