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


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 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 _______

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Check which system packages are installed:
dpkg -l | less

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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

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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)"

Run web server:
/usr/local/nginx/sbin/nginx
/usr/sbin/nginx

Run server:
python runserver.py

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Update user password:
use mysql;
UPDATE user SET password=PASSWORD('whatever') WHERE user='webqtl';
FLUSH PRIVILEGES;

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Redis things

Restart redis server:
sudo /etc/init.d/redis_6379 stop
sudo /etc/init.d/redis_6379 start

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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/

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Start up log:
Go to /tmp and tail -f flask_gn_log

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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)

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Unset ASKPASS when trying to git push

unset SSH_ASKPASS

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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

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ll h*: Finds items in the directory starting with h

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du -hms * | sort -n : Gives size used by different directories
-h: human readable
-m: in megabytes (default)
-s: summarize

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rm -rfv

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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)

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tidyp - Improves/beautifies html code
tidyp -m -i -w 100 index_page.html

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ps -ax - View processes

kill (process #)

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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

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Using Yolk

Install Yolk:
pip install yolk

Check packages installed in this virtual environment:
yolk -l

Checks packages that have updates available:
yolk -U

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Python stuff:

Classes should always inherit "object"
To iterate through dictionary items: for X, Y in MyDictionary.items():

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Create symbolic link:
ln -s dir_to_link_to linking_dir

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Reboot server
sudo reboot

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Using grep:

grep -ir (search string) (directory)

-i ignores case
-r searches recursively through subdirectories of directory you specify

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MySQL Things -

Create fulltext (MATCH AGAINST syntax) index:
CREATE FULLTEXT INDEX __________ ON Table (Column);