Checkout from github

Use source tree on development machines or git on servers to checkout.

Table of Contents For SourceTree(clone repository): For Git command line(Test and Prod): Update files from current branch(either develop or master) To switch to a branch

For SourceTree(clone repository):

URL: https://username@github.com/TabakoffLab/PhenoGen.git
Destination: /usr/share/tomcat/webapps/PhenoGen
Bookmark Name: PhenoGen

Advanced:
Get working copy: true
Checkout branch: develop  (All development should occur on development except hotfixes)
Recurse submodules: true

For Git command line(Test and Prod):

Update files from current branch(either develop or master)

Note: We will generally try to keep master on compbio, but at the begining current files are in develop so it is checked out on compbio. See switching branches for directions on moving from one branch to another. PhenoGen will always be the master branch.

1. Login as tomcat and cd to PhenoGen or PhenoGenTEST.
2. run

git status

Check to make sure no files have been modified on compbio. Files will be listed as either modified, untracked(additional files not checked in), removed, etc.

If anything changed you can either discard:

git checkout -- <file>

or commit:

git add <file>
git commit

Then pull files from GitHub by using the following:

git pull origin <branch> 
ex. git pull origin develop or git pull origin master

depending on the branch being used.

To switch to a branch

1. Login as tomcat and cd to PhenoGen or PhenoGenTEST.
2. run

git status

Check to make sure no files have been modified on compbio. Files will be listed as either modified, untracked(additional files not checked in), removed, etc.

If anything changed you can either discard:

git checkout -- <file>

or commit:

git add <file>
git commit

Then checkout files from GitHub by using the following:

git checkout origin/<branch> 

ex. git checkout origin/develop or git checkout origin/master

depending on the branch being used.