TPP 5.0.0: Installing on Ubuntu 16.04
From SPCTools
 | Note that this recipe will likely not be exactly applicable to different versions of TPP and different distributions of Linux, but perhaps can be a useful head start. For other versions of TPP, 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 |
Before we begin
First some general notes
- We assume a fresh installation of Ubuntu 16.04 as a starting point.
- This recipe was tested on a fresh Ubuntu 16.04 LTS instance running on Azure in November 2016
- We assume that there is an ordinary user account named 'tpp' that will be used as the primary account. This account will need sudo privileges
- This installation assumes you are installing to
/local/tpp/, if you want to install anywhere else, change accordingly - This installation assumes you are using Apache 2.4 as your web server
- The gray blocks are commands to be typed in at the shell directly. You should be able to copy and paste them a line at a time.
Installation
Installing prerequisite packages
Use the ubuntu package manager to install all the dependencies
sudo apt --yes install subversion sudo apt --yes install make sudo apt --yes install g++ sudo apt --yes install g++-4.9 sudo apt --yes install build-essential sudo apt --yes install zlib1g-dev sudo apt --yes install libghc-bzlib-dev sudo apt --yes install gnuplot sudo apt --yes install unzip sudo apt --yes install expat sudo apt --yes install libexpat1-dev
Using an old compatibility version of gcc
Although later TPP versions can use gcc 5, the version of Boost and ProteoWizard bundled with TPP 5.0.0 seems to require gcc 4.x. Use the below commands to force an older version of gcc (assumes you installed it above!)
ll /usr/bin/gcc* /usr/bin/g++* sudo rm /usr/bin/g++ sudo rm /usr/bin/gcc sudo ln -s g++-4.9 /usr/bin/g++ sudo ln -s gcc-4.9 /usr/bin/gcc ll /usr/bin/gcc* /usr/bin/g++*
Creating a suitable place to compile and install
In this recipe, we install in /local. You may wish to install in a different location, and the recipe should be adjusted accordingly. This also assumes that you will use an account 'tpp' and group 'tpp'. Maybe you'll use a different account.
sudo mkdir /local cd /local sudo mkdir tpp data svn sudo chown tpp.tpp tpp data svn
Downloading the source code from svn
cd /local/svn svn checkout svn://svn.code.sf.net/p/sashimi/code/trunk/trans_proteomic_pipeline cd /local/svn/trans_proteomic_pipeline
Create a new file /usr/local/src/TPP-4.5.2/src/Makefile.config.incl and populate it with
TPP_ROOT=/usr/local/tpp/ TPP_WEB=/tpp/ ## for Boost BOOST_INCL=-I/usr/include/boost/ BOOST_LIBDIR=/usr/lib BOOST_LIBSPEC=-gcc43-mt LINK=shared LIBEXT=so PERL_LIB_CORE= /usr/lib/perl/5.10/CORE/
Build TPP
$ make && make install
Copy any files from /usr/local/src/TPP-4.5.2/perl to /usr/local/tpp/bin if they don't exist there already
$ cp -n /usr/local/src/TPP-4.5.2/perl/* /usr/local/tpp/bin
Configuring your installation for use
Add local configuration data to /usr/local/tpp/cgi-bin/tpp_gui_config.pl. Add the following lines immediately after the line # SET TPP_GUI DEFAULTS HERE. Nothing along these paths can be a symlink, because the TPP web client (Petunia) resolves absolute paths and checks those against the config, which means symlinks will look like they're outside of the allowed directories. You can probably get around this with some funky apache configuration using URL rewrites, but that's too complex to go into here, and not necessary generally. Note the trailing slashes, they are important!
'base_dir' => '/usr/local/tpp/', 'www_root' => '/usr/local/tpp/', 'data_dir' => '/usr/local/tpp/data/', 'tppbin' => '/usr/local/tpp/bin/',
Create the data directory and set permissions and ownership so that apache can use it properly
$ cd /usr/local/tpp $ mkdir data $ mkdir data/parameters $ cp /usr/local/tpp/bin/isb_default_* /usr/local/tpp/data/parameters $ chown -R www-data:www-data /usr/local/tpp/data $ chmod -R 0660 /usr/local/tpp/data $ chmod -R a+X /usr/local/tpp/data
Setting up apache
Now we need to tell apache about the TPP installation. Create a new file /etc/apache2/sites-available/tpp-x.y.z and populate with
<VirtualHost *:80>
# directory to store data for web browser viewing
Alias /tpp/data "/usr/local/tpp/data"
<Directory "/usr/local/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/tpp/html"
<Directory "/usr/local/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/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/tpp/cgi-bin"
<Directory "/usr/local/tpp/cgi-bin">
#AllowOverride AuthConfig Limit
AllowOverride All
Options Indexes +FollowSymLinks MultiViews ExecCGI +Includes
AddHandler default-handler .jpg .png .css .ico .gif
AddHandler cgi-script .cgi .pl
Order allow,deny
Allow from all
SetEnv WEBSERVER_ROOT /usr/local/
#SetEnv WEBSERVER_ROOT /var/www
</Directory>
# Enables Lorikeet spectrum display program to work for linux
Alias /ISB /usr/local/tpp
</VirtualHost>
TPP produces pepxml files but links to them as .shtml in the putunia gui. We need to enable the SSI includes module to make these links work, which is not enabled by default in ubuntu server. You can see whether you already have the includes module enabled by running
$ apache2ctl -M
If the list contains "include_module" then you've already got it enabled, if not, enable it by running
$ a2enmod include
Finally, we enable the virtual host we've just created
$ a2ensite tpp-x.y.z $ /etc/init.d/apache2 restart
And now you're good to go ... head on over to http://localhost/tpp/cgi-bin/tpp_gui.pl; And you can give up your root shell now by issuing the command
$ exit
Installing the tutorial data (optional)
If you want to test your installation using the SPC demo/tutorial data (yeast ORF data) then there are a few extra steps. First create a demo directory in the data area
$ mkdir /usr/local/tpp/data/demo
Extract all the example files (mzXML, tandem params, fasta database) to /usr/local/tpp/data/demo
You'll also need to create a download directory for SpectraST libraries.
$ mkdir -p /usr/local/tpp/data/dbase/speclibs
Set the permissions and ownership
$ chown -R www-data:www-data /usr/local/tpp/data/demo /usr/local/tpp/data/dbase $ chmod -R 0660 /usr/local/tpp/data/demo /usr/local/tpp/data/dbase $ chmod -R a+X /usr/local/tpp/data/demo /usr/local/tpp/data/dbase
The tandem.xml parameters file has a hard coded path that is windows specific. You will need to change the windows path to isb_default_input_kscore.xml in tandem.xml to the correct Linux path. The file can normally be found in linux instalaltions at /usr/local/tpp/bin/isb_default_input_kscore.xml, but if you've followed these instructions, you will have copied it to /usr/local/data/parameters already.
Replace "C:\InetPub\wwwroot\ISB\data\parameters\isb_default_input_kscore.xml" with "/usr/local/tpp/data/parameters/isb_default_input_kscore.xml" in the tandem.xml file.
