TPP:Installing on Ubuntu 7.04
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 | For TPP versions 4.8 and later please see the README and INSTALL_LINUX files found in source code distribution for instructions on how to build TPP for the Linux platform. |
Contents |
Disclaimer
These instructions are provided with no guarantees of any kind. These steps worked for me. I hope they work for you but don’t hold me responsible if you make your system inoperable by following these directions.
Background
You will need to have the basic programming packages installed beforehand. Get them by typing the following at the command line:
sudo apt-get install build-essential
When prompted to, enter your user password.
Prerequisite Packages
There are several packages that you need to have installed. The list is provided below. You can find them for Ubuntu using the search feature of this webpage: http://packages.ubuntu.com/
| Package Name | Maintainer | Ubuntu Packages to get |
|---|---|---|
| libgd | www.boutell.com/gd | libgd-dev |
| libpng | www.libpng.org | libpng12-dev |
| zlib | www.gzip.org/zlib | zlib1g-dev |
| boost | www.boost.org | libboost* |
| expat | expat.sourceforge.net | libexpat1-dev |
| gnuplot | www.gnuplot.info | gnuplot |
All of these packages can be installed with this command: sudo apt-get install
package name. You can check to see if you have the libraries installed using this
command: dpkg -l package name
Install Apache Server
For whatever reason, the apache version for Ubuntu 7.04 from the repositories
did not work for me so I compiled mine from source. I used version 2.2.4 and
installed it to /usr/local/apps/apache2. I downloaded the source code from http://httpd.apache.org/download.cgi.
Once you have the source code, these are the commands I typed:
sudo su
tar xzf httpd-2.2.4.tar.gz
cd httpd-2.2.4
./configure --prefix=/usr/local/apps/apache2
make
make install
Start apache: /usr/local/apps/apache/bin/apachectl -k start. Open your
browser and go to http://localhost . If everything is okay, you should see a
webpage that says ”It works!”.
Now modify the apache server configuration file. At the end of this HowTo
is the httpd.conf file that I used. You can copy and paste the text into a blank
file and save it as httpd.conf.tpp. Then backup the default apache2 httpd.conf
file and replace it with mine. Here are the commands for after you’ve saved my
httpd.conf file as httpd.conf.tpp:
cd /usr/local/apps/apache2/conf
mv httpd.conf httpd.conf.original
mv /current/directory/of/httpd.conf.tpp /usr/local/apps/apache2/conf
ln -s httpd.conf.tpp httpd.conf
Restart the httpd daemon:
/usr/local/apps/apache/bin/apachectl -k restart
Go back to http://localhost and see if you still get the same webpage.
Compiling TPP
Download the TPP package here. As of this writing, the current version is 3.2.1. Once you have the tarball here's what you do:
tar xzf TPP_v3.2.1_SQUALL.zip
cd trans_proteomic_pipeline/src
SVN Version
Alternatively, you can get the latest source code via SVN. I've found that installing the SVN release is sometimes better so if you want to use this code here is what you do.
(Note: You need SVN installed to do this so make sure you have it with sudo apt-get svn
Once you have SVN installed. Type:
svn co https://sashimi.svn.sourceforge.net/svnroot/sashimi/trunk/trans_proteomic_pipeline --username=anonymous
cd trans_proteomic_pipeline/src
This will download the trans_protemic_pipeline directory to your computer.
Using your favorite editor, open up the Makefile.incl file and set TPP ROOT variable to be where you want the installation to go. In my case I wanted to install it to /usr/local/apps/tpp
so that is the value I used. When you’re done, save your changes.
Back at the terminal, from within the src directory type:
make configure
make
sudo make install
As a final step, I created a data directory within my TPP install that is "world accessible". This means anyone can dump data in to this directory for running/viewing proteomics data through the pipeline. I've included the commands for making the directory here:
sudo mkdir /usr/local/apps/tpp/data
sudo chmod 777 /usr/local/apps/tpp/data
Note that the directory is completely accessible to everyone so don't put confidential or mission-critical stuff in this folder.
I did run into one minor nuisance: the nice command in Ubuntu 7.04 is installed at /usr/bin/nice. TPP expects to find it at /bin/nice. To deal with this, I just added a link:
sudo ln -s /usr/bin/nice /bin/nice
This is by no means an exhaustive HowTo and additions/improvement/comments are welcome.
Original Author: Damian Fermin (dfermin at the University of Michigan, Ann Arbor)
Custom httpd.conf file
This is the httpd.conf file I used for my implementation of TPP. It worked for me, I hope it works for you but again this file is provided with no guarantee of any kind.
# This file hosts 2 servers from localhost: 1) TPP and 2) CPAS
# where Apache2 install actually lives on filesystem
ServerRoot "/usr/local/apps/apache2"
# Fully qualified name for server
ServerName localhost
# User accounts to use for Apache processes
<IfModule !mpm_netware_module>
User daemon
Group daemon
</IfModule>
# Contact info. for when people break the machine
ServerAdmin dfermin@umich.edu
# Sets the file Apache will server if a directory is requested
<IfModule dir_module>
DirectoryIndex index.html
</IfModule>
# Prevents access to .htaccess and .htpasswd files
<FilesMatch "^\.ht">
Order allow,deny
Deny from all
Satisfy All
</FilesMatch>
# Default MIME type the server will use for documents if it can't
# figure one out for a given file extension
DefaultType text/plain
<IfModule mime_module>
TypesConfig conf/mime.types
AddType application/x-compress .Z
AddType application/x-gzip .gz .tgz
AddType text/html .shtml
AddHandler server-parsed .shtml
AddOutputFilter INCLUDES .shtml
</IfModule>
# Secure (SSL/TLS) connections
<IfModule ssl_module>
SSLRandomSeed startup builtin
SSLRandomSeed connect builtin
</IfModule>
## Ports to listen on for TPP
Listen 80
NameVirtualHost 127.0.0.1:80
## Ports to listen on for CPAS
#Listen 8080
#NameVirtualHost 127.0.0.1:8080
######################### TPP Server Configuration ############################
<VirtualHost 127.0.0.1:80>
## IP address _AND_ port to access this server on
ServerName 127.0.0.1:80
DocumentRoot /usr/local/apps/tpp
SetEnv WEBSERVER_ROOT /usr/local/apps/tpp
# file where errors are recorded and what level of recording is done
ErrorLog logs/tpp-errors.log
LogLevel warn
# Access logs
<IfModule log_config_module>
# Directives defining formatting of access log output
LogFormat "%h %l %u %t \"%r\" %>s %b \"%{Referer}i\" \"%{User-Agent}i\"" combined
LogFormat "%h %l %u %t \"%r\" %>s %b" common
<IfModule logio_module>
# You need to enable mod_logio.c to use %I and %O
LogFormat "%h %l %u %t \"%r\" %>s %b \"%{Referer}i\" \"%{User-Agent}i\" %I %O" combinedio
</IfModule>
CustomLog logs/tpp_access_log common
</IfModule>
## Global directives for TPP configuration
<Directory "/usr/local/apps/tpp">
Options Indexes FollowSymLinks
AllowOverride None
Order allow,deny
Allow from all
</Directory>
# directory to store data for web browser viewing
Alias /tpp/data "/usr/local/apps/tpp/data"
<Directory "/usr/local/apps/tpp/data">
AllowOverride None
Options Indexes FollowSymLinks Includes
Order allow,deny
Allow from all
</Directory>
# directory for tpp's html resources (css, js, images, etc)
Alias /tpp/html "/usr/local/apps/tpp/html"
<Directory "/usr/local/apps/tpp/html">
AllowOverride None
Options Includes Indexes FollowSymLinks MultiViews
Order allow,deny
Allow from all
</Directory>
# directory for tpp's schema resources
<Directory "/usr/local/apps/tpp/schema">
AllowOverride None
Options Includes Indexes FollowSymLinks MultiViews
Order allow,deny
Allow from all
</Directory>
# directory for tpp's executable files
ScriptAlias /tpp/cgi-bin/ "/usr/local/apps/tpp/cgi-bin/"
<Directory "/usr/local/apps/tpp/cgi-bin">
AllowOverride AuthConfig Limit
Options Indexes FollowSymLinks MultiViews ExecCGI +Includes
Order allow,deny
Allow from all
SetEnv WEBSERVER_ROOT /usr/local/apps/tpp
</Directory>
</VirtualHost>
##############################################################################
########################## CPAS Configuration ################################
# Not relevant to this TPP HowTo so you can delete this section
##############################################################################
