#!/bin/bash

###########################################
# The pipeline is located here :
pipePath="/t1-data/data/hugheslab/jelenatools/CCseqBasic/CM5"
###########################################
# This is the name we give our sample (no fancy characters, don't start the name with a number)

Sample="testSample"

#############################################

# The fastq files are located here (these cannot be .gz packed files)

# This is the genome build for the run :

Genome="mm9dpnMasked"

# Supported genomes (time of writing 08oct2018) :
# mm9 mm10 hg18 hg19 hg38 danRer7 danRer10 galGal4 dm3 dm6 mm10balb mm9PARP hg19hindMasked mm9dpnMasked
# The 'masked' genomes save time by mapping to RE-fragment ends only (recommended for HUGE designs only)

# This is the oligo coordinate input file (containing the dpnII fragments within which your biotinylated capture oligos are) :
# Make this file with this tutorial : http://sara.molbiol.ox.ac.uk/public/telenius/captureManual/Generating_Oligo_Coordinate_File_For_CaptureC_analyser.pdf

OligoFile="/t1-data/user/hugheslab/telenius/developmentAndTesting/CM5rainbowtest_240918/oligofile_few.txt"

# We are now here (the current directory) - the directory we are now running the pipe :

rundir=$( pwd )

# This is the path to the public folder we want to put the data into (this folder can exist, but it does not need to) :
PublicPath="/public/telenius/capturetests/cm5test_240918/${Sample}"

# Reuse the blat runs from here (CM5 runs demand blat results - can be constructed with the same script, by adding flag --onlyBlat to the run command below) :

reusedir="/t1-data/user/hugheslab/telenius/runsAndAnalysis/damien7000oligos_181217/2_monsterBlatRuns/combined"

#############################################
# We are now here (the current directory) - the directory we are now running the pipe :

rundir=$( pwd )


# Tell where we are - print it to output :

echo "Running pipe.sh in folder ${rundir}"

# Tell the command to user - print it to output :

echo "${pipePath}/pipeRainbow.sh -o "${OligoFile}" -s "${Sample}" --pf "${PublicPath}" --genome ${Genome} --chunkmb 1012 --BLATforREUSEfolderPath ${reusedir} --wobblyEndBinWidth 20 "


# Run the command :

${pipePath}/pipeRainbow.sh -o "${OligoFile}" -s "${Sample}" --pf "${PublicPath}" --genome ${Genome} --chunkmb 1012 --BLATforREUSEfolderPath ${reusedir} --wobblyEndBinWidth 20


# Tell the user that we are now finished :

echo
date
echo "All done !"
echo