#! /bin/bash

#######################################################################################
# This file is part of geniac.
# 
# Copyright Institut Curie 2020.
# 
# This software is a computer program whose purpose is to perform
# Automatic Configuration GENerator and Installer for nextflow pipeline.
# 
# You can use, modify and/ or redistribute the software under the terms
# of license (see the LICENSE file for more details).
# 
# The software is distributed in the hope that it will be useful,
# but "AS IS" WITHOUT ANY WARRANTY OF ANY KIND.
# Users are therefore encouraged to test the software's suitability as regards
# their requirements in conditions enabling the security of their systems and/or data.
# 
# The fact that you are presently reading this means that you have had knowledge
# of the license and that you accept its terms.
#######################################################################################


### <<<< MODIFY BELOW WITH YOUR CONFIGURATION

### information about your repository
GIT_CONTAINER_BRANCH="devel"

### information about nf-geniac
GIT_SUBMODULE_REPO="https://github.com/bioinfo-pf-curie/geniac"
GIT_SUBMODULE_DIR="geniac"
GIT_SUBMODULE_SHA1="209fc1b"
GIT_SUBMODULE_BRANCH="release"

GIT_COMMIT_MSG="[MODIF] add nf-geniac as a submodule using commit ${GIT_SUBMODULE_SHA1}"

### END: MODIFY BELOW WITH YOUR CONFIGURATION >>>

### prerequisites
git config --global status.submoduleSummary true
git config --global diff.submodule log


### Add the submodule in your git repository
git submodule add ${GIT_SUBMODULE_REPO} ${GIT_SUBMODULE_DIR}

### Activate the use of the submodule in the repository
git submodule update --init --recursive


##################################
### cd the submodule directory ###
##################################


cd ${GIT_SUBMODULE_DIR}

### check information about the submodule (which is a git repository inside the git repository)
git branch -vv 

### checkout the branch that contains the commit (or version) we want to use
git checkout ${GIT_SUBMODULE_BRANCH}

### download the git submodule repository
git fetch

### checkout the commit (or version) we want to use as a Detached HEAD
git checkout ${GIT_SUBMODULE_SHA1}


### check information about the submodule (we should be on a Detached HEAD with the expected commit)
git branch -vv 


#####################################################
### cd the root directory of your main repository ###
#####################################################

cd ..

git status
git branch -vv
git add ${GIT_SUBMODULE_DIR}
git commit -m "${GIT_COMMIT_MSG}"
git push origin ${GIT_CONTAINER_BRANCH}