We added a lot more support for the Trans Proteomic Pipeline to 1.4. In the process I decided to drop the .exe from the executable names when running them from the pipeline. That way the TPP programs work as built on both 'nix and Windows systems. Previously, I was using 'Tandem2XML.exe' always, so that is probably how you have it on your system.

The following instructions were supposed to make it into our installation help for 'nix, but I can't find them, so here they are:

1. Get the sources for the Sashimi 'Trans Proteomic Pipeline' project. The current download is not recent enough. You must get the sources from anonymous CVS:

https://sourceforge.net/cvs/?group_id=69281

2. Make the following modifications to <root>/src/Makefile.inc:

• Add a line with XML_ONLY=1
• Modify TPP_ROOT to point to the location you intend to install the binaries. This location must be on your PATH.

3. Run 'make configure all install' at a command prompt.

You need to do this not only to fix the Tandem2XML issue, but also to get new TPP components like ProteinProphet and XPress that we now support.

Sorry this wasn't clearer in the release doc's.

The instructions have been available here since the release:

https://cpas.fhcrc.org/Wiki/home/help/1.4/page.view?name=configTomcat

But I recognize they may be a little difficult to find. If you click on the Portal tab in Help, you can search the docs from there.

I tried it and now it goes a bit further but it still gives an error after invoking protein prophet. Something with the perl interpreter. I am attaching the log file. Regards,

Metodi

Try "ls /usr/bin/perl" and "which perl" on your system. Seems like you must not have "/usr/bin/perl". Some systems have it at "/usr/local/bin/perl". Most Linux installs have /usr/bin/perl. Figure out where yours is, and edit ProteinProphet.pl (first line) to point to it. Or you can try get perl into the desired location.

I checked perl. It is ok. Is there anyway to disable the use of ProteinProphet by CPAS?

Well, if "perl -v" fails, then ProteinProphet will not run. Still, I'd keep looking at why ProteinProphet is failing to run on your system. Do you get the same error when your execute "ProteinProphet.pl" from a command prompt? Just type "ProteinProphet.pl" at a command prompt (assuming it is on your path). You should get the usage message. If you get this same "bad interpreter" message, start trying to get a really simple perl script to work, check permissions on ProteinProphet.pl, etc.

If it works, then definitely check permissions on ProteinProphet.pl, it may be that the user you run Tomcat under doesn't have permissions to run ProteinProphet.pl, or perl…

ProteinProphet.pl does not work. Gives "bad interpreter" etc. Simple script does not work either. However if I type: perl ProteinProphet.pl It gives the expected output. Same with simple scripts: perl simple script.pl executes properly.

Hmmm… How about the output for:

1. ls -l ProteinProphet.pl
2. ls -l SimpleScript.pl
3. ls -l /usr/bin/perl
4. which perl
5. whoami
6. groups

Of course, if you have a local 'nix expert, it might be easier for them to figure this out, than for me to try to do it remotely.

> ls -l ProteinProphet.pl -rwxr-xr-x 1 metodi users 185076 2006-06-08 17:39 ProteinProphet.pl

> ls -l script.pl -rwxr--r-- 1 metodi users 44 2006-06-08 18:06 script.pl

> ls -l /usr/bin/perl -rwxr-xr-x 3 root root 1295595 2005-12-17 03:27 /usr/bin/perl

Thanks a lot for the help.

Well, that all looks fine. Does anything change if you modify the first line to read:

#!/usr/bin/perl -w

?

Bingo! ProteinProphet now runs. Why is this (-w) helping. Isn't it just to enable warnings? Thanks a lot. That was great help! Metodi

Huh. I was just hoping it would give us more information. At one point I ended up with a version of ProteinProphet.pl on a Linux system that had some Windows line endings. I remembered that I got the same useless message about the interpreter until I added -w, and then things became a lot clearer, but it didn't fix the problem as in your case.

Anyway, glad it works. Enjoy 1.4!

I just run into the same problem. The perl script has the window end of the line. What make this tricky is that it appears to be a new issue in the current TPP code. I am supprised that Linux can not recognize Window's end of line. In the end, use dos2unix will fix these files into unix files.