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

or

do a sparse checkout (not recommenced without solid understandng how git works) http://stackoverflow.com/questions/600079/is-there-any-way-to-clone-a-git-repositorys-sub-directory-only

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

How to use it?

1. Copy dge_master_template.sh into and rename into something meaningful (e.g. dge_mouse_helin.sh)
2. Adjust DGE_HOME 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.