Get git: sudo apt-get install git-core =========================================== Clone code from git repository: git clone http://github.com/zsloan/genenetwork.git gene Pull from branch in git repository: git pull origin flask(or whatever the branch is) **"apt-cache search" searches for text in the description for various packages, while "apt-file search" searches for files within the packages** Search for package with a specified file that can be installed with apt-get apt-file search _______ Install from requirements.txt: pip install -r gene/wqflask/requirements.txt -t ve27 =========================================== Installing virtualenv: sudo pip install virtualenv Tell virtualenv which directory to use: virtualenv ve27 Start up virtual environment: source ~/ve27/bin/activate =========================================== Installing yaml Install libyaml-dev: sudo apt-get install libyaml-dev Install yaml: pip install pyyaml =========================================== Install MySQL Client To fix error "mysql_config not found" while installing packages with pip: sudo apt-get install libmysqlclient-dev =========================================== Installing QTL Reaper wget http://downloads.sourceforge.net/project/qtlreaper/qtlreaper/1.1.1/qtlreaper-1.1.1.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fqtlreaper%2Ffiles%2Flatest%2Fdownload&ts=1358975786&use_mirror=iweb mv -v qtlreaper-1.1.1.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fqtlreaper%2Ffiles%2Flatest%2Fdownload&ts=1358975786&use_mirror=iweb qtlreaper-1.1.1.tar.gz tar xvf qtlreaper-1.1.1.tar.gz (to unzip) python setup.py build sudo mkdir /home/zas1024/ve27/include/python2.7/Reaper sudo chown /home/zas1024/ve27/include/python2.7/Reaper (or whereever the directory is; the problem involved the fact that doing "sudo python setup.py install" doesn't install within the virtualenv) python setup.py install =========================================== Installing numarray 1.5.2 wget http://downloads.sourceforge.net/project/numpy/Old%20Numarray/1.5.2/numarray-1.5.2.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fnumpy%2Ffiles%2FOld%2520Numarray%2F1.5.2%2Fnumarray-1.5.2.tar.gz%2Fdownload&ts=1358978306&use_mirror=superb-dca2 mv -v numarray-1.5.2.tar.gz?r=http:%2F%2Fsourceforge.net%2Fprojects%2Fnumpy%2Ffiles%2FOld%20Numarray%2F1.5.2%2Fnumarray-1.5.2.tar.gz%2Fdownload numarray-1.5.2.tar.gz tar xvf numarray-1.5.2.tar.gz sudo python setup.py install =========================================== Installing R sudo apt-get install r-base-dev =========================================== Install Parallel Python (pp) wget http://www.parallelpython.com/downloads/pp/pp-1.6.3.tar.gz tar xvf pp-1.6.3.tar.gz python setup.py install ========================================== Install requests pip install requests ========================================== Install logging_tree pip install logging_tree ========================================== To get server running: !If having seemingly inexplicable problems with imports, make sure I've started the environment! Start up virtual environment: source ~/ve27/bin/activate To set WQFLASK_SETTINGS environment variable: export WQFLASK_SETTINGS=~/gene/wqflask/cfg/zach_settings.py (or wherever file is located) To change screen environment variable (if man not working or to get color, for example): export TERM=screen To search for commands in history if necessary: history | grep "(whatever is being searched for)" Run web server: /usr/local/nginx/sbin/nginx Run server: python runserver.py ===========================================