TPP:Installing on Ubuntu 7.04

From SPCTools

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/

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 (http://sourceforge.net/project/showfiles. php?group_id=69281&package_id=126912. As of this writing, the current version is 3.0.3. Once you have the tarball here's what you do:

tar xzf TPP_v3.0.3_SQUALL.zip
cd trans_proteomic_pipeline/src

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)