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-get is an Ubuntu system-wide package manager, while pip is a Python-only system for python packages **** Upgrade system packages for security updates, etc: apt-get upgrade **"apt-cache search" searches for text in the description for various packages, while "apt-file search" searches for files within the packages** Show information about given result item returned by apt-cache search: apt-cache show _______ Search for package with a specified file that can be installed with apt-get apt-file search _______ ============================================ Check which system packages are installed: dpkg -l | less ============================================ NEVER USE SUDO WITH PIP To fix error "mysql_config not found": sudo apt-get install libmysqlclient-dev Create requirements.txt file: pip freeze > requirements.txt (or whatever filename) Install from requirements.txt: pip install -r gene/wqflask/requirements.txt -t ve27 ============================================ To get server running: !If having seemingly inexplicable problems with imports, make sure I've started the environment! Note: Virtual environment is not activated when running as root Start up virtual environment: source ~/ve27/bin/activate Deactivate virtual environment: deactivate (just type deactivate) 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 /usr/sbin/nginx Run server: python runserver.py =========================================== Start screen session: byobu -RD (to start) control-a then :multiuser on control-a then :acladd sam More info on sharing byobu screen with other users: http://wiki.networksecuritytoolkit.org/nstwiki/index.php/HowTo_Share_A_Terminal_Session_Using_Screen control-a c to create channel type: screen -list for sessions screen -r zas1024/25679.byobu or if only one: screen -r zas1024/ =========================================== Start up log: Go to /tmp and tail -f flask_gn_log =========================================== Coffeescript Stuff: coffee -c (filename) coffee -c -w . (to watch for changes and recompile in current directory; the "." is for current directory) coffee --help (for information about setting options) =========================================== Unset ASKPASS when trying to git push unset SSH_ASKPASS =========================================== htop: Gives information on processes, cpu/memory load, etc dstat: Also gives various system information, resource usage, etc df: Reports file system disk space usage =========================================== ll h*: Finds items in the directory starting with h =========================================== tidyp - Improves/beautifies html code tidyp -m -i -w 100 index_page.html =========================================== ps -ax - View processes kill (process #) =========================================== 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 tar xvf qtlreaper-1.1.1.tar.gz (to unzip) python setup.py build python setup.py install =========================================== Using Yolk Install Yolk: pip install yolk Check packages installed in this virtual environment: yolk -l Checks packages that have updates available: yolk -U =========================================== Python stuff: Classes should always inherit "object" To iterate through dictionary items: for X, Y in MyDictionary.items(): =========================================== Create symbolic link: ln -s dir_to_link_to linking_dir =========================================== Reboot server sudo reboot =========================================== Using grep: grep -ir (search string) (directory) -i ignores case -r searches recursively through subdirectories of directory you specify