TPP:5.0 Installation
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Revision as of 20:57, 7 October 2016 JoeS (Talk | contribs) (→New Windows install) Next diff → |
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| This assumes that you do not have a previous version of TPP installed on your system. | This assumes that you do not have a previous version of TPP installed on your system. | ||
| - | As of version 5.0.0, no dependencies are required to install TPP on a modern Windows system. A customized version of the '''perl''' language and '''Apache''' web server are included and installed by default; users can choose to use other versions, but this has not been fully tested and may lead to unstable behavior. | + | As of version 5.0.0, no dependencies are required to install TPP on a modern Windows system. A customized version of the '''Perl''' language and the '''Apache''' web server are included and installed by default; users can choose to use other versions, but this has not been fully tested and may lead to unstable behavior. |
| - | * Download the [https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v5.0%20%28Typhoon%29%20rev%200/ latest version of the TPP installer for windows] and run it. | + | * Download the [https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v5.0%20%28Typhoon%29%20rev%200/ latest version of the TPP installer for Windows] and run it. |
| * After you '''accept''' the license agreement, you will be asked to select a location to install TPP and its components. The default is '''C:\TPP\''', but can be changed to any other location. | * After you '''accept''' the license agreement, you will be asked to select a location to install TPP and its components. The default is '''C:\TPP\''', but can be changed to any other location. | ||
| - | * You will then be asked to select a web '''port number''' for TPP to use. The default value '''10401''' should work fine in most cases. You can enter any other legal port number instead. | + | * You will then be asked to select a web server '''port number''' for TPP to use. The default value '''10401''' should work fine in most cases. You can enter any other legal port number instead. |
| - | Do note that this will make all links in TPP look like this: | + | Do note that this will make all links in TPP look like this: |
| - | http://www.myhost.org:10401/tpp/cgi-bin/tpp_gui.pl | + | http://www.myhost.org:10401/tpp/cgi-bin/tpp_gui.pl |
| * You will then be asked to select the location of your data, which can be on the local drive or an external drive. A few example locations: | * You will then be asked to select the location of your data, which can be on the local drive or an external drive. A few example locations: | ||
| ** Local drive data installation (default for new installations): '''C:\TPP\data\''' | ** Local drive data installation (default for new installations): '''C:\TPP\data\''' | ||
| ** Use old TPP data location: '''C:\Inetpub\wwwroot\ISB\data\''' | ** Use old TPP data location: '''C:\Inetpub\wwwroot\ISB\data\''' | ||
| - | ** Data on another drive: '''E:\data\proteomics\''' | + | ** Data on another drive, e.g.: '''E:\data\proteomics\''' |
| * Lastly, you will be asked to choose which extra components to install: | * Lastly, you will be asked to choose which extra components to install: | ||
| ** '''Apache web server''': needed for graphical user interfaces. May not need if you already have another server installed and running, or are not using TPP interfaces. | ** '''Apache web server''': needed for graphical user interfaces. May not need if you already have another server installed and running, or are not using TPP interfaces. | ||
| - | ** '''ProteoWizard''': needed for RAW->mzML file conversions; includes 3rd party vendor libraries and special licences. Please make yourself familiar with these if you choose to install this component. | + | ** '''ProteoWizard''': needed for RAW->mzML file conversions; includes 3rd party vendor libraries and special licenses. Please make yourself familiar with these if you choose to install this component. |
| ** '''Download and install dependencies for ProteoWizard''': automatically install required components. If left out, you may need to update your system to perform certain file conversions. | ** '''Download and install dependencies for ProteoWizard''': automatically install required components. If left out, you may need to update your system to perform certain file conversions. | ||
| - | ** '''Strawberry Perl''': Custom distribution of the perl language; recommended. You may omit and try to use an existing version of perl, but this is not well tested and may lead to unstable behavior. | + | ** '''Strawberry Perl''': Custom distribution of the Perl language; *strongly* recommended. You may omit and try to use your own installation of Perl, but this is not well tested and may lead to unstable behavior. |
| * Reboot when prompted. | * Reboot when prompted. | ||
| - | |||
| == Upgrading from 4.8.x on Windows == | == Upgrading from 4.8.x on Windows == | ||
Revision as of 20:57, 7 October 2016
TPP 5.0 (Typhoon) is the latest release of the popular proteomics analysis pipeline. More information can be found here: TPP:5.0.0_Release_Notes.
Contents |
New Windows install
This assumes that you do not have a previous version of TPP installed on your system.
As of version 5.0.0, no dependencies are required to install TPP on a modern Windows system. A customized version of the Perl language and the Apache web server are included and installed by default; users can choose to use other versions, but this has not been fully tested and may lead to unstable behavior.
- Download the latest version of the TPP installer for Windows and run it.
- After you accept the license agreement, you will be asked to select a location to install TPP and its components. The default is C:\TPP\, but can be changed to any other location.
- You will then be asked to select a web server port number for TPP to use. The default value 10401 should work fine in most cases. You can enter any other legal port number instead.
Do note that this will make all links in TPP look like this: http://www.myhost.org:10401/tpp/cgi-bin/tpp_gui.pl
- You will then be asked to select the location of your data, which can be on the local drive or an external drive. A few example locations:
- Local drive data installation (default for new installations): C:\TPP\data\
- Use old TPP data location: C:\Inetpub\wwwroot\ISB\data\
- Data on another drive, e.g.: E:\data\proteomics\
- Lastly, you will be asked to choose which extra components to install:
- Apache web server: needed for graphical user interfaces. May not need if you already have another server installed and running, or are not using TPP interfaces.
- ProteoWizard: needed for RAW->mzML file conversions; includes 3rd party vendor libraries and special licenses. Please make yourself familiar with these if you choose to install this component.
- Download and install dependencies for ProteoWizard: automatically install required components. If left out, you may need to update your system to perform certain file conversions.
- Strawberry Perl: Custom distribution of the Perl language; *strongly* recommended. You may omit and try to use your own installation of Perl, but this is not well tested and may lead to unstable behavior.
- Reboot when prompted.
Upgrading from 4.8.x on Windows
For best restuls, it is strongly recommended that you uninstall TPP, ActiveState perl and the Apache web server -- unless you are using either of the last two components for other purposes. Once you have done this, please follow the steps described above for a new Windows install; pay close attention to the location of the data directory, as you may choose to use the location of your existing data for easy transition to the new TPP.
Installing on Linux
Please follow the instructions included in the BUILD_LINUX file found at the top-level of the distribution.
Installing on OSX
As of this writing, we do not provide explicit support for OSX. Please share your experience with us if you are able to install it. We otherwise plan on providing this in the near future.
