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diff --git a/doc/notes.txt b/doc/notes.txt deleted file mode 100644 index f8ce2759..00000000 --- a/doc/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 - |