// Andril Case Study - GLOBAL CONFIGURATIONS
// author: Marko Laakso, Riku Louhimo

// Enables gene expression analysis
doGeneExpression = true

// Enables transcript expression analysis
doTranscriptExpression = true

// Enables microRNA expression analysis
doMiRNAExpression = true

// Enables copy number analysis
doArrayCGH = true

/* Anduril installation */
andurilHome = $ANDURIL_HOME

// Root of the project data storage
//dataDir = "/storageExt/tcga-glioblastoma"
dataDir = "data"

// Gene expression data
// NOTE: The second and the last lines of this file were removed manually.
prenormalizedGeneExpression = dataDir+"/expression/Expression-Genes/BI__HT_HG-U133A/Level_2/broad.mit.edu__HT_HG-U133A__probeset_rma"

/** Transcript expression matrix */
transcriptExpressionFileName = dataDir+"/exon-normalized/Expression-Exon/LBL_HuEx-1_0-st-v2/Level_2/TranscriptExpression_v56"

/** Gene level transcript expression matrix */
genelevelExpressionFileName = dataDir+"/exon-normalized/Expression-Exon/LBL_HuEx-1_0-st-v2/Level_2/GeneExpression_v56"

/** Array CGH data */
arrayCGHdatadir = dataDir+"/acgh/acgh-data/cangem/DataFiles/"

/** Annotation file for transcript expression matrix */
transcriptAnnotationFileName = dataDir+"/exon-normalized/Expression-Exon/LBL_HuEx-1_0-st-v2/Level_2/TranscriptExprAnnotation_v56"

/** Clinical parameters for the patients */
patientMetadataFileName = dataDir+"/patient-metadata.csv"

/**
  Database configurations for Ensemble database~\cite{flicek2008}.
  The exact content can be seen in Section~\ref{propertiesDoc}.
 */
ensembl = INPUT(path="ensemblHS.properties")

/** Database configuration for Ensembl variation database. */
snpdb = INPUT(path="ensemblSNP.properties")

/** Settings for SNPHelistin database (see Section~\ref{propertiesDoc}) */
genotypeDB = INPUT(path="csv/snpstorage.properties")

miRNAExprNormalized = INPUT(path=dataDir+"/mirna/Expression-miRNA/UNC__H-miRNA_8x15K/Level_2/unc.edu__H-miRNA_8x15K__Quantile_Normalized_Log2")
miRNAProbeAnnot = INPUT(path=dataDir+"/mirna/agilent_G4470A_probes_CIBEX.csv")
miRNANames = INPUT(path=dataDir+"/mirna/miRBase_Sequences_rel9.1.csv")
miRNATargets = INPUT(path=dataDir+"/mirna/miRBase_Targets_v4_hsa.csv")

/** A very short description of this study */
abstract = INPUT(path="abstract")

authors = "Kristian Ovaska,Marko Laakso,Riku Louhimo,Erkka Valo,Viljami Aittom\\\"aki,Sampsa Hautaniemi"