TPP 4.8.0 Release is now available

[Joseph Slagel]

Announcing the official release of Trans-Proteomic Pipeline (TPP) 4.8.0 "PHILAE"

We are proud to offer a update to the Trans-Proteomic Pipeline (TPP) software, release 4.8.0 (4.8 revision).  The software is available for Windows as well as Linux (and unofficially) through OSX source from all the usual locations (please see the section below, "Getting the software").  Most users are recommended to use the Windows installer, which installs and configures the TPP and other required software (such as a web server).  For advanced users who need to customize the TPP, or for those who run on Linux or OS X, you can download the source code.


== Release Notes ==

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

"http://tools.proteomecenter.org/wiki/index.php?title=TPP:4.8.0_Release_Notes"


== Getting the TPP Software ==

* Download the TPP version 4.8.0 native windows installer from the Sashimi SourceForge project file release page:

  "http://sourceforge.net/http://sourceforge.net/projects/sashimi/files/Trans-Proteomic Pipeline (TPP)"

* Everyone is encouraged to read and contribute to our wiki, at
  "http://tools.proteomecenter.org/wiki/"

* For guides to installing and using our software, please see our wiki:
  "http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP"

* For downloading the source code, please go to the following link:
  "http://sourceforge.net/projects/sashimi/files/" and find the 4.8.0 source code .zip package;
or, check out the code directly from svn:
  "svn co svn://svn.code.sf.net/p/sashimi/code/tags/release_4-8-0"

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

== Acknowledgements ==

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

--

Joe Slagel
Institute for Systems Biology
jsl...@systemsbiology.org

[Alejandro]

Thank you very much to you all, for continuing this work. 

Alejandro

[Alfonso Olaya Abril]

Introducir código aquí...

Hi, im new in TPP, and after proving differents things, I lost my tandem_params.xml (that it is bassically the default sample because I introduced only a few changes, such as variable modifications in oxidation of methionine and deamidation of glutamine and arginine...), I am trying to create a new one (could I do in "TextEdit" and saving as .xml?), but I starting programming too, so It is so difficult for me just now. Could you send me that file? I can`f find it... My email es b22o...@uco.es

Thank you very much!

[Vladimir Gorshkov]

Hi,

Thank you very much for your work on TPP.

I'm sorry to say, but there are serious bugs in TPP 4.8 installer for windows.
1. The installer search for Apache installation only in one specific folder ( C:\Program Files (x86)\Apache Software Foundation\Apache2.3 ), thus if Apache is installed in any other location it fails. The default installation folder for Apache server supplied with the installer is C:\Program Files (x86)\Apache Software Foundation\Apache2.2

2. The installer overwrites PATH environment variable to "C:\Intepub\tpp-bin" instead of adding the value to the PATH existing in the system. This bug is specifically bad, since it leads to malfunction of a lot of other software in the system.

3. There seems to be hardcoded location for perl installation as well.

This issues make it impossible and somehow dangerous to use the installer.
Therefore the only suitable option is to compile everything from the source, which sounds a bit to complicated.

The better option was to distribute TPP as simple zipped binaries. As far as I can judge, the installer just unpack files to hardcoded folder, and modify some variables in system path and apache conf. Zipped binares and a decent installation instruction would serve the same way much better.

Best regards,
Vladimir

[MD]

Hi Joe,

I am trying to install 4.8 on linux and getting the following error. I also tried 4.71 , and both on ubuntu 12.04 and 14.04. . Can you please help? 

tu-x86_64 ZLIB_INCL=""  ZLIB_LIB=-lz  STATIC_LIBSTDCPP=

make[1]: Entering directory `/home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/extern/gzstream'

g++    -I. -O  -c -o Ubuntu-x86_64gzstream.o gzstream.cpp

ar cr /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../build/Ubuntu-x86_64/libgzstream.a Ubuntu-x86_64gzstream.o 

make[1]: Leaving directory `/home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/extern/gzstream'

uncompressing HDF5 library

mkdir -p /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../build/Ubuntu-x86_64/hdf5-1.8.6

cd /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../build/Ubuntu-x86_64/hdf5-1.8.6; cd ..; tar zxf /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/hdf5-1.8.6.tar.gz; \

for P in /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/hdf5-1.8.6.gcc47patch /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/hdf5-1.8.6.mingwpatch; do \

  echo "applying HDF5 patch $P"; \

  patch -s -p0 < $P; \

done

applying HDF5 patch /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/hdf5-1.8.6.gcc47patch

/bin/sh: 4: patch: not found

applying HDF5 patch /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/hdf5-1.8.6.mingwpatch

/bin/sh: 4: patch: not found

make: *** [/home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../build/Ubuntu-x86_64/hdf5-1.8.6] Error 127

root@trans-proteomic-pipeline:/home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src# 

Thank you

Regards

Mohammad

[Joseph Slagel]

It appears as if you are missing the following file:

/home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/hdf5-1.8.6.gcc47patch

Can you look to see what *patch files you have in this directory?  And did you download the source tar archive or did you check out the code from the sourceforge svn repository?

-Joe

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[Mohammad T Islam]

Hi Joe,

Thanks for your reply. hdf5-1.8.6.gcc47patch is available in the extern folder.

Ubuntu 14.04
ubuntu@trans-proteomic-pipeline-server:~$ ls -al /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/*patch
-rwxrwxr-x 1 51842 1100 1820 Nov  7  2013 /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/boost_1_54_0.mingwpatch
-rw-rw-r-- 1 51842 1100  967 May 30  2014 /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/boost_1_54_0.ubuntupatch
-rw-rw-r-- 1 51842 1100  944 Dec 28  2012 /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/hdf5-1.8.6.gcc47patch
-rw-rw-r-- 1 51842 1100 7042 Sep  5  2012 /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/hdf5-1.8.6.mingwpatch

Ubuntu 12.04
ubuntu@trans-proteomic-pipeline:~$ ls -al /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/*patch
-rwxrwxr-x 1 51842 1100 1820 Nov  7  2013 /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/boost_1_54_0.mingwpatch
-rw-rw-r-- 1 51842 1100  967 May 29  2014 /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/boost_1_54_0.ubuntupatch
-rw-rw-r-- 1 51842 1100  944 Dec 28  2012 /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/hdf5-1.8.6.gcc47patch
-rw-rw-r-- 1 51842 1100 7042 Sep  5  2012 /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/hdf5-1.8.6.mingwpatch

I followed the sourceforge site link from the wiki and downloaded the TPP_4.8.0-src.tgz file.

Direct link for this file was

http://downloads.sourceforge.net/project/sashimi/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v4.8%20%28philae%29%20rev%200/TPP_4.8.0-src.tgz?r=http%3A%2F%2Ftools.proteomecenter.org%2Fwiki%2Findex.php%3Ftitle%3DSoftware%3ATPP&ts=1432642452&use_mirror=softlayer-sng


Best Regards
Mohammad

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[Joseph Slagel]

I'm sorry, I should have read more closely.  The line:

/bin/sh: 4: patch: not found

seems to suggest that you don't have the "patch" program on your system.  Try running

sudo apt-get update && sudo apt-get install patch

to update your system and install the patch program.

[Mohammad T Islam]

Hi Joe,

Thanks a lot! After installing patch I was able to complete the TPP installation. I haven't used TPP before so I will go through the tutorial soon. On a side note, I noticed the tutorials are windows based. Are there any linux specific user guide?

Thank you

Best Regards
Mohammad

[Joseph Slagel]

Mohammad,

For the most part the tutorial should work on either platform.  You'll have to change the paths obviously as they'll be different.  Just shout out to the mailing list if you run into problems and you're sure to get help.

-Joe