TPP 5.2.0: Installing on Ubuntu 18.04 LTS
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| Revision as of 22:56, 22 October 2018 Edeutsch (Talk | contribs) ← Previous diff |
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| Line 61: | Line 61: | ||
| echo "TPP_BASEURL = /tpp" >> site.mk | echo "TPP_BASEURL = /tpp" >> site.mk | ||
| echo "TPP_DATADIR = /local/data" >> site.mk | echo "TPP_DATADIR = /local/data" >> site.mk | ||
| + | echo "TPP_PORT = 10401" >> site.mk | ||
| </pre> | </pre> | ||
| Line 81: | Line 82: | ||
| sudo cpan make install | sudo cpan make install | ||
| printf '\n' | sudo cpan install Bundle::CPAN | printf '\n' | sudo cpan install Bundle::CPAN | ||
| + | (this takes a while. At one point you need to hit [ENTER] to accept the 'exit') | ||
| sudo cpan install CGI | sudo cpan install CGI | ||
| sudo cpan install XML::Parser | sudo cpan install XML::Parser | ||
| Line 101: | Line 103: | ||
| === Configuring the Apache web server === | === Configuring the Apache web server === | ||
| - | The following assumes you will install on port 10401. Substitute 10401 for 80 if you want to install on the default port. | + | The following assumes you will install on port 10401. Substitute 10401 for 80 if you want to install on the default port or some other port. |
| + | |||
| + | NOTE: If you are installing TPP on a cloud-based system such as AWS or Azure, you will very likely need to configure your network security rules (via the cloud computing console/portal) to allow | ||
| + | inbound traffic to port 10401, else attempts to point a web browser to it will yield no response. | ||
| <pre>sudo apt --yes install apache2 | <pre>sudo apt --yes install apache2 | ||
| cd /local/tpp/conf | cd /local/tpp/conf | ||
| - | cat httpd-tpp.conf | sed 's/_TPP_PORT_/10401/' > httpd-tpp-1.conf | + | cat httpd-2.4-tpp.conf | sed 's/_TPP_PORT_/10401/' > httpd-2.4-tpp-1.conf |
| - | cat httpd-tpp-1.conf | sed 's/ScriptInterpreterSource/#ScriptInterpreterSource/' > httpd-tpp-2.conf | + | |
| - | vi httpd-tpp-2.conf | + | # Check your location with: http://www.whatsmyip.org/ and then configure the permission rules accordingly |
| - | Comment out: | + | cat httpd-2.4-tpp-1.conf | sed 's/Require ip 10/Require ip 174.250.12/' > httpd-2.4-tpp-2.conf |
| - | # PassEnv TPP_HOME | + | |
| - | # PassEnv TPP_DATADIR | + | |
| - | UNcomment these lines (and make sure they have leading slashes!): | + | # Alternatively, you can allow traffic from anywhere. This might expose your server to some security vulnerabilities: |
| - | SetEnv TPP_HOME /local/tpp | + | cat httpd-2.4-tpp-1.conf | sed 's/#Require all granted/Require all granted/' > httpd-2.4-tpp-2.conf |
| - | SetEnv TPP_DATADIR /local/data | + | |
| - | SetEnv TPP_BASEURL /tpp | + | |
| - | SetEnv TPP_DATAURL /tpp/data | + | |
| - | </pre> | + | |
| - | 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 access to localhost (127.0.0.1) and IP addresses 174.*.*.*. Access to all has been commented out: | + | # And make sure that the TPP_DATAURL has a leading slash, or there will be problems with the web interface links: |
| - | + | cat httpd-2.4-tpp-2.conf | sed 's/TPP_DATAURL tpp\/data/TPP_DATAURL \/tpp\/data/' > httpd-2.4-tpp-3.conf | |
| - | <pre> | + | |
| - | <Directory "/local/tpp"> | + | |
| - | AllowOverride None | + | |
| - | Require ip 127.0.0.1 | + | |
| - | Require ip 174 | + | |
| - | # Require all granted | + | |
| - | </Directory> | + | |
| </pre> | </pre> | ||
| - | Also do the same for the data directory: | ||
| - | |||
| - | <pre> | ||
| - | <Directory "/local/data"> | ||
| - | Options Includes Indexes MultiViews | ||
| - | Require ip 127.0.0.1 | ||
| - | Require ip 174 | ||
| - | # Require all granted | ||
| - | |||
| - | AddType text/html .shtml | ||
| - | AddHandler server-parsed .shtml | ||
| - | </Directory> | ||
| - | </pre> | ||
| Next set up some needed Apache modules and restart: | Next set up some needed Apache modules and restart: | ||
| Line 155: | Line 133: | ||
| <pre>cd /etc/apache2/conf-available | <pre>cd /etc/apache2/conf-available | ||
| - | sudo cp -p /local/tpp/conf/httpd-tpp-2.conf httpd-tpp.conf | + | sudo cp -p /local/tpp/conf/httpd-2.4-tpp-3.conf httpd-tpp.conf |
| cd ../conf-enabled | cd ../conf-enabled | ||
| sudo ln -s ../conf-available/httpd-tpp.conf | sudo ln -s ../conf-available/httpd-tpp.conf | ||
| Line 169: | Line 147: | ||
| </pre> | </pre> | ||
| - | 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. | + | And now you're good to go ... Point your web browser 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. |
| + | |||
| + | If you get a response "Internal Server Error", you'll need to look at the contents of /var/log/apache2/error.log to see what went wrong. If the cause is not apparent, post the error log to the support group for assistance. | ||
| + | |||
| + | If you get *no response*, i.e. just hangs, this probably means that your firewall rules or cloud-based inbound traffic security rules have not been configured to allow inbound traffic to 10401. This is not likely | ||
| + | the problem on a fresh Ubuntu machine, but probably is the result of your cloud provider and IT provide security system. | ||
| Line 219: | Line 202: | ||
| [Add Files] Select Yeast_UPS_cRAP.fasta | [Add Files] Select Yeast_UPS_cRAP.fasta | ||
| [Run Comet Search] | [Run Comet Search] | ||
| + | Wait a few moments and [Refresh] until the job is done | ||
| [TPP Tools] [Analyze Peptides] | [TPP Tools] [Analyze Peptides] | ||
| Line 224: | Line 208: | ||
| - Check box next to UPS1_50000amol_R1.pep.xml | - Check box next to UPS1_50000amol_R1.pep.xml | ||
| - (Select) | - (Select) | ||
| - | - Check box next to "Use accurate mass binning" | + | - Under -PEPTIDEPROPHET OPTIONS- check box next to "Use accurate mass binning" |
| + | - Under -IPROPHET OPTIONS- Check box next to "RUN iProphet" | ||
| - Scroll to bottom and (Run XInteract) | - Scroll to bottom and (Run XInteract) | ||
| - | - [Refresh] | + | - Wait a few moments and [Refresh] until the job is done |
| - Make sure no errors | - Make sure no errors | ||
| - | - click on [PepXML] link in /local/data/tests/QuickYeastUPS1/interact.pep.xml [ PepXML ] | + | - click on [PepXML] link in /local/data/tests/QuickYeastUPS1/interact.ipro.pep.xml [ PepXML ] |
| - Click on a probability and view the plots | - Click on a probability and view the plots | ||
| - Go back to the PepXML Viewer tab | - Go back to the PepXML Viewer tab | ||
| - Click on a value in the Ions column | - Click on a value in the Ions column | ||
| + | |||
| </pre> | </pre> | ||
| Finis! | Finis! | ||
Revision as of 16:26, 23 October 2018
 | Note that this recipe will likely not be exactly applicable to different versions of TPP or 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
This recipe describes installing TPP release 5.2.0.
First some general notes
- We assume a fresh installation of Ubuntu 18.04 LTS as a starting point (LTS stands for Long Term Support, which means that this version of Ubuntu will be stable and supported for several years).
- This recipe was tested on a fresh Azure cloud computing platform instance running Ubuntu 18.04 LTS in October 2018
- 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 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
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
Pulling the TPP 5.2.0 source code from SourceForge
cd /local/svn svn checkout svn://svn.code.sf.net/p/sashimi/code/tags/release_5-2-0
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/release_5-2-0 echo "INSTALL_DIR = /local/tpp" > site.mk echo "TPP_BASEURL = /tpp" >> site.mk echo "TPP_DATADIR = /local/data" >> site.mk echo "TPP_PORT = 10401" >> site.mk
Compile the whole package. 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. It has been reported that sometimes just doing another `make all` will allow completion of compilation. Try that first before trying something more complex. Otherwise, try to determine why the compilation failed. Perhaps some prerequisite software is not installed on your system. If you can't figure it out, post the operating system version, TPP version, and compilation error messages to spctools-discuss and someone can help you.
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 18.04 LTS that we tried on:
export PERL_MM_USE_DEFAULT=1
yes | sudo cpan install automatically
sudo cpan make install
printf '\n' | sudo cpan install Bundle::CPAN
(this takes a while. At one point you need to hit [ENTER] to accept the 'exit')
sudo cpan install CGI
sudo cpan install XML::Parser
sudo cpan install FindBin::libs
yes | sudo cpan install JSON
Now test to make sure all modules are installed:
cd /local/tpp/bin export PERL5LIB=/local/tpp/lib/perl ./test_tpi.plIf you get any NOT FOUND errors, then go back to cpan and install them.
If you have no interest in using the web interfaces, then you're done. Happy TPPing. However, if you want the GUI web interfaces, continue on to install and configure Apache .
Configuring the Apache web server
The following assumes you will install on port 10401. Substitute 10401 for 80 if you want to install on the default port or some other port.
NOTE: If you are installing TPP on a cloud-based system such as AWS or Azure, you will very likely need to configure your network security rules (via the cloud computing console/portal) to allow inbound traffic to port 10401, else attempts to point a web browser to it will yield no response.
sudo apt --yes install apache2 cd /local/tpp/conf cat httpd-2.4-tpp.conf | sed 's/_TPP_PORT_/10401/' > httpd-2.4-tpp-1.conf # Check your location with: http://www.whatsmyip.org/ and then configure the permission rules accordingly cat httpd-2.4-tpp-1.conf | sed 's/Require ip 10/Require ip 174.250.12/' > httpd-2.4-tpp-2.conf # Alternatively, you can allow traffic from anywhere. This might expose your server to some security vulnerabilities: cat httpd-2.4-tpp-1.conf | sed 's/#Require all granted/Require all granted/' > httpd-2.4-tpp-2.conf # And make sure that the TPP_DATAURL has a leading slash, or there will be problems with the web interface links: cat httpd-2.4-tpp-2.conf | sed 's/TPP_DATAURL tpp\/data/TPP_DATAURL \/tpp\/data/' > httpd-2.4-tpp-3.conf
Next set up some needed Apache modules and restart:
sudo a2enmod rewrite sudo a2enmod cgid 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 Ubuntu 16.04.
cd /etc/apache2/conf-available sudo cp -p /local/tpp/conf/httpd-2.4-tpp-3.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 ... Point your web browser 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.
If you get a response "Internal Server Error", you'll need to look at the contents of /var/log/apache2/error.log to see what went wrong. If the cause is not apparent, post the error log to the support group for assistance.
If you get *no response*, i.e. just hangs, this probably means that your firewall rules or cloud-based inbound traffic security rules have not been configured to allow inbound traffic to 10401. This is not likely the problem on a fresh Ubuntu machine, but probably is the result of your cloud provider and IT provide security system.
Testing the installation with a sample dataset (optional)
If you want to test your installation with a search and a PeptideProphet processing, try this recipe:
Navigate to:
http://xxx.xxx.xxx.xxx:10401/tpp/cgi-bin/tpp_gui.pl
- Login with guest and password
## In the Petunia interface in the Web browser:
[Files]
[Create new directory] tests
Go into tests
[TPP Tools] [Fetch Datasets]
Choose target directory for downloaded files
[Add Files] Go to the top level /local/data
- Check box next to tests
- (Select)
Specify Dataset ID
Paste into URL box: http://www.peptideatlas.org/export/refData/QuickYeastUPS1.zip
(Fetch Dataset)
Wait a few moments and [Refresh] until the job is done
Click on [this directory] and there should only be a subdirectory "QuickYeastUPS1"
[Files]
- Go to /local/data/params/
- Check box next to comet.params
- Click (Copy) button
- Go to /local/data/tests/QuickYeastUPS1
- Click (Paste) button
- On the same line as comet.params, click [Params]
Make the following changes (they might already be set, but check):
peptide_mass_tolerance = 20
peptide_mass_units = 2
isotope_error = 3
- (Save Search Parameters File)
[Pipeline: Comet]
[TPP Tools] [Comet Search]
Choose mz[X]ML Input Files
[Add Files] Select /local/data/tests/QuickYeastUPS1/UPS1_50000amol_R1.mzML
Choose Comet Parameters File
[Add Files] Select comet.params
Choose a sequence database
[Add Files] Select Yeast_UPS_cRAP.fasta
[Run Comet Search]
Wait a few moments and [Refresh] until the job is done
[TPP Tools] [Analyze Peptides]
- (Add Files)
- Check box next to UPS1_50000amol_R1.pep.xml
- (Select)
- Under -PEPTIDEPROPHET OPTIONS- check box next to "Use accurate mass binning"
- Under -IPROPHET OPTIONS- Check box next to "RUN iProphet"
- Scroll to bottom and (Run XInteract)
- Wait a few moments and [Refresh] until the job is done
- Make sure no errors
- click on [PepXML] link in /local/data/tests/QuickYeastUPS1/interact.ipro.pep.xml [ PepXML ]
- Click on a probability and view the plots
- Go back to the PepXML Viewer tab
- Click on a value in the Ions column
Finis!
