aboutsummaryrefslogtreecommitdiff
path: root/misc/gn_installation_notes.txt
blob: 11bda48c24139bc768789a58ac128590eb1e7d75 (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
UFW - default firewall confirguation tool for Ubuntu; eases iptables firewall configuration

Enable UFW:
sudo ufw enable
Check status of UFW:
sudo ufw status verbose

Limit ssh:
sudo ufw limit ssh

Enable http, https:
sudo ufw allow http
sudo ufw allow https

===========================================

http://evilrouters.net/2011/02/18/using-etckeeper-with-git-on-ubuntu/

Install etckeeper:
sudo apt-get install etckeeper

Edit /etc/etckeeper/etckeeper.conf to comment out VCS="bzr" and comment in VCS="git"

Initialize repository:
sudo etckeeper init

Do initial commit:
sudo etckeeper commit "Initial commit."

===========================================

Get git:

sudo apt-get install git

===========================================

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 _______

============================================

Create trash directory:
mkdir ~/.trash

============================================

Using dpkg

Check which system packages are already installed:
dpkg -l | less

===========================================

Installing virtualenv:
sudo pip install virtualenv

Tell virtualenv which directory to use:
virtualenv ve27

Start up virtual environment:
source ~/ve27/bin/activate

===========================================

Install libmysqlclient-dev (Mysql-Python dependency)
sudo apt-get install libmysqlclient-dev

Install python-dev (numpy dependency)
sudo apt-get install python-dev

Install scipy dependencies:
sudo apt-get install libatlas-base-dev gfortran g++

===========================================

Install pip:
sudo apt-get install python-pip

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

===========================================

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)
mkdir /home/zas1024/ve27/include/python2.7/Reaper
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 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

============================================

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

===========================================

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

==========================================

Install colordiff (just to make it easier to view differences in files, not necessary for GN)

sudo apt-get install colordiff

==========================================

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

===========================================