From 7be6c2c94c99148667a05f400ca47df1c472d964 Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Thu, 24 Jan 2013 17:46:19 -0600
Subject: Added a lot to the notes in the process of setting up on the new
 server

---
 misc/gn_installation_notes.txt | 38 ++++++++++++++++++++++++++++++++++++--
 misc/notes.txt                 | 18 ++++++++++++++++++
 2 files changed, 54 insertions(+), 2 deletions(-)

diff --git a/misc/gn_installation_notes.txt b/misc/gn_installation_notes.txt
index 54e8fcee..173f2819 100644
--- a/misc/gn_installation_notes.txt
+++ b/misc/gn_installation_notes.txt
@@ -27,7 +27,18 @@ sudo pip install virtualenv
 Tell virtualenv which directory to use:
 virtualenv ve27
 
+Start up virtual environment:
+source ~/ve27/bin/activate
+
+===========================================
 
+Installing yaml
+
+Install libyaml-dev:
+sudo apt-get install libyaml-dev
+
+Install yaml:
+pip install pyyaml
 
 ===========================================
 
@@ -43,8 +54,11 @@ 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)
-sudo python setup.py build
-sudo python setup.py install
+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)
+python setup.py install
 
 ===========================================
 
@@ -63,6 +77,26 @@ sudo apt-get install r-base-dev
 
 ===========================================
 
+Install Parallel Python (pp)
+
+wget http://www.parallelpython.com/downloads/pp/pp-1.6.3.tar.gz
+tar xvf pp-1.6.3.tar.gz
+python setup.py install
+
+==========================================
+
+Install requests
+
+pip install requests
+
+==========================================
+
+Install logging_tree
+
+pip install logging_tree
+
+==========================================
+
 To get server running:
 
 !If having seemingly inexplicable problems with imports, make sure I've started the environment!
diff --git a/misc/notes.txt b/misc/notes.txt
index ab71a99f..e60102fc 100644
--- a/misc/notes.txt
+++ b/misc/notes.txt
@@ -4,9 +4,19 @@ git clone http://github.com/zsloan/genenetwork.git gene
 Pull from branch in git repository:
 git pull origin flask(or whatever the branch is)
 
+
+**** 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 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 _______
 
@@ -25,9 +35,14 @@ 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=~/gene/wqflask/cfg/zach_settings.py (or wherever file is located)
 
@@ -128,4 +143,7 @@ Python stuff:
 Classes should always inherit "object"
 To iterate through dictionary items: for X, Y in MyDictionary.items():
 
+===========================================
 
+Create symbolic link:
+ln -s dir_to_link_to linking_dir
-- 
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