#!/bin/bash

###########################################
# The statistics pipeline is located here :
pipePath="/t1-data/data/hugheslab/jelenatools/CC/statisticsCis"
###########################################

# This is wrapper around Marieke Oudelaar's script capture_R_analysis1.pl
# ( which is a combination of James Davies' original statistical analyses for captureC data)

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

# This is neither CC3 or CC4 output folder,
# located in /t1-data/usr/....../Promoter_capture
#
# Promoter_capture
#    |
#    | CONDITION-samples (3 replicates)
#    |
#    |-- Analysis_INSERT_EB5
#    |   `-- CCanalyser_gff_files_of_INSERT_EB5
#    |-- Analysis_INSERT_EB6
#    |   `-- CCanalyser_gff_files_of_INSERT_EB6
#    |-- Analysis_INSERT_EB7
#    |   `-- CCanalyser_gff_files_of_INSERT_EB7
#    |
#    | CONTROL-samples (3 replicates)
#    |
#    |-- Analysis_WT_Sp5
#    |   `-- CCanalyser_gff_files_of_WT_Sp5
#    |-- Analysis_WT_Sp6
#    |   `-- CCanalyser_gff_files_of_WT_Sp6
#    |-- Analysis_WT_Sp15
#    |   `-- CCanalyser_gff_files_of_WT_Sp15
#

pathToUpstreamFolder="/t1-data/usr/....../Promoter_capture"
withoutPipelineSampleFolders="Analysis_INSERT_EB5/CCanalyser_gff_files_of_INSERT_EB5,Analysis_INSERT_EB6/CCanalyser_gff_files_of_INSERT_EB6,Analysis_INSERT_EB7/CCanalyser_gff_files_of_INSERT_EB7,Analysis_WT_Sp5/CCanalyser_gff_files_of_WT_Sp5,Analysis_WT_Sp6/CCanalyser_gff_files_of_WTN_Sp6,Analysis_WT_Sp15/CCanalyser_gff_files_of_WT_Sp15"
condition="INSERT" # Part of the CONDITION folder name which identifies it as "condition" folder
control="WT" # Part of the CONDITION folder name which identifies it as "condition" folder

# Then you select which oligos of interest you want to analyse.
# These are oligo names from your oligo file, except for combined globines check the gff name separately.
oligos="Mitof,SOX2,nanog"

# Give oligo file, where the script can read "which chromosome is cis"
oligoFile="/t1-data/full/path/to/usedOligoFile.txt"
# ( should contain AT LEAST the oligos listed in 'oligos' above )

# In which genome your sample was mapped ?
genome="mm9"

# Which name you would like to give your sample (and your public data hub) ?
name="myAnalysis"

# Where would you like to put it in your public directory ?
# (this dir does not need to exist beforehand)
publicFolder="/public/username/capturedata/analysis"


#############################################
# 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 statisticsRunner.sh in folder ${rundir}"


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

echo
echo ${pipePath}/statisticsRunner.sh
echo "            --genome ${genome} " 
echo "            --pf ${publicFolder} "
echo "            --condition ${condition} "
echo "            --control ${control} "
echo "            --name ${name} "
echo "            --path ${pathToUpstreamFolder} "
echo "            --nonPipelineFolders ${withoutPipelineSampleFolders} "
echo "            --oligos ${oligos} "
echo "            --oligoFile ${oligoFile} "
echo


# Run the command :

${pipePath}/statisticsRunner.sh --genome ${genome} --pf ${publicFolder} --condition ${condition} --control ${control} --name ${name} --path ${pathToUpstreamFolder} --nonPipelineFolders ${withoutPipelineSampleFolders} --oligos ${oligos} --oligoFile ${oligoFile}



# Tell the user that we are now finished :

echo "All done !"