TPP on linux command line

[alastair.s...@googlemail.com]

I'm interested in running the TPP from the linux command line for a few reasons (flexibility + using the computing power of our linux server, the administers of which aren't keen on an apache webserver).

I can get some of the individual programs and scripts to run, but I'm struggling with some others (eg PeptideProphet and iProphet). Are there any examples of command line uses of TPP around that I can use to guide myself?

Many thanks,

Alastair

Max-Planck Institute for Molecular Plant Physiology

[David Shteynberg]

Hello Alastair,

The TPP gui interface (which is a simple windows install) provides the command lines for the tools it runs and can be used to train yourself on commandline TPP.  Also, running the PeptideProphetParser (PeptideProphet) and InterProphetParser (iProphet) on the commandline without additional flags should provide you with detailed usage statements for running the tools.

Thanks,

-David

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[alastair.s...@googlemail.com]

Good advice. Many thanks, Alastair

Am Montag, 25. Juni 2018 18:48:37 UTC+2 schrieb David Shteynberg:

Hello Alastair,

The TPP gui interface (which is a simple windows install) provides the command lines for the tools it runs and can be used to train yourself on commandline TPP.  Also, running the PeptideProphetParser (PeptideProphet) and InterProphetParser (iProphet) on the commandline without additional flags should provide you with detailed usage statements for running the tools.

Thanks,

-David

On Mon, Jun 25, 2018 at 6:53 AM, alastair.skeffington via spctools-discuss <spctools...@googlegroups.com> wrote:

I'm interested in running the TPP from the linux command line for a few reasons (flexibility + using the computing power of our linux server, the administers of which aren't keen on an apache webserver).

I can get some of the individual programs and scripts to run, but I'm struggling with some others (eg PeptideProphet and iProphet). Are there any examples of command line uses of TPP around that I can use to guide myself?

Many thanks,

Alastair

Max-Planck Institute for Molecular Plant Physiology

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[Chris Waizenegger]

Hi David,

Where in the GUI would I find the command line call for each tool? Perhaps I am missing something obvious. I am in a similar situation to Alastair whom originally posted this question, and it seems he was satisfied with your reply so I figure I'm on the right track here...

Thanks,

Chris

On Monday, June 25, 2018 at 9:48:37 AM UTC-7, David Shteynberg wrote:

Hello Alastair,

The TPP gui interface (which is a simple windows install) provides the command lines for the tools it runs and can be used to train yourself on commandline TPP.  Also, running the PeptideProphetParser (PeptideProphet) and InterProphetParser (iProphet) on the commandline without additional flags should provide you with detailed usage statements for running the tools.

Thanks,

-David

On Mon, Jun 25, 2018 at 6:53 AM, alastair.skeffington via spctools-discuss <spctools...@googlegroups.com> wrote:

I'm interested in running the TPP from the linux command line for a few reasons (flexibility + using the computing power of our linux server, the administers of which aren't keen on an apache webserver).

I can get some of the individual programs and scripts to run, but I'm struggling with some others (eg PeptideProphet and iProphet). Are there any examples of command line uses of TPP around that I can use to guide myself?

Many thanks,

Alastair

Max-Planck Institute for Molecular Plant Physiology

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[Luis Mendoza]

Hi Chris,

Once you run a command, you can see the exact command line that was run on the Job Output window (after the "EXECUTING:" string).  You can also view old commands, as long as their output has not been deleted.

Hope this helps,

--Luis

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[Chris Waizenegger]

Thanks Luis!

With some effort to get the parameters files properly filled up, and converting some of the file locations to be accurate to their locations for a Linux install, I've been able to get some work done.

Frustratingly, I have yet to find much documentation as to how to do so. Simple enough to figure out alone, but it would be nice to be able to skip right to processing data. Oh well!

Cheers,

Chris