Git Repository

Git_repository.sh

# Create git repository and push to remote
cd workspace/Clinical_genomics_framework/
git init
git add .
git commit -m "Clinical genomics framework"
echo "# Clinical_genomics_framework" >> README.md
git add README.md
git commit -m "Readme file"

Create a repo online using browser  then push local to remote

git remote add origin https://github.com/nilesh-tawari/Clinical_genomics_framework.git
git push -u origin master

RESOURCE: https://stackoverflow.com/questions/37937984/git-refusing-to-merge-unrelated-histories

# configure git repo
git config user.name "nilesh-tawari"
git config user.email "EMAIL"

# tracked files
git ls-tree --name-only --full-tree -r HEAD

# clean the history
git clone --mirror https://github.com/nilesh-tawari/fusion_list.git
cd fusion_list.git/
java -jar ../../bfg-1.13.0.jar  --delete-files CosmicBreakpointsExport.tsv.gz
java -jar ../../bfg-1.13.0.jar  --delete-files CosmicFusionExport.tsv.gz
git reflog expire --expire=now --all && git gc --prune=now --aggressive
git push



# sync fork with master REF: https://help.github.com/articles/syncing-a-fork/

git remote -v
git remote add upstream https://github.com/macarthur-lab/clinvar.git
git remote -v
git fetch upstream
git checkout master
git merge upstream/master
git status
git add .
git commit -m "check snsps"
git push origin master