Git

Installation

Redhat EL 6.0

Simple installation:

yum install git

Using git.hpc.ufl.edu

As an example we'll use the awesome group, administrative user (set up by HPC staff) admin and a regular user student.

admin@linux64

The admin user on a remote machine linux64 can do the following

• Check out the admin repository

git clone awesome@git.hpc.ufl.edu:gitosis-admin.git

• Add more users e.g. 'student' with a public key student.pub

cd gitosis-admin
cp ~/student.pub keydir/
git add keydir/*
git commit -m "added user student"
git push

• Create a new repository denovo for de novo assembly scripts and set access to users admin and student

cd gitosis-admin
vim gitosis.conf

Add:

[group awesome]
writable = denovo
members = admin student

• Commit and push

git add *
git commit -m "Set up a new repository denovo for use by admin and student"
git push

• Create a local working tree for the denovo project:

cd
mkdir denovo
cd denovo
git init
git remote add origin awesome@hpc.ufl.edu:denovo.git

• Add and edit some files
• Commit and push to the Git server

git add *
git commit -m "Initial import"
git push origin master

Output:

Initialized empty Git repository in /git/awesome/repositories/denovo.git/
Counting objects: 3, done.
Writing objects: 100% (3/3), 231 bytes, done.
Total 3 (delta 0), reused 0 (delta 0)
To awesome@git.hpc.ufl.edu:denovo.git
* [new branch]      master -> master

student@linux64

• Clone the denovo repository

git clone awesome@git.hpc.ufl.edu:denovo.git

Output:

Cloning into denovo...
remote: Counting objects: 3, done.
remote: Total 3 (delta 0), reused 0 (delta 0)
Receiving objects: 100% (3/3), done.

• Work in the git working tree

cd denovo

Edit and add files

• Commit and push the changes to the repository

git add *
git commit -m "The changes I made"
git push