EVscope/EVscope.conf at main · TheDongLab/EVscope · GitHub

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# ==============================================================================
# CONFIGURATION FILE FOR THE EVSCOPE PIPELINE
# Version: 1.0.0
# ==============================================================================

# --- A. Core Paths ---
# IMPORTANT: Set this to the absolute path of your EVscope installation directory.
EVscope_PATH="/path/to/EVscope"

# --- B. Tool Paths & Environments ---
CIRI2_PERL_SCRIPT="${EVscope_PATH}/soft/CIRI_v2.0.6/CIRI2.pl"
BBSPLIT_SCRIPT="${EVscope_PATH}/soft/bbmap/bbsplit.sh"
RSEM_CALC_EXPR="${EVscope_PATH}/soft/RSEM_v1.3.3/rsem-calculate-expression"
KRAKEN_DB="${EVscope_PATH}/soft/kraken2/standard_krakendb"
KRAKEN_TOOLS_DIR="${EVscope_PATH}/soft/KrakenTools"

# --- C. Conda Environments ---
PICARD_ENV="picard_env"
KRAKEN2_ENV="kraken2_env"
MULTIQC_ENV=""
CORE_PYTHON_ENV=""

# --- D. Java Memory ---
# Used for Picard/Java tools. Default is 250g if left empty.
JAVA_MEM="250g"

# --- E. Reference Genomes & Indices ---
HUMAN_GENOME_FASTA="${EVscope_PATH}/references/genome/hg38/hg38.p14.whole.genome.fa"
MYCOPLASMA_GENOME_FASTA="${EVscope_PATH}/references/genome/mycoplasma/mycoplasma_ge.fa"
ECOLI_GENOME_FASTA="${EVscope_PATH}/references/genome/ecoli/E.coli_ge.fa"

RSEM_BOWTIE2_INDEX="${EVscope_PATH}/references/index/RSEM_bowtie2_index_3659642_RNNAs/RSEM_REF_HG38_3659642_RNNAs"
STAR_INDEX="${EVscope_PATH}/references/index/Index_STAR-2.7.10b_sjdbOverhang99_GeneCode45"
BWA_INDEX="${EVscope_PATH}/references/index/Index_BWA_V0.7.18/hg38.p14.whole.genome.fa"

# --- F. General Annotation ---
PIPELINE_BIN_DIR="${EVscope_PATH}/bin"
TOTAL_GENE_GTF="${EVscope_PATH}/references/annotations_HG38/HG38_3659642_combined_RNAs_with_gold_standard_piRNAs.gtf"
TOTAL_GENE_REFFLAT="${EVscope_PATH}/references/annotations_HG38/HG38_3659642_combined_RNAs_with_gold_standard_piRNAs.refflat"
TOTAL_GENEID_META="${EVscope_PATH}/references/annotations_HG38/3659642_HG38_geneID_Symbol_RNAtype_with_gold_standard_piRNAs.tsv"
GENCODE_V45_GTF="${EVscope_PATH}/references/annotations_HG38/gencode.v45.chr_patch_hapl_scaff.annotation_UCSC.gtf"
GENCODE_V45_REFFLAT="${EVscope_PATH}/references/annotations_HG38/gencode.v45.chr_patch_hapl_scaff.annotation_UCSC.refflat"
GENCODE_V45_non_overlapping_exon_BED="${EVscope_PATH}/references/annotations_HG38/3_gencode.v45.chr_patch_hapl_scaff.annotation_UCSC.non_overlapping_exon_only.bed"
HUMAN_RRNA_INTERVAL="${EVscope_PATH}/references/annotations_HG38/GeneCodeV45_combined_Nucl_Mt_rRNA_589.interval_list"
ENCODE_BLACKLIST_BED="${EVscope_PATH}/references/annotations_HG38/Encode_hg38-blacklist.v2.bed"

# --- G. Step 18: Merged SAF for meta-gene region counting ---
# Single merged SAF with 7 mutually exclusive regions (801,166 features).
# GeneID format: {region}__region_{N}  (e.g. exon__region_1, intron__region_42)
# Regions: 5UTR, 3UTR, exon, intron, promoter, downstream, intergenic
# Priority: 5UTR > 3UTR > exon > intron > promoter > downstream > intergenic
export STEP18_MERGED_SAF="${EVscope_PATH}/references/annotations_HG38/HG38_all7_metagene_noOverlap.saf"
# Region labels for output (order matters for pie chart)
export STEP18_REGION_LABELS="5UTR,3UTR,exon,intron,promoter,downstream,intergenic"

# --- H. Step 26a: BED files for RNA Type Density Plot ---
export STEP26_RNATYPE_BEDS=(
    "${EVscope_PATH}/references/annotations_HG38/HG38_protein_coding.bed"
    "${EVscope_PATH}/references/annotations_HG38/HG38_tRNAs.bed"
    "${EVscope_PATH}/references/annotations_HG38/HG38_rRNAs.bed"
    "${EVscope_PATH}/references/annotations_HG38/HG38_Y_RNAs.bed"
    "${EVscope_PATH}/references/annotations_HG38/HG38_snoRNAs.bed"
    "${EVscope_PATH}/references/annotations_HG38/HG38_snRNAs.bed"
    "${EVscope_PATH}/references/annotations_HG38/HG38_scaRNAs.bed"
    "${EVscope_PATH}/references/annotations_HG38/HG38_vault_RNAs.bed"
    "${EVscope_PATH}/references/annotations_HG38/HG38_lncRNAs.bed"
    "${EVscope_PATH}/references/annotations_HG38/HG38_TEC_protein_coding.bed"
    "${EVscope_PATH}/references/annotations_HG38/HG38_IG_genes.bed"
    "${EVscope_PATH}/references/annotations_HG38/HG38_TR_genes.bed"
    "${EVscope_PATH}/references/annotations_HG38/HG38_misc-sncRNAs.bed"
    "${EVscope_PATH}/references/annotations_HG38/HG38_miRNAs.bed"
    "${EVscope_PATH}/references/annotations_HG38/HG38_pseudogenes.bed"
    "${EVscope_PATH}/references/annotations_HG38/HG38_ERVs.bed"
    "${EVscope_PATH}/references/annotations_HG38/HG38_LINEs.bed"
    "${EVscope_PATH}/references/annotations_HG38/HG38_SINEs.bed"
    "${EVscope_PATH}/references/annotations_HG38/HG38_piRNAs_gold_standard.bed"
)
export STEP26_RNATYPE_LABELS="[protein_coding,tRNAs,rRNAs,Y_RNAs,snoRNAs,snRNAs,scaRNAs,vault_RNAs,lncRNAs,TEC_protein_coding,IG_genes,TR_genes,misc-sncRNAs,miRNAs,pseudogenes,ERVs,LINEs,SINEs,piRNAs]"

# --- I. Step 26b: BED files for Meta-Gene Density Plot ---
export STEP26_METAGENE_BEDS=(
    "${EVscope_PATH}/references/annotations_HG38/HG38_promoter_upstream2000bp_noOverlap.bed"
    "${EVscope_PATH}/references/annotations_HG38/HG38_5UTR_noOverlap.bed"
    "${EVscope_PATH}/references/annotations_HG38/HG38_exon_noOverlap.bed"
    "${EVscope_PATH}/references/annotations_HG38/HG38_intron_noOverlap.bed"
    "${EVscope_PATH}/references/annotations_HG38/HG38_3UTR_noOverlap.bed"
    "${EVscope_PATH}/references/annotations_HG38/HG38_downstream_2kb_noOverlap.bed"
    "${EVscope_PATH}/references/annotations_HG38/HG38_intergenic_noOverlap.bed"
)
export STEP26_METAGENE_LABELS="[Promoters,5'UTR,Exon,Intron,3'UTR,Downstream,Intergenic]"

# --- J. Deconvolution Refs ---
GTEX_SMTS_REF="${EVscope_PATH}/references/deconvolution_HG38/human_ref_GTEx_v10_SMTS_AVG_TPM.csv"
Monaco2020_ImmuneCell_REF="${EVscope_PATH}/references/deconvolution_HG38/human_ref_Monaco2020_ImmuneCell_AVG_TPM.csv"
BRAIN_SC_REF="${EVscope_PATH}/references/deconvolution_HG38/human_ref_brain_single_cell_atlasV1_31superclusters_AVP_CPM.csv"