diff options
| -rw-r--r-- | misc/gn_installation_notes.txt | 112 | ||||
| -rw-r--r-- | wqflask/other_config/nginx_conf/penguin.conf | 42 | ||||
| -rw-r--r-- | wqflask/other_config/wqflask-nginx.conf | 83 |
3 files changed, 109 insertions, 128 deletions
diff --git a/misc/gn_installation_notes.txt b/misc/gn_installation_notes.txt index e31273b1..11bda48c 100644 --- a/misc/gn_installation_notes.txt +++ b/misc/gn_installation_notes.txt @@ -49,30 +49,6 @@ apt-file search _______ ============================================ -Install pip: -sudo apt-get install python-pip - -REMEMBER TO SOURCE VE BEFORE INSTALLING - -Comment out in requirements.txt: -Reaper -numarray - -Install from requirements.txt (after activating virtualenv): -pip install -r gene/misc/requirements.txt - -When it hits error with install MySQL-Python, install libmysqlclient-dev: -sudo apt-get install libmysqlclient-dev - -When hits error with numpy install python-dev: -sudo apt-get install python-dev - -When hits error with scipy: -sudo apt-get install libatlas-base-dev gfortran g++ - - -============================================ - Create trash directory: mkdir ~/.trash @@ -85,19 +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 @@ -109,20 +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 =========================================== @@ -145,6 +119,54 @@ 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 + +============================================ + +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 diff --git a/wqflask/other_config/nginx_conf/penguin.conf b/wqflask/other_config/nginx_conf/penguin.conf new file mode 100644 index 00000000..822556d3 --- /dev/null +++ b/wqflask/other_config/nginx_conf/penguin.conf @@ -0,0 +1,42 @@ +server { + # Modeled after http://flask.pocoo.org/docs/deploying/wsgi-standalone/ + listen 80; + + server_name penguin.uthsc.edu; + + access_log /var/log/nginx/access.log; + error_log /var/log/nginx/error.log; + + location ^~ /css/ { + root /gene/wqflask/wqflask/static/; + } + + location ^~ /javascript/ { + root /gene/wqflask/wqflask/static/; + } + +# location ^~ /image/ { +# root /gene/wqflask/wqflask/static/; +# } + + location ^~ /images/ { + root /gene/wqflask/wqflask/static/; + } + + ### New - added by Sam + #location ^~ /static/ { + # root /gene/wqflask/wqflask/static/; + #} + + location / { + proxy_pass http://127.0.0.1:5000/; + proxy_redirect off; + + proxy_set_header Host $host; + proxy_set_header X-Real-IP $remote_addr; + proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; + + proxy_read_timeout 40m; + } +} + diff --git a/wqflask/other_config/wqflask-nginx.conf b/wqflask/other_config/wqflask-nginx.conf deleted file mode 100644 index 4e6fd0d9..00000000 --- a/wqflask/other_config/wqflask-nginx.conf +++ /dev/null @@ -1,83 +0,0 @@ -server { - # Modeled after http://flask.pocoo.org/docs/deploying/wsgi-standalone/ - listen 80; - - server_name gn2python.genenetwork.org; - - access_log /var/log/nginx/access.log; - error_log /var/log/nginx/error.log; - - location ^~ /css/ { - root /gene/wqflask/wqflask/static/; - } - - location ^~ /javascript/ { - root /gene/wqflask/wqflask/static/; - } - -# location ^~ /image/ { -# root /gene/wqflask/wqflask/static/; -# } - - location ^~ /images/ { - root /gene/wqflask/wqflask/static/; - } - - ### New - added by Sam - #location ^~ /static/ { - # root /gene/wqflask/wqflask/static/; - #} - - location / { - proxy_pass http://127.0.0.1:5000/; - proxy_redirect off; - - proxy_set_header Host $host; - proxy_set_header X-Real-IP $remote_addr; - proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; - - proxy_read_timeout 40m; - } -} - -server { - # Modeled after http://flask.pocoo.org/docs/deploying/wsgi-standalone/ - listen 80; - - server_name gn2python_lei.genenetwork.org; - - access_log /var/log/nginx/lei_access.log; - error_log /var/log/nginx/lei_error.log; - - location ^~ /css/ { - root /gene/wqflask/wqflask/static/; - } - - location ^~ /javascript/ { - root /gene/wqflask/wqflask/static/; - } - -# location ^~ /image/ { -# root /gene/wqflask/wqflask/static/; -# } - - location ^~ /images/ { - root /gene/wqflask/wqflask/static/; - } - - ### New - added by Sam - #location ^~ /static/ { - # root /gene/wqflask/wqflask/static/; - #} - - location / { - proxy_pass http://127.0.0.1:5001/; - proxy_redirect off; - - proxy_set_header Host $host; - proxy_set_header X-Real-IP $remote_addr; - proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; - - proxy_read_timeout 40m; - } -} |