README.md

# RNA-Seq DGE Workflow

git checkout-index -a -f --prefix=/destination/path/

## How to use install it?

export the directory from git into your project
git archive --format=tar --remote=git-srv1:/local/git/bioinformatics master dge_workflow/ | tar -xf -

http://stackoverflow.com/questions/160608/do-a-git-export-like-svn-export
cd /somewhere
git init
git remote add origin git-srv1:/local/git/bioinformatics
git config core.sparsecheckout true
echo "dge_workflow/" >> .git/info/sparse-checkout
git pull origin master

or


do a sparse checkout
http://stackoverflow.com/questions/600079/is-there-any-way-to-clone-a-git-repositorys-sub-directory-only

git init <repo>
cd <repo>
git remote add -f origin <url>
This creates an empty repository with your remote. Then do:

git config core.sparsecheckout true
Now you need to define which files/folders you want to actually check out. This is done by listing them in .git/info/sparse-checkout, eg:

echo "some/dir/" >> .git/info/sparse-checkout




## How to use it?




1) Optionally rename dge_master.sh to something like dge_mouse_helin.sh
2) Adjust paths in master script
3) Run on madmax
4) Adjust reports if necessary


## How to backport changes into it?

Clone it, change it, push and commit it.