Merge branch 'flask' of http://github.com/zsloan/genenetwork into flask

1 files changed, 46 insertions, 2 deletions

diff --git a/misc/notes.txt b/misc/notes.txt
index 2ae9710b..e60102fc 100644
--- a/misc/notes.txt
+++ b/misc/notes.txt
@@ -4,23 +4,45 @@ 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 _______
+
 To fix error "mysql_config not found":
 sudo apt-get install libmysqlclient-dev
 
+Create requirements.txt file:
+pip freeze > requirements.txt (or whatever filename)
+
 Install from requirements.txt:
 pip install -r gene/wqflask/requirements.txt -t ve27
 
-
-
 ============================================
 
 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)
 
@@ -97,9 +119,31 @@ kill (process #)
 
 ===========================================
 
+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
+tar xvf qtlreaper-1.1.1.tar.gz (to unzip)
+python setup.py build
+python setup.py install
+
+===========================================
+
+Using Yolk
+
+Check packages installed in this virtual environment:
+yolk -l
+
+Checks packages that have updates available:
+yolk -U
+
+===========================================
+
 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