TPP 4.5.2: Installing on Ubuntu 10.04.3
From SPCTools
Contents |
Before we begin
First some general notes
- Run all these commands as root, we recommend running
sudo sufor convenience. - This installation assumes you are installing to
/usr/local/tpp/, if you want to install anywhere else, change accordingly - This installation assumes you are using apache 2 as your web server
- Where a block is presented with lines beginning with a dollar ($), these 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 prerequisites
Use the ubuntu package manager to install all the dependencies
$ apt-get install g++ subversion vim apache2 libbz2-dev swig expat libpng12-dev $ apt-get install gnuplot libperl-dev libxml-parser-perl build-essential libgd2-xpm libgd2-xpm-dev libboost-all-dev $ apt-get install libboost-dev libboost-doc boost-build
Extracting and building the source
Extract TPP-4.6.1-src.tgz to /usr/local/src
$ cd /usr/local/src $ tar xzf TPP-4.6.1-src.tgz
Create a new file /usr/local/src/TPP-4.6.1/trans_proteomic_pipeline/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-4.6.1/trans_proteomic_pipeline/perl to /usr/local/tpp/bin if they don't exist there already
$ cp -nv /usr/local/src/TPP-4.6.1/trans_proteomic_pipeline/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 $ chown -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>
</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.
