diff options
Diffstat (limited to 'misc')
| -rw-r--r-- | misc/gn_installation_notes.txt | 237 | ||||
| -rw-r--r-- | misc/notes.txt | 42 | ||||
| -rw-r--r-- | misc/requirements.txt | 34 |
3 files changed, 283 insertions, 30 deletions
diff --git a/misc/gn_installation_notes.txt b/misc/gn_installation_notes.txt index bad21226..6329586f 100644 --- a/misc/gn_installation_notes.txt +++ b/misc/gn_installation_notes.txt @@ -1,6 +1,37 @@ +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-core +sudo apt-get install git =========================================== @@ -16,9 +47,10 @@ git pull origin flask(or whatever the branch is) Search for package with a specified file that can be installed with apt-get apt-file search _______ -Install from requirements.txt: -pip install -r gene/wqflask/requirements.txt -t ve27 +============================================ +Create trash directory: +mkdir ~/.trash ============================================ @@ -29,19 +61,6 @@ dpkg -l | less =========================================== -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 virtualenv: sudo pip install virtualenv @@ -53,20 +72,31 @@ source ~/ve27/bin/activate =========================================== -Installing yaml +Install libmysqlclient-dev (Mysql-Python dependency) +sudo apt-get install libmysqlclient-dev -Install libyaml-dev: -sudo apt-get install libyaml-dev +Install python-dev (numpy dependency) +sudo apt-get install python-dev -Install yaml: -pip install pyyaml +Install scipy dependencies: +sudo apt-get install libatlas-base-dev gfortran g++ =========================================== -Install MySQL Client +Install pip: +sudo apt-get install python-pip -To fix error "mysql_config not found" while installing packages with pip: -sudo apt-get install libmysqlclient-dev +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/misc/requirements.txt =========================================== @@ -75,10 +105,7 @@ 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) -python setup.py build -sudo mkdir /home/zas1024/ve27/include/python2.7/Reaper -sudo chown /home/zas1024/ve27/include/python2.7/Reaper (or whereever the directory is; the problem -involved the fact that doing "sudo python setup.py install" doesn't install within the virtualenv) +mkdir /home/zas1024/ve27/include/python2.7/Reaper python setup.py install =========================================== @@ -92,6 +119,153 @@ 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 @@ -132,7 +306,7 @@ Start up virtual environment: source ~/ve27/bin/activate To set WQFLASK_SETTINGS environment variable: -export WQFLASK_SETTINGS=~/gene/wqflask/cfg/zach_settings.py (or wherever file is located) +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 @@ -146,4 +320,9 @@ Run web server: Run server: python runserver.py +=========================================== + +To do full upgrade (as opposed to apt-get upgrade) +sudo aptitude full-upgrade + ===========================================
\ No newline at end of file diff --git a/misc/notes.txt b/misc/notes.txt index 92ed267b..91a0e67c 100644 --- a/misc/notes.txt +++ b/misc/notes.txt @@ -92,6 +92,15 @@ python runserver.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'; @@ -117,7 +126,7 @@ pylint --help Start screen session: -If "no option -R": +If "no option -R" or running for first time: byobu-select-backend 2. screen @@ -236,6 +245,11 @@ 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 @@ -255,7 +269,33 @@ grep -ir (search string) (directory) =========================================== +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 + diff --git a/misc/requirements.txt b/misc/requirements.txt new file mode 100644 index 00000000..ec02a2c2 --- /dev/null +++ b/misc/requirements.txt @@ -0,0 +1,34 @@ +BeautifulSoup==3.2.1 +Flask==0.9 +Flask-Login==0.1.3 +Flask-Mail==0.7.6 +Flask-Principal==0.3.4 +Flask-SQLAlchemy==0.16 +Flask-Security==1.6.0 +Flask-WTF==0.8.3 +Jinja2==2.6 +MySQL-python==1.2.4 +PyYAML==3.10 +#Reaper==1.0 +Reindent==0.1.1 +SQLAlchemy==0.8.0 +WTForms==1.0.3 +Werkzeug==0.8.3 +apache-libcloud==0.12.3 +argparse==1.2.1 +blinker==1.2 +itsdangerous==0.17 +logging-tree==1.2 +logilab-astng==0.24.3 +logilab-common==0.59.1 +#numarray==1.5.2 +numpy==1.7.0 +passlib==1.6.1 +pp==1.6.3 +pylint==0.27.0 +redis==2.7.2 +requests==1.1.0 +scipy==0.11.0 +simplejson==3.0.7 +wsgiref==0.1.2 +yolk==0.4.3 |