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-rw-r--r--misc/gn_installation_notes.txt122
-rw-r--r--misc/notes.txt48
2 files changed, 168 insertions, 2 deletions
diff --git a/misc/gn_installation_notes.txt b/misc/gn_installation_notes.txt
new file mode 100644
index 00000000..173f2819
--- /dev/null
+++ b/misc/gn_installation_notes.txt
@@ -0,0 +1,122 @@
+Get git:
+
+sudo apt-get install git-core
+
+===========================================
+
+Clone code from git repository:
+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-cache search" searches for text in the description for various packages, while
+"apt-file search" searches for files within the packages**
+
+Search for package with a specified file that can be installed with apt-get
+apt-file search _______
+
+Install from requirements.txt:
+pip install -r gene/wqflask/requirements.txt -t ve27
+
+===========================================
+
+Installing virtualenv:
+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
+
+===========================================
+
+Install MySQL Client
+
+To fix error "mysql_config not found" while installing packages with pip:
+sudo apt-get install libmysqlclient-dev
+
+===========================================
+
+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)
+python setup.py install
+
+===========================================
+
+Installing numarray 1.5.2
+
+wget http://downloads.sourceforge.net/project/numpy/Old%20Numarray/1.5.2/numarray-1.5.2.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fnumpy%2Ffiles%2FOld%2520Numarray%2F1.5.2%2Fnumarray-1.5.2.tar.gz%2Fdownload&ts=1358978306&use_mirror=superb-dca2
+mv -v numarray-1.5.2.tar.gz?r=http:%2F%2Fsourceforge.net%2Fprojects%2Fnumpy%2Ffiles%2FOld%20Numarray%2F1.5.2%2Fnumarray-1.5.2.tar.gz%2Fdownload numarray-1.5.2.tar.gz
+tar xvf numarray-1.5.2.tar.gz
+sudo python setup.py install
+
+===========================================
+
+Installing R
+
+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!
+
+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)
+
+To change screen environment variable (if man not working or to get color, for example):
+export TERM=screen
+
+To search for commands in history if necessary:
+history | grep "(whatever is being searched for)"
+
+Run web server:
+/usr/local/nginx/sbin/nginx
+
+Run server:
+python runserver.py
+
+=========================================== \ No newline at end of file
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