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 custom site.mk file with something like the following. After pasting in the three data lines, hit CTRL-D.
cat > site.mk INSTALL_DIR = /local/tpp BASE_URL = /tpp TPP_DATA = /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 allIf 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 IO::Uncompress::Gunzip
(this might already be included in Bundle::CPAN, or maybe not)
install XML::Parser
(need to hit [ENTER] twice to answer silly questions)
quit
Now test to make sure all modules are installed:
cd /local/tpp/cgi-bin perl 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. 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 it's name or IP address, e.g. http://40.83.177.49:10401/tpp/cgi-bin/tpp_gui.pl. Note that the above installation assumbed installation on port 10401. If you chose a different port, then adjust the above URLs accordingly.
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.
