Ron,

I believe you can add the default parameters to the file, default_input.xml file at the pipeline root and they will be used for each search in that pipeline.


-Brian

Hi Brian,

I also thought that you should be able to add the default parameters to the file but the file mascot_default_input.xml is not present at the pipeline root. I can easily create the file and edit the contents accordingly but it concerned me that the file is not already present at the pipeline root. It especially concerned me since when we create a Mascot search protocol; the default parameters are being drawn down into the Mascot search protocol but yet I can not find this file anywhere within the CPAS installation.

Is it possible that this default search parameter file is actually hosted up on the Mascot server that CPAS is connecting to? If so, then CPAS is simply downloading the contents of this xml file as the default parameters for a Mascot Search Protocol?

Thanks for your help.

Ron

Ron,

LabKey does not download the default parameters from the mascot server. The default parameters for the pipeline are read from the file default_input.xml, which is written into the PIPE_ROOT/.labkey/protocols/xtandem directory at pipeline root creation time.

I recommend putting your default parameters in the file default_input.xml and running a test job to see if they are picked up correctly.

Thank you,

Brian

Brian,

My pipeline root is set to E:\home via this procedure:

Admin >.....Go to Module >......More Modules >.......Pipeline

From here I clicked on "Set up"

I then entered in this value: E:\home for the "Use a default based on the site-level root"

On that file store I have this set of folders: E:\home\@files\.labkey

but there is nothing else below the .labkey folder.

Is this where the mascot_default_input.xml should be located?

thanks

Ron

Ron,

The way you are accessing Data Pipeline is certainly valid, however, the folder you working in, needs to be configured as a MS2 Folder type for the server to create all the MS2 default search parameter files.

For the folder, where you would like to setup your pipeline root, please set the folder type to be "MS2". You can do that by hitting the "Folder Settings" link in the Manage Project section of the Navigation Pane (ie the left pane).

Once this is done, you can go back to you Pipeline set up page using the same method as above and you should see a link to

1) Set the X!Tandem Specific Settings [This link will allow you to set the default parameters for all X!Tandem searches in this pipeline]

2) Set the Mascot Specific Settings [This link will allow you to set the default parameters for all Mascot searches in this pipeline]
 -- You will not see this link, unless you have successfully setup your mascot server configuration within the LabKey Server (via the Site Settings Admin console)


These links allow you to edit the default_input.xml and mascot_default_input.xml files through the LabKey Server UI.

Thank you,

Brian



PS YO

Thanks Brain, it all worked perfectly once I followed your instructions.

Brain,

Once I set up the pipeline as an MS2 folder, the home page is now displaying MS2 web parts (data pipeline, MS2 Experiments and Protein Search). Is there a way to not show these web parts on the home page of the web site?

The other issue is now tt looks like I have misconfigured the pipeline when establishing it with an MS2 folder.

When a search is initiated; the following error now appears:

Could not find the default sequence database path : /E:/databases/mascot/Sprot/mascot/Sprot

Can you please offer a suggestion on how I might correct this problem?

thanks

Ron

Ron,

About the home page problem: My recommendation is for you to

1) Create a new folder in the Home Project.
2) Configure the new folder to be of type MS2
3) Configure pipeline, again, in this folder.
4) In the Home project, root folder, change the Home Project back to being a Collaboration folder.

Now when you want to perform go MS2 searches, you go to this new sub-folder. There are other ways to do this, but I think this one will give you the best results.



About the Search problem: I will more a little more information about the error. Can you send me the labkey.log file for your server. The file is located in the "logs" subdirectory of the Tomcat installation directory.

Thank you,

Brian

Thanks Brian, attached please find the requested labkey.log file.

Ron,
It looks like the Mascot search is failing on the mascot server. The Mascot server is sending back an error code of "3". You might find more information in the logs of your mascot server or in the log file from the job.

Thanks,

Brian

Thanks Brian. I will start investigating that problem as well. Unfortunately, I am also unable to start local X-Tandem searches since modifying the enterprise pipeline to support a default mascot parameter file. The error that I am receiving is:

Could not find the default sequence database path : /E:/home/EntPip/@files/databases/mascot/Sprot/mascot/Sprot/

It looks to me like a part of the path (/mascot/sprot/) is being inserted twice.

thanks for your help

Ron

Ron,

This can one of 2 things.

First it could be that the Sequence Database path is set incorrectly in your Data Pipeline configuration. Goto the Data Pipeline Processing Setup page for your pipeline. On this page, there is a link named, "Set FASTA root" where you specify the location on the web server where FASTA sequence files will be located. If you click on that link, is it set to valid directory on your web server? If not, then that could be your problem too.


Second, I recommend creating a new, test folder to determine if your default parameter changes are the problem. Create a new sub-folder of the home project. Do not make the changes to the default mascot parameter file, like you have done in your current pipeline. Now attempt a X!Tandem search, do you see the same error message? If not, then it must have been one of the changes that you have made. I recommend adding the same changes to the pipeline configuration in this new, test folder, one by one, till you determine which parameter is incorrectly set.


-Brian

Brian,

I have not made any changes to the default mascot parameter file. I am using it exactly as created at the time that the pipeline root folder was designated as folder type "MS2".

I have set the fasta root to: E:\home\EntPip\@files\databases\mascot\Sprot

So why does CPAS generate this error when trying to create an X-Tandem search: ?

Could not find the default sequence database path : /E:/home/EntPip/@files/databases/mascot/Sprot/mascot/Sprot/

It looks to me like a part of the path (/mascot/sprot/) is being inserted twice.

Ron

Ron,

I am sorry for any confusion on my part. I am not sure why your server is experiencing these problems. Is E:\home\EntPip\@files\databases\mascot\Sprot a directory or a file?

Can you do 2 things for me.

1) send me the job log file for this failed job.
2) Implement a workaround of
   1: Change fasta root to be E:\home\EntPip\@files\databases
   2: Move fasta file(s) used in the search(es) to E:\home\EntPip\@files\databases
   3: retry the xtandem search.


If you are unable to successfully perform a search after #2, lets jump on a web conference so that I can review your configuration and get you working again.

Thank you,

Brian Connolly