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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
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Using dpkg
Check which system packages are already installed:
dpkg -l | less
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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
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
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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
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Installing R
sudo apt-get install r-base-dev
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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
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Install requests
pip install requests
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Install logging_tree
pip install logging_tree
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Install colordiff (just to make it easier to view differences in files, not necessary for GN)
sudo apt-get install colordiff
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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
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