Wrote code that can get a dataset's type for every single GN

dataset; previously we could not view traits in datasets that
were not in the DBType table in the database

1 files changed, 113 insertions, 35 deletions

diff --git a/misc/gn_installation_notes.txt b/misc/gn_installation_notes.txt
index 2607f2b5..7545a5b8 100644
--- a/misc/gn_installation_notes.txt
+++ b/misc/gn_installation_notes.txt
@@ -49,15 +49,6 @@ apt-file search _______
 
 ============================================
 
-Install pip:
-sudo apt-get install python-pip
-
-Install from requirements.txt:
-pip install -r gene/wqflask/requirements.txt -t ve27
-
-
-============================================
-
 Create trash directory:
 mkdir ~/.trash
 
@@ -70,19 +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
 
@@ -94,20 +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
 
 ===========================================
 
@@ -116,10 +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
 
 ===========================================
@@ -133,6 +119,98 @@ 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;
+
+============================================
+
+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
@@ -173,7 +251,7 @@ 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