#!/bin/bash
# 11-1-2019 JHZ

# Settings and environment variables

function module ()
{
  eval `/usr/bin/modulecmd bash $*`
}

function MRC_Epid()
{
  export SHOME=/genetics/bin
  export PATH=/genetics/bin:/usr/local/bin:$PATH:/genetics/data/software/bin
  export R_LIBS=/usr/local/lib/R/site-library/:/genetics/bin/R:/usr/local/lib64/R/library:/genetics/data/software/R
  export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib64/R/lib:/genetics/data/software/lib
  export HRC=/gen_omics/data/EPIC-Norfolk/HRC/binary_ped
  export bfile=$HRC/HRC
  export remove_sample=$HRC/exclude.id
  export exclude_snp=$HRC/exclude.snps
}

function cardio()
# Clusters at CEU
{
  module load gcc/5.2.0
  module load matlab/r2014a
  module load mpfr/3.1.4
  module load python/2.7.10
  export SHOME=/scratch/jhz22
  export CYTOSCAPE=$SHOME/Cytoscape_v3.5.1
  export PARTITION=long
}

cardio

## Pipeline
# Location and reference data
export FM_location=$SHOME/FM-pipeline
# GEN files named chr{chr}_{start}_{end}.gen.gz
export GEN_location=$FM_location/1KG/FUSION
# sample file
export sample_file=$FM_location/1KG/FUSION.sample
# Complementary files for fgwas
export fgwas_location_1kg=$SHOME/fgwas/1000-genomes
## software flags: 1=enable
export CAVIAR=1
export CAVIARBF=0
export clumping=1
export FM_summary=1
export GCTA=1
export JAM=1
export LocusZoom=0
export fgwas=1
export finemap=1

## Other environment variables
# parallel processes
export threads=1
# LD calculations
export LD_MAGIC=0
export LD_PLINK=0
# Rscript as in getCredible.r