gin-scripts/create_research_repositories/add_submodule.sh

#!/usr/bin/env bash

. .//setgin.sh

## this will be taken for the previous code
projectname="testproject" 
projectdir=${HOME}/datasets/${projectname}

##Inputs if made a function:

submodule="raw_data"
folder="10_raw_data2"

## create repo with readme, no issues

echo "Creating ${submodule} submodule ${projectname}.${submodule}"
createrepot ${projectname}.${submodule}
addrepototeam ${projectname}.${submodule} ${projectteam}
issuetrackeroption ${projectname}.${submodule} false

## add repo to parent (cloned version)
git -C ${projectdir} submodule add  git@${ginssh}:/${organisation}/${projectname}.${submodule} ${folder}
git -C ${projectdir} submodule sync

## not working: initialise git annex in submodule
git -C ${projectdir} submodule foreach git annex init

## add to .gitmodules file and sync parent with server

datalad -C ${projectdir} add --to-git .gitmodules --message "Initialise submodules"
datalad -C ${projectdir} publish --recursive

## sync via gin to have submodules on gin server

cd ${projectdir}
gin sync