That would be great, Bill. I am currently reviewing code contributed by Wong Chee Hong of Singapore to add Mascot support (both cluster, and single local machine) to CPAS. Adding Sequest is definitely on our list.

Do you have access to our subversion server yet? If you really are planning on writing this code, you will want it.

Once you have it, probably the quickest way to understand how you might implement this would be to look at branches/integ_mascot (the integration branch for Chee Hong's Mascot work). You would be plugging in Sequest support in a lot of the same places. Just look at the log for the branch to see what's been modified.

This branch is not complete. We are still in the process of reviewing and revising. But it is a good start, and certainly shows how to plug into the CPAS data pipeline.

Hi Bill,

My team made an effort to write up some document for our Mascot support effort. I will post them here and hopefully you find them useful.

These 2 docs are related to the cluster support.

1. cluster-pipeline.doc - describe basic cluster pipeline setup and how to support new scheduler
2. cluster-pipeline-changes.doc - describe changes made to cluster-pipeline code to support Mascot

Here are the last 2 documents related to mini-pipeline support.

1. CPAS-changes.doc - describe changes made to CPAS java code to support Mascot
2. CPAS-support-search-engines.doc - describe changes need to support another search engine in CPAS with Mascot support as specific example.

These documents are by no way complete but capture the gist of what we have done and thoughts that we formed.

I would also like to re-iterate my belief: if you have enhanced the pipeline to support another search engine, the CPAS community will like to hear from you and encourage you to contribute it. Your generous contribution will greatly benefit researchers in the community.

Thanks so much. This is all great information. I have been using the SVN repositiory and I am currently in the process of checking out the integ_mascot project. I hope we'll be able to deliver. I'll be in touch.

Bill

integ_mascot is building okay. I'd like to install it in the lab and see if I can get it to work with our mascot server before I try anything new. Is it ready to do that? If so, is there and example xar?

Thanks, Bill

Hi Bill,

I suggest that you start with mini-pipeline first. Use the "Test Mascot" (from "Manage Site", "Admin Console") to make sure CPAS can contact your mascot server. If the parameters work, save them in the Site's setting. (From "Manage Site", "Admin Console", "Customize Site")

You can use the sample .mzXML files from CPAS's get started to start a search. The xar will be created from the CPAS UI (starting with the "Pipeline" Tab, then "Process and Upload Data" button). You can then take a look at them. If you try the X!Tandem search too, and take a look at the "MS2" tab's "Protocol Column", you should see "Mascot Analysis" and "X!Tandem Analysis".

If all these work, turn on cluster-pipeline support by checking "Has pipeline cluster" via "Manage Site", "Admin Console", "Customize Site". Then, repeat the search test via "Pipeline" tab. You can use the X!Tandem search as a base line to make sure that your cluster-pipeline work, then test the Mascot search afterward.

For cluster-pipeline to work, your cluster scheduler/queueing system has to be either Torque or SGE for now.

All the best!

Cheers, Chee-Hong.

A couple of questions: We don't have security turned on. Your document says that you have code for servers with the security disabled. Can you please give me more details?

Our server is version 2.0.05. I think the current version is 2.1. Will this be a problem?

Thanks, Bill

Logics to handle servers with security disabled is already in the existing code. It is untested as our production server is too busy for us to try that.

Our server version is 2.1.03. I do not think we will run into problem here. But, as we have not tested on version 2.0.05, we can't tell for sure.

You may also want to practise cautious if you have valuable data.

Thanks for trying out and helping to test this untested feature.

Cheers, Chee-Hong.

I am running the testMascot.gm form. It queries URL: http://myserver/mascot/cgi/login.pl?..... but because we have security disabled there is no login.pl. I'm looking at MascotClient line 88, startSession(). There does not appear to be any conditional code for security disabled servers. How do you prefer me to proceed?

Thanks, Bill

Bill, sorry that the code did not work out for the security disabled case. May I trouble you to locate the cgi directory and report the list of files found in it?

Thanks, Chee-Hong.

No problem, thanks for the help.
By the way, have you been using the unit tests (ant targt drt)? I'm having some trouble getting them to pass with this branch. See the end of thread; https://cpas.fhcrc.org/announcements/home/support/details.view?rowId=456

Also, I just figured out that we're exactly 12 hours different. I'll start checking email between 8am and 10am your time so we can make quicker progress. I attached a file with the directory listing in case the listing below does not fomat well.

Thanks,
Bill

 Directory of C:\Inetpub\Mascot\cgi

03/25/2005 05:42p <DIR> .
03/25/2005 05:42p <DIR> ..
01/30/2004 07:45p 11,496 browser.pl
01/30/2004 07:45p 23,396 common_subs.pl
01/30/2004 07:45p 456,192 cygwin1.dll
01/30/2004 07:45p 4,416 daemon.pl
03/23/2005 04:58p 10,162 exprotbcl.pl
01/30/2004 07:45p 25,539 form_defaults.pl
01/30/2004 07:45p 5,122 getseq.pl
01/30/2004 07:45p 4,304 get_params.pl
01/30/2004 07:45p 1,475,092 htsearch.exe
01/30/2004 07:45p 2,498 index.pl
12/07/2001 07:31a 49,152 lcq_dta.exe
05/05/2004 07:18a 11,105 lcq_dta_shell.pl
06/07/2004 10:03a 10,730 lcq_dta_shell.pl.bak
01/30/2004 07:45p 12,903 mass_error.pl
05/05/2004 07:18a 119,628 master_results.pl
06/07/2004 10:03a 107,755 master_results.pl.bak
08/23/2004 05:00a 241,664 ms-geterror.exe
09/14/2004 02:43p 241,664 ms-geterror.exe.bak
01/30/2004 07:45p 2,738 msbiotools_batch_helper.pl
01/30/2004 07:45p 5,739 msbiotools_protein_get.pl
01/30/2004 07:45p 7,141 msbiotools_protein_view.pl
01/30/2004 07:45p 33,778 msbiotools_prot_cov_get.pl
01/30/2004 07:45p 2,024 msbiotools_results.pl
01/30/2004 07:45p 5,386 msbiotools_sequence_get.pl
05/05/2004 07:18a 11,722 msms_gif.pl
06/07/2004 10:03a 11,721 msms_gif.pl.bak
03/06/2002 07:52p 401,462 msvcp60.dll
03/06/2002 07:52p 290,869 msvcrt.dll
01/30/2004 07:45p 5,068 nph-daemon_helper.pl
08/23/2004 05:00a 2,228,224 nph-mascot.exe
09/14/2004 02:43p 2,228,224 nph-mascot.exe.bak
09/11/2003 06:46p 60 null
05/05/2004 07:18a 87,148 peptide_view.pl
06/07/2004 10:03a 86,066 peptide_view.pl.bak
05/05/2004 07:18a 57,976 protein_view.pl
06/07/2004 10:03a 54,341 protein_view.pl.bak
01/30/2004 07:45p 15,125 score_gif.pl
01/30/2004 07:45p 57,423 search_form.pl
04/04/2003 05:57p <DIR> sequest
03/25/2005 02:59p 811 tryit.pl
03/25/2005 05:41p 858 tryit2.pl
03/25/2005 05:48p 889 tryit3.pl
06/18/2002 02:34p <DIR> _vti_cnf
              41 File(s) 8,407,611 bytes
               4 Dir(s) 41,542,320,128 bytes free

 Directory of C:\Inetpub\Mascot\cgi\_vti_cnf

06/18/2002 02:34p <DIR> .
06/18/2002 02:34p <DIR> ..
06/18/2002 02:34p 180 browser.pl
06/18/2002 02:34p 181 cygwin1.dll
06/18/2002 02:34p 180 form_defaults.pl
06/18/2002 02:34p 179 getseq.pl
06/18/2002 02:34p 179 get_params.pl
06/18/2002 02:34p 182 htsearch.exe
06/18/2002 02:34p 179 index.pl
06/18/2002 02:34p 180 lcq_dta_shell.pl
06/18/2002 02:34p 180 mass_error.pl
06/18/2002 02:34p 181 master_results.pl
06/18/2002 02:34p 181 ms-geterror.exe
06/18/2002 02:34p 179 msbiotools_protein_get.pl
06/18/2002 02:34p 179 msbiotools_protein_view.pl
06/18/2002 02:34p 179 msbiotools_results.pl
06/18/2002 02:34p 179 msbiotools_sequence_get.pl
06/18/2002 02:34p 180 msms_gif.pl
06/18/2002 02:34p 181 msvcp60.dll
06/18/2002 02:34p 181 msvcrt.dll
06/18/2002 02:34p 180 nph-daemon_helper.pl
06/18/2002 02:34p 181 nph-mascot.exe
06/18/2002 02:34p 180 peptide_view.pl
06/18/2002 02:34p 180 protein_view.pl
06/18/2002 02:34p 180 score_gif.pl
06/18/2002 02:34p 180 search_form.pl
              24 File(s) 4,321 bytes
               2 Dir(s) 41,542,320,128 bytes free

 Directory of C:\Inetpub\Mascot\cgi\sequest

04/04/2003 05:57p <DIR> .
04/04/2003 05:57p <DIR> ..
12/05/2001 06:51a 331,855 displayions.exe
06/18/2001 10:44a 36,128 flicka.pl
12/03/2001 02:51p 10,903 showout.pl
               3 File(s) 378,886 bytes
               2 Dir(s) 41,542,320,128 bytes free

I just checked in changes to the integ_mascot branch that should get the DRT passing again. It does appear that Chee Hong has not been running this. There were 3 separate issues. I am sure it was just an oversight, and that he'll be using the tests in the future.

Thanks to Brendan for getting DRT to pass again. Bill has kindly helped out with the testing. Together, we have enhanced the code to work with Mascot Server v2.0.x. Thanks, Bill!

The changes have been committed to svn "branches/integ_mascot" and you are welcome to try it out.

I have attached a document to describe the expected interactions and also notes on preparation before engaging the Mascot features.