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TPP patch wnels2  2010-01-07 12:41
Status: Closed
 
I'm upgrading to 9.3 on a CentOS 5 server. I checked out https://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_4-3-1 with svn and downloaded your patch.
From the ~/release_4-3-1/trans_proteomic_pipeline directory I ran patch -p0 -i ~/TPP4_3_1.patch. The TPP patches worked but not the xtandem patches.

Thanks,
Bill

[labkey@berkelium trans_proteomic_pipeline]# patch -p0 -i /root/Desktop/TPP4_3_1.patch
(Stripping trailing CRs from patch.)
patching file extern/xtandem/src/mpmods.cpp
Hunk #1 FAILED at 170.
Hunk #2 FAILED at 189.
Hunk #3 FAILED at 203.
Hunk #4 FAILED at 247.
Hunk #5 FAILED at 283.
Hunk #6 FAILED at 318.
6 out of 6 hunks FAILED -- saving rejects to file extern/xtandem/src/mpmods.cpp.rej
(Stripping trailing CRs from patch.)
patching file extern/xtandem/src/mprocess.cpp
Hunk #1 FAILED at 161.
Hunk #2 FAILED at 256.
Hunk #3 FAILED at 283.
Hunk #4 FAILED at 881.
Hunk #5 FAILED at 1203.
Hunk #6 FAILED at 1285.
Hunk #7 FAILED at 1508.
Hunk #8 FAILED at 1836.
Hunk #9 FAILED at 1852.
Hunk #10 FAILED at 2118.
Hunk #11 FAILED at 2638.
Hunk #12 FAILED at 2948.
Hunk #13 FAILED at 2990.
Hunk #14 FAILED at 3161.
Hunk #15 FAILED at 3333.
Hunk #16 FAILED at 3537.
Hunk #17 FAILED at 3762.
Hunk #18 FAILED at 3898.
18 out of 18 hunks FAILED -- saving rejects to file extern/xtandem/src/mprocess.cpp.rej
(Stripping trailing CRs from patch.)
patching file extern/xtandem/src/mprocess.h
Hunk #1 FAILED at 282.
Hunk #2 FAILED at 302.
Hunk #3 FAILED at 318.
Hunk #4 FAILED at 331.
Hunk #5 FAILED at 401.
5 out of 5 hunks FAILED -- saving rejects to file extern/xtandem/src/mprocess.h.rej
(Stripping trailing CRs from patch.)
patching file extern/xtandem/src/mscore.cpp
Hunk #1 FAILED at 153.
Hunk #2 FAILED at 206.
Hunk #3 FAILED at 527.
Hunk #4 FAILED at 703.
Hunk #5 FAILED at 1357.
Hunk #6 FAILED at 1570.
Hunk #7 FAILED at 1692.
7 out of 7 hunks FAILED -- saving rejects to file extern/xtandem/src/mscore.cpp.rej
(Stripping trailing CRs from patch.)
patching file extern/xtandem/src/mscore.h
Hunk #1 FAILED at 381.
Hunk #2 FAILED at 468.
2 out of 2 hunks FAILED -- saving rejects to file extern/xtandem/src/mscore.h.rej
(Stripping trailing CRs from patch.)
patching file extern/xtandem/src/mscore_s.cpp
(Stripping trailing CRs from patch.)
patching file extern/xtandem/src/mscore_s.h
(Stripping trailing CRs from patch.)
patching file extern/xtandem/src/mscorepam.h
Hunk #1 FAILED at 283.
Hunk #2 FAILED at 322.
2 out of 2 hunks FAILED -- saving rejects to file extern/xtandem/src/mscorepam.h.rej
(Stripping trailing CRs from patch.)
patching file extern/xtandem/src/msequenceserver.h
Hunk #1 FAILED at 161.
1 out of 1 hunk FAILED -- saving rejects to file extern/xtandem/src/msequenceserver.h.rej
(Stripping trailing CRs from patch.)
patching file extern/xtandem/src/msequtilities.cpp
Hunk #1 FAILED at 389.
Hunk #2 FAILED at 419.
2 out of 2 hunks FAILED -- saving rejects to file extern/xtandem/src/msequtilities.cpp.rej
(Stripping trailing CRs from patch.)
patching file extern/xtandem/src/msequtilities.h
Hunk #1 FAILED at 192.
Hunk #2 FAILED at 238.
2 out of 2 hunks FAILED -- saving rejects to file extern/xtandem/src/msequtilities.h.rej
(Stripping trailing CRs from patch.)
patching file extern/xtandem/src/p3.cpp
Hunk #1 FAILED at 175.
Hunk #2 FAILED at 187.
Hunk #3 FAILED at 258.
Hunk #4 FAILED at 271.
Hunk #5 FAILED at 607.
5 out of 5 hunks FAILED -- saving rejects to file extern/xtandem/src/p3.cpp.rej
(Stripping trailing CRs from patch.)
patching file extern/xtandem/src/resource1.h
(Stripping trailing CRs from patch.)
patching file extern/xtandem/src/stdafx.h
Hunk #1 FAILED at 1.
Hunk #2 FAILED at 10.
Hunk #3 FAILED at 186.
Hunk #4 FAILED at 261.
4 out of 4 hunks FAILED -- saving rejects to file extern/xtandem/src/stdafx.h.rej
(Stripping trailing CRs from patch.)
patching file extern/xtandem/src/tandem.cpp
Hunk #1 FAILED at 175.
Hunk #2 FAILED at 187.
Hunk #3 FAILED at 258.
Hunk #4 FAILED at 271.
4 out of 4 hunks FAILED -- saving rejects to file extern/xtandem/src/tandem.cpp.rej
(Stripping trailing CRs from patch.)
patching file src/Validation/ProteinProphet/ProteinProphet.cpp
(Stripping trailing CRs from patch.)
patching file src/Visualization/xinteract/xinteract.cxx
 
 
Brian Connolly responded:  2010-01-07 13:09
Bill, I ran into the same problem on a Fedora server. Here is the work around that I put together.

Create the Patched Source Code tree

Download the Source code

There are 2 steps in creating the source Download the source code from https://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_4-3-1. The 

mkdir ~/src/searchTools/TPP.4.3.1
cd ~/src/searchTools/TPP.4.3.1
mkdir release_4-3-1
svn checkout https://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_4-3-1 /labkey/src/searchTools/TPP.4.3.1/release_4-3-1

Download the LabKey TPP Patch from https://www.labkey.org/Wiki/home/Documentation/download.view?entityId=aa644dd3-12e8-102a-a590-d104f9cdb538&name=TPP431Patch.zip.


Apply the LabKey TPP Patch:

With all future versions of TPP and Xtandem, patching the source code will not be required. This is only required for v4.3.1. Lets expand and prepare the patch files. 

cd ~/src/searchTools/TPP.4.3.1
unzip TPP431Patch.zip
cd TPP431Patch
tar czf preparePatchFiles.tar.gz .

Apply the patch file 

cd ~/src/searchTools/TPP.4.3.1/release_4-3-1/trans_proteomic_pipeline
tar xzf ~/src/searchTools/TPP.4.3.1/TPP431Patch/preparePatchFiles.tar.gz



Now you can just build the TPP binaries. (Please note that the make command for the TPP also builds the X!Tandem binary. )
 
wnels2 responded:  2010-01-11 10:43
The patch procedure worked great, thanks! The tomcat server is working now but I'm getting errors from globus. I did move the 9.3 binaries to the globus server and restarted globus. I do see the job start using qstat but I get the message below in my log. Attached is a log file of my first search attempt, it shows the modules being extracted with a couple of unusual errors. Thanks, Bill 11 Jan 2010 13:22:13,960 INFO : Completed task 'org.labkey.ms2.pipeline.FastaCheckTask' 11 Jan 2010 13:22:14,111 INFO : Submitting job to Globus SGE with queue labkey: /share/apps/java/jdk1.5.0_12/bin/java -cp /share/apps/cpas/bin/labkey/labkeyBootstrap.jar org.labkey.bootstrap.ClusterBootstrap -modulesdir=/share/apps/cpas/bin/labkey/modules -webappdir=/share/apps/cpas/bin/labkey/labkeywebapp -configdir=/share/apps/cpas/bin/labkey/config file:/home/massspec/cpas/pipeline/projects/UPS/nelson/xtandem/test9_3_Copy4/UPS1-01.job.xml 11 Jan 2010 13:22:32,417 ERROR: Fault received from Globus on "submit" command 11 Jan 2010 13:22:32,451 ERROR: Parameter not supported 11 Jan 2010 13:22:32,459 ERROR: Fault received from Globus 11 Jan 2010 13:22:32,501 ERROR: org.globus.exec.generated.FaultType 11 Jan 2010 13:22:32,517 ERROR: Fault received from Globus 11 Jan 2010 13:22:32,553 ERROR: ProcessDied 11 Jan 2010 13:22:32,562 ERROR: Fault received from Globus 11 Jan 2010 13:22:32,568 ERROR: java.lang.Exception 11 Jan 2010 13:22:32,574 ERROR: Fault received from Globus 11 Jan 2010 13:22:32,580 ERROR: org.oasis.wsrf.faults.BaseFaultType
 
jeckels responded:  2010-01-11 13:35
Hi Bill, This looks like a permission problem. Either the user that's executing the Java process on the cluster node needs to have write permissions to create and modify files in the /share/apps/cpas/bin/labkey/labkeywebapp directory, or you need to manually run: java -jar labkeyBootstrap.jar as a user that has permission. It will give you information on the arguments. This will do the one-time extraction of the resources from the .module files. You will need to do this after every upgrade. Thanks, Josh
 
wnels2 responded:  2010-01-11 13:58
Thanks, it was permissions.
 
wnels2 responded:  2010-01-14 08:20
I ran into an issue with the tpp patch. It is still running ProphetModels.pl and ProtProphModels.pl. If gunplot is not installed on the system there will just be errors in the logfile saying that it can't find gunplot but if it is installed it will create .png files that mess up pipeline clean up and crash the analysis. As a work around I put exit; at the beginning of these scripts. Did I make an error installing the patches? Thanks, Bill
 
Brian Connolly responded:  2010-01-14 09:17
Bill, No you did not make an error. I have just tested on a Fedora server here and can reproduce your behavior. I will be opening a bug about this and will send you the bug number.
 
Brian Connolly responded:  2010-01-27 18:07
Bill, there was problem with the TPP Patch zip file. I have regenerated the zip file and updated our website with the new file (https://www.labkey.org/Wiki/home/Documentation/download.view?entityId=aa644dd3-12e8-102a-a590-d104f9cdb538&name=TPP431Patch.zip)

You will need to rebuild TPP and X!tandem in order to pick up these changes. My suggestion is that start the process from scratch. Meaning to download the source from the subversion repository, apply the updated patch file and then rebuild.

Send me a note if you run into any problems.

Brian
 
wnels2 responded:  2010-01-28 07:41
Hi Brian, I'm not at the lab until late next week. I will install it when I get back and let you know how it went. Thanks for your help. Bill
 
wnels2 responded:  2010-02-05 09:11
The new patch works. The logs are clean. thanks, Bill