TPP 6.1.0 Release is now available

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Luis Mendoza

Jun 3, 2022, 4:23:19 AM6/3/22
Announcing the official release of Trans-Proteomic Pipeline (TPP) 6.1.0 "Parhelion"

We are proud to offer a major update to the Trans-Proteomic Pipeline (TPP) software, release 6.1.0.  The software is available for Windows as well as Linux from all the usual locations (please see the section below, "Getting the TPP Software").  Most users are recommended to use the Windows installer, which installs and configures TPP and other required software, such as a web server.  For advanced users who need to customize TPP, or for those who run on Linux or OS X, the source code can be downloaded.

Release Notes
Release notes on the most important new features, changes, and known issues are available at:

Getting the TPP Software
Download the TPP version 6.1.0 native windows installer from the Sashimi SourceForge project file release page:

Everyone is encouraged to read and contribute to our wiki, at

For guides to installing and using our software, please see our wiki:

For downloading the source code, please go to the following link:  and find the 6.1.0 source code .zip package
or, check out the code directly from svn:
  svn export svn://

For building from source, please refer to the README and INSTALL files in src/ directory of TPP as well as the wiki.

The TPP Team: David, Luis, Mike, Eric, Jimmy, plus all other developers who contributed to this release from ISB.  Thanks to developers and users from the TPP's user community who also provided feedback and code contributions.


Jun 7, 2022, 1:04:43 AM6/7/22
to spctools-discuss
Congrats on the new release.

You will probably want to modify these instructions which still advise to download from trunk.  

I just followed  them.

Should I still expect this to work satisfactorily?


Luis Mendoza

Jun 7, 2022, 1:37:31 AM6/7/22
Hi Malcolm,
Thank you for the congrats, and for catching that in our build notes; we will correct it soon.  In the "Pulling from Sourceforge" section, just follow the commented-out command instead of the last one:
#svn checkout     <----- this one; remove the leading pound sign
svn checkout   <---- not this one

As of tonight, though, the trunk code is still virtually identical to what is tagged as release_6.1.0, so it should work fine.

Let us know if you run into any other issues.

Thank you for using TPP!

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Malcolm Cook

Jun 7, 2022, 6:44:14 PM6/7/22
to spctools-discuss

I am checking out again from the release_6.1.0 since my `make all` is problematic, I want to start over, and `make clean` seems perhaps incomplete in its cleaning.

Alas I encounter this error whose workaround I can not guess:

David Shteynberg

Jun 7, 2022, 6:53:04 PM6/7/22
to spctools-discuss
Hi Malcolm,

Thanks for your interest in the TPP.
I think your url has a mistake in it.  Please try the following command:


Malcolm Cook

Jun 7, 2022, 10:50:29 PM6/7/22
to spctools-discuss
Hi David,

Indeed, the svn link I took from these instructions is incorrect (and probably should be amended), while the link you advise (and appearing above in the announcement) is correct.

BTW - I would offer to amend them myself but am unable to see if I am allowed to have an account on the wiki - seemingly not.

FWIW - I do now find that downloading and expanding the tarball is many times faster then using svn, so I will prefer it going forward.



Eric Deutsch

Jun 7, 2022, 11:47:35 PM6/7/22
to, Eric Deutsch

Hi Malcolm, thank you for the corrections, the page is now updated. Let me know if you find any other problems.




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