## Reference Files
REF_GENOME=/home/mayo/refdata/BOWTIE/H.sapiens.UCSC.hg19/hg19.fa
BOWTIE_REF=/home/mayo/refdata/BOWTIE/H.sapiens.UCSC.hg19/hg19
MIRBASE_HAIRPIN=/home/mayo/refdata/mirbase/v19/hairpin.hsa.dna.fa
MIRBASE_MATURE=/home/mayo/refdata/mirbase/v19/mature.hsa.dna.fa
MIRBASE_GFF=/home/mayo/refdata/mirbase/v19/hsa.gff3
GENCODE_GTF=/home/mayo/refdata/gencode/gencode.v18.annotation.gtf

## Tool Paths
SCRIPT_PATH=/home/mayo/miRNA
MIRDEEP2_PATH=/usr/local/mirdeep/
BOWTIE_PATH=/usr/local/bowtie/
RANDFOLD_PATH=/usr/local/bin/
SQUID_PATH=/usr/local/
VIENNA_PATH=/usr/local/share/ViennaRNA/bin/
PDFAPI2_PM_PATH=/projects/bsi/bictools/apps/miRNA/mirdeep/2.0.0.5/lib/lib/perl5/
JAVA_PATH=/usr/local/bin/java/bin/
NGS_PORTAL_PATH=/projects/bsi/bictools/apps/misc/ngs_dashboard/2.0
PICARD_PATH=/usr/local/picard/
FASTQC_PATH=/usr/local/FastQC
CUTADAPT_PATH=/usr/local/bin/
SAMTOOLS_PATH=/usr/local/bin/
BEDTOOLS_PATH=/usr/local/bedtools/
GATK_JAR=/usr/local/GenomeAnalysisTK.jar
VCFTOOLS_PATH=/projects/bsi/bictools/apps/variant_detection/vcftools/0.1.9/bin/
VCFTOOLS_PERLLIB=/projects/bsi/bictools/apps/variant_detection/vcftools/0.1.9/perl/
HTSEQ_PATH=/projects/bsi/bictools/apps/mrnaseq/htseq/0.5.3p9/bin/
HTSEQ_LIB_PATH=/projects/bsi/bictools/apps/mrnaseq/htseq/0.5.3p9/lib/python2.7/site-packages/
PYTHON_PATH=/usr/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 Human
MIRDEEP2_CLOSE_SPECIES=none
QUANTIFIER_PARAMS=-P -W
BOWTIE_PARAMS=-p 4 -S -q -n 1 -e 80 -l 30 -a -m 5 --best --strata
ADDORREPLACEREADGROUPS_PARAMS=MAX_RECORDS_IN_RAM=1800000 VALIDATION_STRINGENCY=SILENT RGLB=hg19 RGCN=Mayo RGPL=Illumina 
SORTSAM_PARAMS=MAX_RECORDS_IN_RAM=1800000 VALIDATION_STRINGENCY=SILENT
PRINTREADS_PARAMS=-rf ReassignOneMappingQuality -RMQF 255 -RMQT 60
UNIFIEDGENOTYPER_PARAMS=-glm SNP -dcov 1000
HTSEQ_PARAMS=-m intersection-nonempty -q -t exon -s no
QUEUE=ngs-sec -l medp=TRUE

## Memory Parameters
# QSUB
REFERENCE_INDEXES_MEM=-l h_vmem=3G -l h_stack=10M
CUTADAPT_MEM=-l h_vmem=4G -l h_stack=10M
FASTQC_MEM=-l h_vmem=5G -l h_stack=10M
BAMS_MEM=-l h_vmem=4G -l h_stack=10M
MIRDEEP2_MAPPER_MEM=-l h_vmem=4G -l h_stack=10M
MIRDEEP2_MEM=-l h_vmem=6G -l h_stack=10M
VARIANTS_MEM=-l h_vmem=12G -l h_stack=10M
EXPRESSION_REPORTS_MEM=-l h_vmem=1G -l h_stack=10M
DIFF_EXPRESSION_MEM=-l h_vmem=2G -l h_stack=10M
GENCODE_CLASSIFICATION_MEM=-l h_vmem=10G -l h_stack=10M
SAMPLE_SUMMARY_MEM=-l h_vmem=1G -l h_stack=10M
MAIN_DOC_MEM=-l h_vmem=1G -l h_stack=10M
# JVM
ADDORREPLACEREADGROUPS_JVM_MEM=-Xmx6g -Xms512m
SORTSAM_JVM_MEM=-Xmx6g -Xms512m
CREATEDICTIONARY_JVM_MEM=-Xmx1g -Xms512m
UNIFIEDGENOTYPER_JVM_MEM=-Xmx8g -Xms512m
