pasa

## templated variables to be replaced exist as <__var_name__>

# SQLite settings
DATABASE=/public/home/software/test/PASA/pasa.sqlite


#######################################################
# Parameters to specify to specific scripts in pipeline
# create a key = "script_name" + ":" + "parameter" 
# assign a value as done above.

#script validate_alignments_in_db.dbi
validate_alignments_in_db.dbi:--MIN_PERCENT_ALIGNED=75
validate_alignments_in_db.dbi:--MIN_AVG_PER_ID=95
validate_alignments_in_db.dbi:--NUM_BP_PERFECT_SPLICE_BOUNDARY=0

#script subcluster_builder.dbi
subcluster_builder.dbi:-m=50

#BSUB -J pasa
#BSUB -n 20
#BSUB -R span[hosts=1]
#BSUB -o %J.out
#BSUB -e %J.err
#BSUB -q normal
module load PASA/2.5.2
Launch_PASA_pipeline.pl -c alignAssembly.config -C -r -R --ALT_SPLICE -g genome.fa -t all.fa.clean -T -u all.fa -f accession.txt --TDN TCN.acc --transcribed_is_aligned_orient --ALIGNERS blat,gmap --CPU 20