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env.Configure
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MAKEFLOW=/share/home/share/software/cctools-7.1.6/bin/makeflow
PYTHON3=/share/home/share/software/Python-3.8.3/bin/python
PYTHON2=/share/home/share/software/Python-2.7.16/bin/python2
R36=/share/home/share/software/R-3.6.3/bin/R
Rscript36=/share/home/share/software/R-3.6.3/bin/Rscript
JAVA_JRE=/share/home/share/software/java/jre1.8.0_261/bin/java
JAVA_JDK=/share/home/share/software/java/jdk-14.0.2/bin/java
JAVA=/usr/bin/java
CUTADAPT=/share/home/share/software/Python-3.8.3/bin/cutadapt
FASTQC=/share/home/share/software/FastQC/bin/fastqc
TRIMGALORE=/share/home/share/software/TrimGalore-0.6.5/bin/trim_galore
STAR=/share/home/share/software/STAR/bin/Linux_x86_64_static/STAR
RSEMce=/share/home/share/software/RSEM-1.3.3/RSEM/bin/rsem-calculate-expression
BWA=/share/home/share/software/bwa-0.7.17/bin/bwa
SAMTOOLS=/share/home/share/software/samtools-1.10/bin/samtools
SAMBAMBA=/share/home/share/software/sambamba/bin/sambamba
PLOTBAMSTATS=/share/home/share/software/samtools-1.10/bin/plot-bamstats
BEDTOOLS=/share/home/share/software/bedtools2/bin/bedtools
PICARD=/share/home/share/software/GATKtools/gatk/picard-2.23.6.jar
MACS2=/share/home/share/software/Python-3.8.3/bin/macs2
GENRICH=/share/home/share/software/Genrich/bin/Genrich
PRESEQ=/share/home/share/software/preseq_v2.0/bin/preseq
FEATURECOUNTS=/share/home/share/software/subread-2.0.1-Linux-x86_64/bin/featureCounts
IDR=/share/home/share/software/Python-3.8.3/bin/idr
ATAQV=/share/home/share/software/ataqv-1.2.1/bin/ataqv
MKARV=/share/home/share/software/ataqv-1.2.1/bin/mkarv
BAMCOVERAGE=/share/home/share/software/Python-3.8.3/bin/bamCoverage
COMPUTEMATRIX=/share/home/share/software/Python-3.8.3/bin/computeMatrix
PLOTPROFILE=/share/home/share/software/Python-3.8.3/bin/plotProfile
PLOTHEATMAP=/share/home/share/software/Python-3.8.3/bin/plotHeatmap
PLOTFINGERPRINT=/share/home/share/software/Python-3.8.3/bin/plotFingerprint
GENOMECOVERAGEBED=/share/home/share/software/bedtools2/bin/genomeCoverageBed
BEDGRAPHTOBIGWIG=/share/home/share/software/ucsc_app.v401/bin/bedGraphToBigWig
ANNOTATEPEAKS=/share/home/share/software/Homer/bin/annotatePeaks.pl
FINDMOTIFSGENOME=/share/home/share/software/Homer/bin/findMotifsGenome.pl
INDEX=/share/home/share/Repository/GenomeDB/Index/
REFER=/share/home/share/Repository/GenomeDB/Reference/
BWAref_Plasmid20=$INDEX/Plasmid20/BWADB/plasmid20.BP.fasta
GTF_GENCODE_GRCh38=$REFER/Homo_Sapiens/GENCODE/gencode.v34.primary_assembly.annotation.gtf
GTF_ENSEMBL_GRCh38=$REFER/Homo_Sapiens/ENSEMBL/Homo_sapiens.GRCh38.100.gtf
IDX_STAR_ENSEMBL_GRch38_100=$INDEX/Homo_Sapiens/STARDB/ENSEMBL_GRch38_STAR_100
IDX_RSEN_ENSEMBL_GRch38_100=$INDEX/Homo_Sapiens/RSEMDB/ENSEMBL_GRch38_STAR_100/STAR
ATAC_BLACKLIST_HomoSapiens_38=/share/home/share/Repository/GenomeDB/Blacklist/hg38.blacklist.bed
ATAC_BLACKLIST_MusMusculus_38=/share/home/share/Repository/GenomeDB/Blacklist/mm10.blacklist.bed
ATAC_BLACKLIST_MusMusculus_38=/share/home/share/Repository/GenomeDB/Blacklist/mm10.blacklist.merge.bed
GENE_GTF_HomoSapiens_38=/share/home/share/Repository/GenomeDB/Reference/Homo_Sapiens/ENSEMBL/Homo_sapiens.GRCh38.100.gtf
GENE_GTF_MusMusculus_38=/share/home/share/Repository/GenomeDB/Reference/Mus_Musculus/ENSEMBL/Mus_musculus.GRCm38.100.gtf
if [[ $Species == 'hg38' || $Species == 'hg' ]];then
ATAC_BLACKLIST=/share/home/share/Repository/GenomeDB/Blacklist/hg38.blacklist.bed
GENOME_REF=$INDEX/Homo_Sapiens/BWADB/ENSEMBL_GRch38_SMPRIM_BWA/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa
GENE_GTF=$GENE_GTF_HomoSapiens_38
HOMER_REF='hg38'
BWAref=$INDEX/Homo_Sapiens/BWADB/ENSEMBL_GRch38_SMPRIM_BWA/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa
MACS2_GSIZE='hs'
elif [[ $Species == 'hg19' || $Species == 'hg37' ]];then
ATAC_BLACKLIST='ATAC_BLACKLIST_HomoSapiens_38'
GENOME_REF='hg19'
BWAref='hg19'
HOMER_REF='hg19'
MACS2_GSIZE='hs'
elif [[ $Species == 'mm38' || $Species == 'mm10' || $Species == 'mm' ]];then
ATAC_BLACKLIST=$ATAC_BLACKLIST_MusMusculus_38
GENOME_REF=$INDEX/Mus_Musculus/BWADB/ENSEMBL_GRCm38_SMPRIM_BWA/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa
GENE_GTF=$GENE_GTF_MusMusculus_38
BWAref=$INDEX/Mus_Musculus/BWADB/ENSEMBL_GRCm38_SMPRIM_BWA/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa
HOMER_REF='mm10'
MACS2_GSIZE='mm'
elif [[ $Species == 'mm37' || $Species == 'mm9' ]];then
ATAC_BLACKLIST='ATAC_BLACKLIST_MusMusculus_9'
GENOME_REF='mm9'
HOMER_REF='mm9'
BWAref='mm9'
MACS2_GSIZE='mm'
elif [[ $Species == 'plasmid' ]];then
ATAC_BLACKLIST='None'
GENOME_REF=$BWAref_Plasmid20
BWAref=$BWAref_Plasmid20
else
ATAC_BLACKLIST='None'
GENOME_REF='None'
HOMER_REF='hg38'
MACS2_GSIZE='hs'
BWAref='None'
echo "cannot find the speciens atac blacklist!!"
fi