Merge branch 'staging' of github.com:genenetwork/genenetwork2 into development

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+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)
+
+Add all files in current directory branch to be staged to be committed
+git add -A
+
+Git push to my github repository
+git push https://github.com/zsloan/genenetwork.git master
+
+Get the default path being used when a command is typed:
+which _______
+
+Change default path python looks at when importing
+export PYTHONPATH="/home/zas1024/gene/wqflask"
+
+Get the paths checked when a user types a command:
+echo $PATH
+
+Get all environment variables:
+set
+
+
+**** 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 update
+apt-get dist-upgrade (can probably be used in place of apt-get upgrade)
+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=~/zach_settings.py (or wherever file is located)
+
+zach_settings.py is the local config file with the DB_URI
+default_settings.py is the config file with the configuration information that would apply
+to any running instance of GeneNetwork
+
+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)"
+
+Reload web server:
+/usr/sbin/nginx -s reload
+
+Run server:
+python runserver.py
+
+Run sendmail.py
+python send_mail.py
+
+===========================================
+
+UFW - default firewall confirguation tool for Ubuntu; eases iptables firewall configuration
+
+Enable UFW:
+sudo ufw enable
+Check status of UFW:
+sudo ufw status verbose
+
+===========================================
+
+Update user password:
+use mysql;
+UPDATE user SET password=PASSWORD('whatever') WHERE user='webqtl';
+FLUSH PRIVILEGES;
+
+===========================================
+
+Redis things
+
+Restart redis server:
+sudo /etc/init.d/redis_6379 stop
+sudo /etc/init.d/redis_6379 start
+
+===========================================
+
+Run pylint:
+pylint file_name
+
+For options:
+pylint --help 
+
+===========================================
+
+Start screen session:
+
+If "no option -R" or running for first time:
+byobu-select-backend
+2. screen
+
+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
+
+===========================================
+
+du -hms * | sort -n : Gives size used by different directories
+-h: human readable
+-m: in megabytes (default)
+-s: summarize
+
+===========================================
+
+rm -rfv
+
+===========================================
+
+cp -a (archive; copies recursively and doesn't follow symbol links)
+   -i (interactive, prompts before overwrite)
+   -v (verbose)
+   -b (backup)
+   
+mv (same as above, but with no -a)
+
+===========================================
+
+Add user:
+sudo adduser
+Edit /etc/sudoers to give user root privileges
+
+
+===========================================
+
+tidyp - Improves/beautifies html code
+tidyp -m -i -w 100 index_page.html
+
+===========================================
+
+ps ax - View processes
+ps ux (the "u" is for user)
+
+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():
+
+===========================================
+
+Change import path from command line
+export PYTHONPATH=~/gene/wqflask (or whatever)
+
+===========================================
+
+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
+
+===========================================
+
+Command line arguments:
+
+Use argparse to deal with command line arguments (instead of argv or optparse)
+
+===========================================
+
+Change owner/group:
+
+chown zas1024 somefile (change owner of somefile to zas1024)
+chown zas1024: somefile (change owner and group of somefile to zas1024)
+sudo chown root: somefile (change owner/group of somefile to root)
+
+Change permissions:
+
+chmod g-wr (remove write/read privileges for group)
+chmod g+w (add write privileges for group)
+chmod u+rwx (add read, write, and execute privileges for user)
+etc.
+
+===========================================
+
+MySQL Things -
+
+Create fulltext (MATCH AGAINST syntax) index:
+CREATE FULLTEXT INDEX __________ ON Table (Column);
+
+If <4 character searches not working:
+Add ft_min_word_len = 2 (to make te minimum characters 2) to config file
+Rebuild relevant tables with fulltext indexes with "REPAIR TABLE _______ QUICK"
+
+===========================================
+
+To delete all .pyc files (for example if there's some issue you're having trouble resolving):
+find . -name '*.pyc' -delete
+http://stackoverflow.com/questions/785519/how-do-i-remove-all-pyc-files-from-a-project
+