## Reference Files
REF_GENOME=/data5/bsi/refdata/BOWTIE/M.musculus.mm9/mm9.fa
BOWTIE_REF=/data5/bsi/refdata/BOWTIE/M.musculus.mm9/mm9
MIRBASE_HAIRPIN=/data5/bsi/refdata/mirbase/v19/hairpin.mmu.dna.fa
MIRBASE_MATURE=/data5/bsi/refdata/mirbase/v19/mature.mmu.dna.fa

## Tool Paths
SCRIPT_PATH=/projects/bsi/bictools/scripts/miRNA/trunk/
MIRDEEP2_PATH=/projects/bsi/bictools/apps/miRNA/mirdeep/2.0.0.5/
BOWTIE_PATH=/projects/bsi/bictools/apps/alignment/bowtie/0.12.7/
RANDFOLD_PATH=/projects/bsi/bictools/apps/miRNA/mirdeep/2.0.0.5/essentials/randfold-2.0/
SQUID_PATH=/projects/bsi/bictools/apps/miRNA/mirdeep/2.0.0.5/essentials/squid-1.9g/
VIENNA_PATH=/projects/bsi/bictools/apps/miRNA/mirdeep/2.0.0.5/essentials/ViennaRNA-1.8.4/install_dir/bin/
PDFAPI2_PM_PATH=/projects/bsi/bictools/apps/miRNA/mirdeep/2.0.0.5/lib/lib/perl5/
JAVA_PATH=/usr/java/latest/bin/
PICARD_PATH=/projects/bsi/bictools/apps/alignment/picard/1.77/
FASTQC_PATH=/projects/bsi/bictools/apps/qc/FastQC
CUTADAPT_PATH=/projects/bsi/bictools/apps/miRNA/cutadapt/0.9.5/
SAMTOOLS_PATH=/projects/bsi/bictools/apps/alignment/samtools/samtools-0.1.18
BEDTOOLS_PATH=/projects/bsi/bictools/apps/misc/BEDTools/2.15.0/bin/

## Tool Parameters
CUTADAPT_PARAMS=-b AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -b GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT -b GATCTACACGTTCAGAGTTCTACAGTCCGACGATC -b GATCGTCGGACTGTAGAACTCTGAACGTGTAGATC -O 3 -m 17 -f fastq
MAPPER_PARAMS=-e -h -q -m -r 5 -u -v -o 4
MIRDEEP2_PARAMS=-P -t Mouse
MIRDEEP2_CLOSE_SPECIES=none
QUANTIFIER_PARAMS=-P -W
BOWTIE_PARAMS=-p 4 -S -q -n 1 -e 80 -l 18 -a -m 5 --best --strata --sam-RG PL:Illumina --sam-RG LB:hg19  --sam-RG CN:Mayo
SORTSAM_PARAMS=MAX_RECORDS_IN_RAM=1800000 VALIDATION_STRINGENCY=SILENT
QUEUE=ngs-sec -l medp=TRUE

## Memory Parameters
# QSUB
CUTADAPT_MEM=-l h_vmem=4G -l h_stack=10M
CUTADAPT_STATS_MEM=-l h_vmem=1G -l h_stack=10M
BOWTIE_MAPPER_MEM=-l h_vmem=4G -l h_stack=10M
MIRDEEP2_MAPPER_MEM=-l h_vmem=4G -l h_stack=10M
ALIGNMENT_STATS_MEM=-l h_vmem=1G -l h_stack=10M
MIRDEEP2_MEM=-l h_vmem=6G -l h_stack=10M
EXPRESSION_REPORTS_MEM=-l h_vmem=1G -l h_stack=10M
EXPRESSION_STATS_MEM=-l h_vmem=1G -l h_stack=10M
MERGE_STATS_MEM=-l h_vmem=1G -l h_stack=10M
# JVM
SORTSAM_JVM_MEM=-Xmx6g -Xms512m

