#init_vars#

#!/usr/bin/env bash
#
# Script name: init_vars
#
# Description: Script to initalise the variables needed for the pipeline.
#
# Authors: Fidel Alfaro-Almagro, Stephen M. Smith & Mark Jenkinson
#
# Copyright 2017 University of Oxford
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#    http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#

###########################################
#                                         #
#   USER MUST MODIFY THE INDICATED LINES  #
#                                         #
###########################################

# UKBB ROOT DIR LOCATION
export BBDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && cd ..; pwd )"
                                                       #TO BE MODIFIED BY USER

#TODO implement this in the files
export QUEUE_STANDARD="all.q"                                                   #TO BE MODIFIED BY USER
export QUEUE_MORE_MEM="bigmem_16.q"                                             #TO BE MODIFIED BY USER
export QUEUE_MAX_MEM="bigmem_64.q"                                              #TO BE MODIFIED BY USER

#SETUP AFNI
export AFNIDIR=/opt/afni                                                        #TO BE MODIFIED BY USER

#SETUP FREESURFER 
export FREESURFER_HOME=/opt/freesurfer                                          #TO BE MODIFIED BY USER
source $FREESURFER_HOME/SetUpFreeSurfer.sh  > /dev/null

#SETUP FSL  
export FSLDIR=/opt/HCPpipelines-4.1.3/fsl                                       #TO BE MODIFIED BY USER
. $FSLDIR/etc/fslconf/fsl.sh
export FSLCONFDIR="${FSLDIR}/config"
export FSLOUTPUTTYPE="NIFTI_GZ"
export FSLGECUDAQ=cuda.q 

# SET UP MATLAB
export MCROOT="$BBDIR/software/MCR_2017b_glnxa64"
export MCRV="v93"

#Move $FSLDIR/bin before $FREESURFER_HOME in the path
FSLDIRseddable=`echo $FSLDIR | sed 's|/|\\\/|g'`
PATH=`echo $PATH | sed "s|$FSLDIR/bin||g"`
export PATH="$FSLDIR/bin:$PATH"

#SETUP EXTERNAL LIBRARIES
export R_LIBS="$BBDIR/software/env/lib/R/library"
export R_DIR="$BBDIR/software/env/lib/R"


#SET LOCALE FOR FLOATING POINT FORMATTING
export LC_ALL=C

#ENV VARIABLES FOR BIOBANK
export BB_BIN_DIR="$BBDIR/tvb-ukbb"
export FSLGPUDIR="$BB_BIN_DIR/bb_diffusion_pipeline/bb_bedpostx"
export MNI="$FSLDIR/data/standard/MNI152_T1_1mm.nii.gz"
export MNI_mask="$FSLDIR/data/standard/MNI152_T1_1mm_brain_mask.nii.gz"
export MNI_brain="$FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz"
export MNI_dir="$FSLDIR/data/standard"
export templ="$BB_BIN_DIR/templates"
export PYTHONPATH="$BBDIR/software/env/bin/python"
export FSL_FIXDIR="$BB_BIN_DIR/bb_functional_pipeline/bb_fix_dir"

#export SUBJECT_AGE_LIST="BB_BIN_DIR/bb_structural_pipeline/FAST_age_spec/subject_ages.tsv"     #TO BE MODIFIED BY USER
#export AGE_SPECIFIC_TEMPLATE_LIST="$BB_BIN_DIR/bb_structural_pipeline/FAST_age_spec/age_specific_templates.tsv"  
export PARC_IMG="$templ/parcellations/Schaefer2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_1mm.nii.gz"     #TO BE MODIFIED BY USER
export PARC_LUT="$templ/parcellations/Schaefer2018/Schaefer2018_200Parcels_17Networks_LUT.txt"                     #TO BE MODIFIED BY USE
export numROI="100"                                                              #TO BE MODIFIED BY USER
#export SLICE_TIMING_FILE="$BB_BIN_DIR/bb_data/slice_timing_odd_even.txt"
export TRAINING_FILE="tvbbaby_Calgary.RData"                                            #TO BE MODIFIED BY USER

#INCLUDE 3 MAIN BIOBANK DIRECTORIES IN PATH
export PATH="$BB_BIN_DIR/bb_pipeline_tools/:$BB_BIN_DIR/bb_general_tools/:$PATH"


#SET PATH FOR MCR
export LD_LIBRARY_PATH="$MCROOT/$MCRV/runtime/glnxa64:$MCROOT/$MCRV/bin/glnxa64:$MCROOT/$MCRV/sys/os/glnxa64:$MCROOT/$MCRV/sys/opengl/lib/glnxa64:$LD_LIBRARY_PATH"

export MATLAB_COMPILER_RUNTIME="$MCROOT/$MCRV"
# export MATLAB_COMPILER_RUNTIME="/opt/MatlabR2017b/MATLAB_Runtime/v93"         #TO BE MODIFIED BY USER

export XAPPLRESDIR="$MCROOT/$MCRV/X11/app-defaults"

conda activate $BBDIR/software/env