From c0b7da4b4c2bd98353eb980402075318010a79a3 Mon Sep 17 00:00:00 2001 From: Zachary Sloan Date: Tue, 9 Jul 2013 17:07:13 -0500 Subject: Committing installation notes before editing them more --- misc/gn_installation_notes.txt | 24 ++++++++++++++++++------ misc/requirements.txt | 4 ++-- 2 files changed, 20 insertions(+), 8 deletions(-) (limited to 'misc') diff --git a/misc/gn_installation_notes.txt b/misc/gn_installation_notes.txt index 2607f2b5..e31273b1 100644 --- a/misc/gn_installation_notes.txt +++ b/misc/gn_installation_notes.txt @@ -52,8 +52,23 @@ apt-file search _______ Install pip: sudo apt-get install python-pip -Install from requirements.txt: -pip install -r gene/wqflask/requirements.txt -t ve27 +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++ ============================================ @@ -116,10 +131,7 @@ 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 =========================================== diff --git a/misc/requirements.txt b/misc/requirements.txt index 0e892c05..ec02a2c2 100644 --- a/misc/requirements.txt +++ b/misc/requirements.txt @@ -9,7 +9,7 @@ Flask-WTF==0.8.3 Jinja2==2.6 MySQL-python==1.2.4 PyYAML==3.10 -Reaper==1.0 +#Reaper==1.0 Reindent==0.1.1 SQLAlchemy==0.8.0 WTForms==1.0.3 @@ -21,7 +21,7 @@ itsdangerous==0.17 logging-tree==1.2 logilab-astng==0.24.3 logilab-common==0.59.1 -numarray==1.5.2 +#numarray==1.5.2 numpy==1.7.0 passlib==1.6.1 pp==1.6.3 -- cgit v1.2.3 From d56f54d23b9f1621049e4cf62049e17e21b88201 Mon Sep 17 00:00:00 2001 From: Zachary Sloan Date: Wed, 10 Jul 2013 15:34:31 -0500 Subject: Updated gn_installation_notes --- misc/gn_installation_notes.txt | 112 ++++++++++++++++----------- wqflask/other_config/nginx_conf/penguin.conf | 42 ++++++++++ wqflask/other_config/wqflask-nginx.conf | 83 -------------------- 3 files changed, 109 insertions(+), 128 deletions(-) create mode 100644 wqflask/other_config/nginx_conf/penguin.conf delete mode 100644 wqflask/other_config/wqflask-nginx.conf (limited to 'misc') 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 @@ -47,30 +47,6 @@ 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 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: @@ -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; - } -} -- cgit v1.2.3 From 917227e5610374f838f3872df2f6df884cb4a239 Mon Sep 17 00:00:00 2001 From: root Date: Wed, 10 Jul 2013 18:15:20 -0500 Subject: Updated installation notes --- misc/gn_installation_notes.txt | 27 ++++++++++++++++++++++++++- 1 file changed, 26 insertions(+), 1 deletion(-) (limited to 'misc') diff --git a/misc/gn_installation_notes.txt b/misc/gn_installation_notes.txt index 11bda48c..46441b39 100644 --- a/misc/gn_installation_notes.txt +++ b/misc/gn_installation_notes.txt @@ -137,6 +137,31 @@ 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 + +============================================ + Using Yolk Install Yolk: @@ -207,7 +232,7 @@ 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 -- cgit v1.2.3