Adding documentation

2 files changed, 0 insertions, 657 deletions

diff --git a/doc/old/gn_installation_notes.txt b/doc/old/gn_installation_notes.txt
deleted file mode 100644
index efea0309..00000000
--- a/doc/old/gn_installation_notes.txt
+++ /dev/null
@@ -1,346 +0,0 @@
-UFW - default firewall confirguation tool for Ubuntu; eases iptables firewall configuration
-
-Enable UFW:
-sudo ufw enable
-Check status of UFW:
-sudo ufw status verbose
-
-Limit ssh:
-sudo ufw limit ssh
-
-Enable http, https:
-sudo ufw allow http
-sudo ufw allow https
-
-===========================================
-
-http://evilrouters.net/2011/02/18/using-etckeeper-with-git-on-ubuntu/
-
-Install etckeeper:
-sudo apt-get install etckeeper
-
-Edit /etc/etckeeper/etckeeper.conf to comment out VCS="bzr" and comment in VCS="git"
-
-Initialize repository:
-sudo etckeeper init
-
-Do initial commit:
-sudo etckeeper commit "Initial commit."
-
-===========================================
-
-Get git:
-
-sudo apt-get install git
-
-===========================================
-
-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 _______
-
-============================================
-
-Create trash directory:
-mkdir ~/.trash
-
-============================================
-
-Using dpkg
-
-Check which system packages are already installed:
-dpkg -l | less
-
-===========================================
-
-Installing virtualenv:
-sudo pip install virtualenv
-
-Tell virtualenv which directory to use:
-virtualenv ve27
-
-Start up virtual environment:
-source ~/ve27/bin/activate
-
-===========================================
-
-Install libmysqlclient-dev (Mysql-Python dependency)
-sudo apt-get install libmysqlclient-dev
-
-Install python-dev (numpy dependency)
-sudo apt-get install python-dev
-
-Install scipy dependencies:
-sudo apt-get install libatlas-base-dev gfortran g++
-
-===========================================
-
-Install pip:
-sudo apt-get install python-pip
-
-REMEMBER TO SOURCE VE BEFORE INSTALLING 
-
-Comment out in requirements.txt:
-Reaper
-numarray
-
-Before installing from requirements.txt, install numpy separately:
-pip install numpy==1.7.0 (or whatever version we're using)
-
-Install from requirements.txt (after activating virtualenv):
-pip install -r gene/doc/requirements.txt
-
-===========================================
-
-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)
-mkdir /home/zas1024/ve27/include/python2.7/Reaper
-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 nginx
-
-sudo -s
-nginx=stable # use nginx=development for latest development version
-echo "deb http://ppa.launchpad.net/nginx/$nginx/ubuntu lucid main" > /etc/apt/sources.list.d/nginx-$nginx-lucid.list
-apt-key adv --keyserver keyserver.ubuntu.com --recv-keys C300EE8C
-apt-get update 
-apt-get install nginx
-
-Create configuration file in ~/gene/wqflask/other_config/nginx_conf/ (modeled off of the others)
-Create symbolic link to config file in /etc/nginx/sites-enabled/:
-ln -s dir_to_link_to linking_dir
-
-Run nginx:
-sudo /usr/sbin/nginx
-
-============================================
-
-Copy over zach_settings.py to /home/zas1024 directory (or whatever is home directory)
-
-export WQFLASK_SETTINGS=~/gene/wqflask/cfg/zach_settings.py (or wherever file is located)
-
-============================================
-
-Install MySQL Server
-
-sudo apt-get install mysql-server
-
-mkdir /mnt/big
-fdisk /dev/sdb
-m: for help
-n: new partion
-...
-w: write to table and exit
-
-Start MySQL server:
-service mysql start
-
-Stop MySQL server:
-service mysql stop
-
-Change root password:
-mysql> UPDATE mysql.user SET Password=PASSWORD('your password') WHERE User='root';
-
-Setup accounts in MySQL (first need to delete anonymous/non-root accounts):
-#; use mysql;
-#; select * from user;
-#; delete from user where Host!="localhost";
-#; delete from user where User!="root";
-#; update user set Password = Password('yourpassword') where User='root';
-#; GRANT ALL ON *.* TO 'yourusername'@'%' IDENTIFIED BY 'yourpassword';
-#; select * from user;
-
-Use Percona to optimise my.cfg file:
-https://tools.percona.com/wizard
-
-To check # CPUs:
-grep -c processor /proc/cpuinfo
-
-To check memory, can use htop
-
-============================================
-
-Check RSA key:
-ssh-keygen -l -f /etc/ssh/ssh_host_rsa_key
-
-03:2c:d7:01:01:f0:31:3a:c8:df:e4:98:62:2c:59:d2  root@penguin (RSA)
-
-============================================
-
-Installing redis server
-
-In the dls directory:
-$ wget http://redis.googlecode.com/files/redis-2.6.14.tar.gz
-$ tar xzf redis-2.6.14.tar.gz
-$ cd redis-2.6.14
-$ make
-
-Run redis (from inside redis-2.6.14 directory):
-src/redis-server
-
-For the rest of the installation instructions, refer to:
-http://redis.io/topics/quickstart
-
-To continue installation (from the README):
-
-In order to install Redis binaries into /usr/local/bin just use:
-
-    % make install
-
-Make install will just install binaries in your system, but will not configure
-init scripts and configuration files in the appropriate place. This is not
-needed if you want just to play a bit with Redis, but if you are installing
-it the proper way for a production system, we have a script doing this
-for Ubuntu and Debian systems:
-
-    % cd utils
-    % ./install_server
-
-The script will ask you a few questions and will setup everything you need
-to run Redis properly as a background daemon that will start again on
-system reboots.
-
-In the redis config file (/etc/redis/6379.conf) uncomment the following line:
-bind 127.0.0.1
-
-This is so only the local computer has access
-
-============================================
-
-Check RSA key:
-ssh-keygen -l -f /etc/ssh/ssh_host_rsa_key
-
-03:2c:d7:01:01:f0:31:3a:c8:df:e4:98:62:2c:59:d2  root@penguin (RSA)
-
-============================================
-
-Using Yolk
-
-Install Yolk:
-pip install yolk
-
-Check packages installed in this virtual environment:
-yolk -l
-
-Checks packages that have updates available:
-yolk -U
-
-===========================================
-
-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 R
-
-sudo apt-get install r-base-dev
-
-===========================================
-
-Installing rpy2
-
-pip install rpy2
-
-===========================================
-
-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
-
-==========================================
-
-Install colordiff (just to make it easier to view differences in files, not necessary for GN)
-
-sudo apt-get install colordiff
-
-==========================================
-
-Install NTP (network time protocol)
-
-sudo apt-get install ntp
-
-==========================================
-
-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==============
-
-Install requests
-
-pip install requests
-
-=======================
-
-To set WQFLASK_SETTINGS environment variable:
-export WQFLASK_SETTINGS=~/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
-
-===========================================
-
-To do full upgrade (as opposed to apt-get upgrade)
-sudo aptitude full-upgrade
-
-===========================================
diff --git a/doc/old/notes.txt b/doc/old/notes.txt
deleted file mode 100644
index f8ce2759..00000000
--- a/doc/old/notes.txt
+++ /dev/null
@@ -1,311 +0,0 @@
-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
-