Setting Up Git

Getting Git

Installation on Windows workstation

Download the installer at: https://git-scm.com/download/win

Options:

• Choosing the default editor used by Git. I use vim as the default editor. However, while vim is the standard editor for Unix systems it has a fairly high learning curve. For first time users, a more intuitive editor such as Notepad++ might be more appropriate until you become familiar with using vim.
• Adjusting your PATH environment. I think that "Use Git from the Windows Command Prompt." This allows you to use git from the command prompt and will not override Windows tools.
• Choosing the HTTPS transport backend. Use the OpenSSL library
• Configuring the line ending conversions. Select "Checkout Windows as-is, commit Unix-style line endings," this is necessary for cross-platform compatibility.

Installation on MacOSX

The easiest way to get git is to install Xcode Command line tools. Since we have a lot of large files, we will need to install LFS. On OSX this is

brew install git-lfs

hipergator

If you are using the hipergator cluster, git is already packaged as a module.

$ module load git

For installing git-lfs, I'm not sure if that is installed on hipergator. I'll tell you when i find out.

Ohio Supercomputing Center(OSC)

git push produces a GTK-askpass error, which produces an error because it is trying to connect to an X11 terminal and typically we do not login with an X11 terminal. To suppress these errors add the following line to your .profile or .bashrc or .bash_profile. [1]

unset SSH_ASKPASS 

Compiling git from source

This was more of a problem when HPC were administer often by research groups. These days most HPCs have professional administrators who have already set this up. The steps here are probably pretty stale, but I have provided a link because it might be useful to sombody!

• Compiling git from source.

References

[1] https://blog.codonomics.com/2011/04/how-to-disable-gnome-ssh-askpass.html

Setting up Git

git config --global user.name "Eugene Ragasa"

git config --global user.email "eragasa@ufl.edu"

for git on windows

git config --global credential.helper wincred

for git on linux

git config --global credential.helper cache

References:

[1] https://help.github.com/articles/set-up-git/

[2] https://help.github.com/articles/caching-your-github-password-in-git/#platform-windows

[3] https://help.github.com/articles/caching-your-github-password-in-git/

Compiling From Source

[I have not done this in a while so the dependencies are possibly wrong]

Since I primarily develop on a cluster, I generally develop and run application from a Linux command line. On some clusters, it is possible that git may not be installed on your HPC system. Since we will be compiling from source, we should get the latest release from the GitHub source repository.

• Git Source Repository

These directions will create a git binary in $HOME/usr/local/git/bin/git, which will need to create:

mkdir $HOME/usr/local

Build Curl

wget https://curl.haxx.se/download/curl-7.47.1.tar.gz tar -xf curl-7.47.1.tar.gz mkdir $HOME/usr/local/curl 

cd curl-7.47.1 ./configure --prefix=$HOME/usr/local/curl 

make 

make install  

Build expat

wget http://downloads.sourceforge.net/expat/expat-2.1.0.tar.gz 

tar -xf expat-2.1.0.tar.gz mkdir $HOME/usr/local/expat 

cd expat-2.1.0 ./configure --prefix=$HOME/usr/local/expat 

make 

make install  

Build Git

wget https://github.com/git/git/archive/v2.6.4.tar.gz 

tar -xf v2.6.4 mkdir $HOME/usr/local/git 

cd git-2.6.4 make configure ./configure --prefix=$HOME/usr/local/git --with-curl=$HOME/usr/local/curl --with-expat=$HOME/usr/local/expat 

make 

make install

You may have a problem with connecting to github. This is an unsecure way to update because it leaves you vulnerable to man-in-the-middle attacks.

git config --global http.sslVerify false