TPP 5.x development: 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.

1 Before we begin
2 Installation
3 Installing the tutorial data (optional)

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Before we begin

This recipe describes installing the latest development branch of TPP after the release of 5.0.0. This contains additional fixes and features not found in the official release version. The installation procedure is a little different than the official release 5.0.0.

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 February 2017
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.

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Installation

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Installing prerequisite packages

Use the ubuntu package manager to upgrade any outdated packages and then install all the dependencies

sudo apt update
sudo apt --yes upgrade
sudo apt --yes install subversion
sudo apt --yes install make
sudo apt --yes install g++
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

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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

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Downloading the very latest source code from svn

cd /local/svn
svn checkout svn://svn.code.sf.net/p/sashimi/code/trunk/trans_proteomic_pipeline

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Compiling the source code

Create a custom site.mk file with something like the following. After pasting in the three data lines, hit CTRL-D.

cd /local/svn/trans_proteomic_pipeline
cat > site.mk
INSTALL_DIR = /local/tpp
TPP_BASEURL = /tpp
TPP_DATADIR = /local/data

First make libgd.

make libgd

Then make everything else. This will start by unpacking Boost and ProteoWizard and compile all that and then compile the TPP. This takes quite a while.

make all

If the above completed without error, then you're ready to proceed. If the compilation stopped with an error, you will need to troubleshoot. Perhaps some prerequisite is not installed on your system. It is rumored that sometimes just doing another `make all` will allow completion of compilation.

Next, install it!

make install

Next you'll need to make sure that all the Perl modules are available. The following works on the fresh version of Ubuntu 16.04 that we tried on:

sudo cpan
      (answer yes)
  make install
  install Bundle::CPAN
      (this takes a long time. At one point you need to hit [ENTER] to accept the 'exit')
  install CGI
  install XML::Parser
  install FindBin::libs
  quit

Now test to make sure all modules are installed:

cd /local/tpp/cgi-bin
./tpp_gui.pl

If it compiles and you get an error about being unable to find HomePath then you're fine. However, if you get an error not being able to find a module, then go back to cpan and install it.<P>

If you have no interest in using the web interface, then you're done. Happy TPPing. However, if you want the web interface, install and configure Apache. The following assumes you will install on port 10401. Substitute 10401 for 80 if you want to install on the default port.

sudo apt --yes install apache2
cd /local/tpp/conf
cat httpd-tpp.conf | sed 's/_TPP_PORT_/10401/' > httpd-tpp-1.conf
cat httpd-tpp-1.conf | sed 's/ScriptInterpreterSource/#ScriptInterpreterSource/' > httpd-tpp-2.conf

vi httpd-tpp-2.conf
Comment out:
#    PassEnv TPP_HOME
#    PassEnv TPP_DATADIR
UNcomment and add beginning slashes:
   SetEnv TPP_HOME    /local/tpp
   SetEnv TPP_DATADIR /local/tpp/data
   SetEnv TPP_BASEURL /tpp
   SetEnv TPP_DATAURL /tpp/data

Next configure the permission access to the server. If only the localhost should be able to access the interface (e.g. installation on a laptop running Linux then only grant access to 127.0.0.1. Or you can just give access to a range of IP addresses. Or you could grant world access if you have collaborators everywhere accessing the system. This confers some additional possible security risks. In this example, we've used the Apache 2.4 syntax to grant world access:

<Directory "/local/tpp">
    AllowOverride None
    Require all granted
#    Order deny,allow
#    Deny from all
#    Allow from 127.0.0.0/255.0.0.0 ::1/128
#   Order allow,deny
#   Allow from all

Next set up some needed Apache modules:

sudo a2enmod rewrite
sudo a2enmod cgi
sudo service apache2 restart

Next install this config file. This may vary among distributions, but this seems like a nice way to do it on our test instance.

cd /etc/apache2/conf-available
sudo cp -p /local/tpp/conf/httpd-tpp-2.conf httpd-tpp.conf
cd ../conf-enabled
sudo ln -s ../conf-available/httpd-tpp.conf
sudo service apache2 reload

If that reload generated an error, you'll need to troubleshoot your configuration. Next, set some appropriate permissions for the web server to write. With the first command, verify that your Apache server is running as the user www-data. If it's running as a different user, then substitute that.

ps aux | grep apache
set tmpUser=www-data
cd /local/tpp
sudo chown -R $tmpUser.$tmpUser data log users

And now you're good to go ... head on over to http://localhost:10401/tpp/cgi-bin/tpp_gui.pl or if this is installed on a different machine, use its name or IP address, e.g. http://40.83.177.49:10401/tpp/cgi-bin/tpp_gui.pl. Note that the above installation assumes installation on port 10401. If you chose a different port, then adjust the above URLs accordingly.

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Installing the tutorial data (optional)

If you want to test your installation using the SPC demo/tutorial data (yeast data) then there are a few extra steps. First create a demo directory in the data area

mkdir /local/tpp/data/demo

Extract all the example files (mzXML, tandem params, fasta database) to /local/tpp/data/demo

[STOPPED HERE. WHERE DID THESE FILES MAGICALLY COME FROM??]

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.

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