Some notes about using Git

Untrack Files In Git Repos Without Deleting Them

1. Do this on all machines

   echo "FILE_NAME" >> .gitignore

   git rm --cached FILE_NAME

   or git rm -r --cached folderName

   For examples: git rm -r --cached .Rproj.user

   git add -u

   git commit -m "removing files from version control"

2. Sync with your git server, pull to sync and push to register your local change

   git pull

   git push

Merge changes from other to master

#set new branch and change to this new branch
git checkout -b new-branch
 
#merge the changes in new-branch to master 
git merge --no-ff new-branch

git checkout -b bioinformatics-gao-patch-1 master
git pull https://github.com/bioinformatics-gao/PathwaySplice.git patch-1    

#Change back to master
git checkout master    
git merge --no-ff bioinformatics-gao-patch-1
git push origin master

Others http://www.interviewadda.com/shortest-path-nodes-binary-search-tree-bst/

Rename a local and remote branch in git

1. Rename your local branch. If you are on the branch you want to rename:

git branch -m new-name

If you are on a different branch:

git branch -m old-name new-name

2. Delete the old-name remote branch and push the new-name local branch.

git push origin :old-name new-name

3. Reset the upstream branch for the new-name local branch. Switch to the branch and then:

git push origin -u new-name

install from the release version of ChipSeq

install_github("aiminy/ChipSeq")

install from different branch or version of ChipSeq

install_github("aiminy/ChipSeq",ref = '0.99.0')

Search a word(Ex:getResultsFromJunctionSeq) in the history of git

git rev-list --all | GIT_PAGER=cat xargs git grep 'getResultsFromJunctionSeq'

then

git show 49892c3cd0b2e3f0bbd9af3f4f537e01e6836cb4

To deal with the following error

"Permission denied (publickey). fatal: Could not read from remote repository. Please make sure you have the correct access rights"

Perform the follwoing commad on macs:

ssh-keygen -t rsa -C "[email protected]" -b 4096

pbcopy < ~/.ssh/id_rsa.pub

Paste in user setting/SSH keys