Re: [spctools-discuss] TPP 4.8.0 installation issues on Ubuntu 14.04

What Linux platform/version are you trying to built it for? On Wed, Apr 20, 2016 at 7:28 AM, Craig Lawless < craig.lawl...@manchester.ac.uk> wrote: > Please can anyone help. I've never really had any success installing TPP > in previous years on linux and so have avoided until now. > > I am follo

Re: [spctools-discuss] Problems with Makefile TPP v4.8.0

Doesn't look like OBJ_ARCH is set properly now either. Can you run "make info" and check to see what its value is? You might try assigning it a value, something like the following might work: make ARCH=SUSE OBJ_ARCH=$PWD/../build/SUSE On Wed, Apr 13, 2016 at 9:24 AM, Constantin wrote: > I ch

Re: [spctools-discuss] Problems with Makefile TPP v4.8.0

It looks like there is a space between SUSE and LINUX. If so this would explain some of the troubles. Easiest thing to do is set ARCH_DISTRO to something without a space, say "SUSE". You can do this directly on the command line as so: make ARCH_DISTRO=SUSE Or in the src/ directory you can add

Re: [spctools-discuss] Problems with Makefile TPP v4.8.0

What's the output for the following command? lsb_release -i -s || cut -d ' ' -f1 /etc/*release | head -n1 On Tue, Apr 12, 2016 at 9:39 AM, Constantin wrote: > Hi everyone, > > I have some trouble getting the TPP v4.8 to compile on my LINUX > distribution (SUSE LINUX Enterprise Desktop 12). > My

Re: [spctools-discuss] Re: problem to open .pepXML file generated by TPP twa with xml viewer

When you used the extra verbose flag there should have been more output as to what the program was actually updating. Was there? On Tue, Mar 1, 2016 at 8:11 AM, Shiliang Wang wrote: > Hi, Joe: > >Thank you very much. > >I clicked the additional options selection box "Be

Re: [spctools-discuss] Possible to run either msconvert or ReAdw on Linux using WINE?

http://tools.proteomecenter.org/wiki/index.php?title=Msconvert_Wine On Mon, Dec 14, 2015 at 10:16 AM, David Zhao wrote: > Hi there, > > Is it possible to run the raw file conversion tool, such as ReAdW or > msconvert on Linux using WINE or similar? > Thanks, > > David > > -- > You received this

Re: [spctools-discuss] [solved] compiling TPP 4.8.0 on "exotic" 64bit linux (massypup64)

Robert, I'm guessing that this line "cut -d ' ' -f1 /etc/*release | head -n1" buried deep in the TPP Makefile is returning an empty string so when the ARCH is set to the distro + architecture you only get the architecture part. An alternative to changing the Makefile, you should be able to simply

Re: [spctools-discuss] Re: Processing MSGF+ searches

Jesse, Yes, I think David pinpointed an issue. It appears as if you downloaded a developer alpha build of TPP. As an alpha build, its expected to have lots of problems as it gets tested and they get fixed. I'd recommend downloading the latest stable TPP release, 4.8.0, from sourceforge, http:

Re: [spctools-discuss] Re: Problems building boost inside TPP

Amin, Did you run a full clean before trying to rebuild? "make realclean". Can you send the full log if you still see a problem? Joe On Thu, Jun 4, 2015 at 12:21 PM, Amin Momin wrote: > Thanks Joe, That error was resolved. Now I get a different one. Please > give your suggestion. > > Amin >

Re: [spctools-discuss] Re: Problems building boost inside TPP

Amin, While its possible I wouldn't recommend it. From the error message it looks like you may be missing the bzip libraries. Make sure you have bzip and bzip-devel installed on your system (yum bzip-devel). -Joe On Thu, Jun 4, 2015 at 8:41 AM, Amin Momin wrote: > Hi > > I am trying to inst

Re: [spctools-discuss] TPP-4.8.0 compilation error (Linux 64bit): undefined reference to `gdImagePngPtr'

Robert, could you include more of the log? It'd be helpful to see what the exact compilation command is. Tx, Joe On Wed, Jun 3, 2015 at 10:28 PM, Robert Winkler < robert.wink...@bioprocess.org> wrote: > Hi Jimmy, Thanks for the quick reply. David and me re-compiled the libpng > and subsequentl

Re: [spctools-discuss] Re: TPP 4.8.0 Release is now available

Are there > any linux specific user guide? > > Thank you > > Best Regards > Mohammad > > > > > On 30/05/2015 3:00 pm, Joseph Slagel wrote: > > I'm sorry, I should have read more closely. The line: > > /bin/sh: 4: patch: not found > > seems

Re: [spctools-discuss] Re: TPP 4.8.0 Release is now available

20%28philae%29%20rev%200/TPP_4.8.0-src.tgz?r=http%3A%2F%2Ftools.proteomecenter.org%2Fwiki%2Findex.php%3Ftitle%3DSoftware%3ATPP&ts=1432642452&use_mirror=softlayer-sng > > > Best Regards > Mohammad > > > > On 30/05/2015 2:39 am, Joseph Slagel wrote: > > It appears as if

Re: [spctools-discuss] Re: TPP 4.8.0 Release is now available

It appears as if you are missing the following file: /home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/hdf5-1.8.6.gcc47patch Can you look to see what *patch files you have in this directory? And did you download the source tar archive or did you check out the code from the s

Re: [spctools-discuss] TPP 4.8.0 compile fatal error

Hmm, I don't recall that htmldoc was being built on linux by default. On windows I know it isn't. You most likely don't need it so could remove it from the build process. -Joe On Mon, Jan 12, 2015 at 2:58 PM, Brian Hampton wrote: > Hi Joe, > > I was headed down that track thanks to your upda

Re: [spctools-discuss] TPP 4.8.0 compile fatal error

Hi Brian, Do you have the GD dev library installed? and if so you may need to add its location to the makefile as a "-I". Under ubuntu I think you can install it via apt-get install libgd2-dev -Joe On Mon, Jan 12, 2015 at 11:54 AM, Brian Hampton wrote: > Hello, > > I'm trying to compile TPP

Re: [spctools-discuss] Command FAILED RETURN CODE:256

You could download and install ProteoWizard and try its version of msconvert. -Joe On Sun, Dec 7, 2014 at 10:50 PM, lei wrote: > Hello, I want to convert the .yep format into .mzML format using TPP4.8, but > it does not work, here are the error message in the msconvert console. Thanks! > > fo

[spctools-discuss] TPP 4.8.0 Release is now available

Announcing the official release of Trans-Proteomic Pipeline (TPP) 4.8.0 "PHILAE" We are proud to offer a update to the Trans-Proteomic Pipeline (TPP) software, release 4.8.0 (4.8 revision). The software is available for Windows as well as Linux (and unofficially) through OSX source from all the u

Re: [spctools-discuss] Error writing run

Javier, Sounds like it might be a memory/file size issue. First off I'd check the last line of the file to see if it has the mzML end marker. If it isn't "" then you know msconvert didnt' finish converting the original file into mzML. Also, how big is the original file that you are trying to co

[spctools-discuss] FWD: Deprecated CGI endform in tpp_gui.pl caused centos install to fail

- Forwarded Message - *From:* "jj...@users.sf.net" *To:* slage...@users.sf.net *Cc:* jj...@users.sf.net *Sent:* Friday, October 3, 2014 6:31 AM *Subject:* Deprecated CGI endform in tpp_gui.pl caused centos install to fail -- Our install to Centos linux faile

Re: [spctools-discuss] Generation of mzIdentML from TPP results

Hi Robert, I just wanted to followup again on this. I updated the patch to match the latest version of Proteowizard and submitted it to the Proteowizard's developer mailing list in the hope they will review and accept the code. I haven't heard back yet from them, but if your need is still there

Re: [spctools-discuss] X!Tandem searches take too long

I haven't tried it on XP in a while but I'd say there is more likely something else wrong. What does the log for your search(es) say. -Joe On Fri, Aug 1, 2014 at 5:54 AM, Marianne Brannon wrote: > Computer with Microsoft XP operating system. The search finished and the > .tandem files were g

Re: [spctools-discuss] X!Tandem searches take too long

Marianne, What are you running X!Tandem on right now? -Joe On Thu, Jul 31, 2014 at 12:25 PM, Marianne Brannon wrote: > Is there a way to speed up the X!Tandem search? Is there a way to > download X!Tandem on one of our local computers so that the search takes > less time? Any help and info

Re: [spctools-discuss] [PeptideProphet] limitation of input file size?

Yes more than likely you'll have better luck on Linux since it will probably be 64-bit and by default will then be compiled as a 64-bit application. You can simply check the system architecture to make sure. -Joe On Wed, Jul 2, 2014 at 6:25 PM, User wrote: > Thanks, Joe. > > My OS is window 7

Re: [spctools-discuss] [PeptideProphet] limitation of input file size?

What platform are you running TPP on? Windows? If so you will have a 2GB limit as TPP is currently compiled as a 32bit application. -Joe On Wed, Jul 2, 2014 at 2:36 AM, User wrote: > Hi > > I try to run PeptideProphet. > > But i found that, > > if input file size was bigger than 1.5G, it oc

Re: [spctools-discuss] Re: TPP 4.7.0 installation problems on Ubuntu 14.04

14.04. > Since this make gave the mentioned thread.a missing problem, I built the > 1.55 version; however, during compilation of TPP the error returned. > > Might it be an idea to build the libboost 1.54 and to try again? > > Best, Robert > > > On Mo 23 Jun 2014 19:57:2

Re: [spctools-discuss] Re: TPP 4.7.0 installation problems on Ubuntu 14.04

Hi Robert, It sounds like you built your own version of boost as we're still on 1.54.0? If so getting the right packages built and linked with the TPP might be a bit challenging. Any reason for not going with the stock boost that built in TPP? -Joe On Mon, Jun 23, 2014 at 4:16 PM, Robert wro

Re: [spctools-discuss] Generation of mzIdentML from TPP results

Hi Robert, I've prepared a patch containing changes made by Steven Lewis to Proteowizard's idconvert that should produce compliant output. The plan is to eventually incorporate these changes directly into Proteowizard. I could give you the patch and you could apply it to the Proteowizard support

[spctools-discuss] TPP 4.7.1 Release is now available

Announcing the general availability of the Trans-Proteomic Pipeline (TPP) "Polar Vortex" version 4.7.1. This is a maintenance update to the Trans-Proteomic Pipeline (TPP) software which addresses a number of issues identified with version 4.7.0. All TPPusers are advised to upgrade their installat

Re: [spctools-discuss] TPP 4.7.0 installation problems on Ubuntu 14.04

Will, I think this may be a problem with boost that's been reported and fixed. I was able to reproduce the problem and when I applied the change found in this bug report it seemed to go: https://svn.boost.org/trac/boost/changeset/84950 -Joe On Mon, May 12, 2014 at 8:42 AM, Will Fondrie wrot

Re: [spctools-discuss] Using new version of Comet with TPP

Shouldn't be a problem. We're just bundling the comet binaries in TPP -- so no modifications. You may encounter a small change with the parameters but that's easily fixed. -Joe On Mon, Apr 7, 2014 at 2:48 PM, Brian Hampton wrote: > Hello, > > A new version of Comet was released recently. I

Re: [spctools-discuss] Help! - The requested URL (http://localhost/tpp-bin/tpp_gui.pl) was not found on this server.

Suzanne, It might be a problem with where you installed ActivePerl. Can you open a Windows command shell (how to ) and type in the command: which perl.exe and forward on the output? It should look something like: C:\Perl\bin\perl.exe This s

Re: [spctools-discuss] Is there a sequest equivalent or port that runs from linux and/or written in Java?

Try comet: http://comet-ms.sourceforge.net/ On Mon, Mar 31, 2014 at 9:58 AM, David Zhao wrote: > Hi there, > > I'm wondering if there is a port of sequest algorithm to java available > now, or a way to run sequest searches on linux, without having bioworks or > discoverer installed. > Thanks,

Re: [spctools-discuss] Help! - The requested URL (http://localhost/tpp-bin/tpp_gui.pl) was not found on this server.

Hi Janet, Can you send us your Apache log files. They are usually under the Apache HTTP Server folder in your programs menu, or C:\Program Files (x86)\Apache Software Foundation\Apache2.2\logs. -Joe On Sun, Mar 30, 2014 at 6:55 AM, wrote: > Hi > > I have the same error. I've just installed

Re: [spctools-discuss] Re: TPP 4.7.0 is now available

software/78-massypup) > release. > > Best Regards, > > Robert > > > On 05.03.2014 10:28, Joseph Slagel wrote: > > Lorenz, > > That's a good question -- I didn't think of the Amazon images. Recently > I've started maintaining "RE

Re: [spctools-discuss] Re: TPP 4.7.0 is now available

Will do where I can. I should also mention that we've discussed including more of the tools directly in TPP so as to alleviate the headache of maintaining them outside of TPP. (Or at least transfer the headache). So this might be happening in the future. -Joe On Wed, Mar 5, 2014 at 1:08 PM,

Re: [spctools-discuss] Apache user on RHEL for TPP

Brian, What's your TPP_ROOT and TPP_WEB variables in your Makefile.confic.incl (or Makefile) set to? They both need to have a trailing '/' otherwise instead of getting a tpp directory you'll end up with all of files/directories up one level. (I've done this more than once myself btw). As to RHE

Re: [spctools-discuss] Problems getting Petunia to run after install of TPP-4.7

#x27;m finding a number of perl files that are lacking the path to perl a >>> the top of the file. The latest one is ProphetModels.pl. >>> >>> I should recompile, but what do I change to correct this? >>> >>> Thanks in advance, >>> Brian >

Re: [spctools-discuss] Re: TPP 4.7.0 is now available

Lorenz, That's a good question -- I didn't think of the Amazon images. Recently I've started maintaining "READMEs" on the images with their contents. The latest, for 4.6.3 outlines the versions installed: http://tools.proteomecenter.org/wiki/index.php?title=TPP_AMI_4.6.3_README If its lacking

Re: [spctools-discuss] Problems getting Petunia to run after install of TPP-4.7

re lacking the path to perl a the > top of the file. The latest one is ProphetModels.pl. > > I should recompile, but what do I change to correct this? > > Thanks in advance, > Brian > > > > > On Tue, Mar 4, 2014 at 10:49 AM, Joseph Slagel < > joseph.sla..

Re: [spctools-discuss] Re: TPP 4.7.0 is now available

On Mon, Mar 3, 2014 at 12:10 AM, loblum wrote: > Dear Joe > > Could you please specify the versions of the external tools (especially > search engines) you are using? > > XTandem JACKHAMMER (2013.06.15) > Version X! TANDEM Jackhammer TPP (2013.06.15.1 - LabKey, Insilicos, ISB). This is a modifie

Re: [spctools-discuss] Problems getting Petunia to run after install of TPP-4.7

Brian, Interesting. What's the first line in tpp_gui.pl? Does it point to a valid instance of perl on your system? Do the newlines at the end of the line look correct for Linux? And is the executable at the command line by apache (e.g. sudo -u apache /usr/local/tpp/cgi-bin/tpp_gui.pl)? -Joe

[spctools-discuss] TPP 4.7.0 is now available

Announcing the official release of Trans-Proteomic Pipeline (TPP) 4.7.0 "Polar Vortex" We are proud to offer a major update to the Trans-Proteomic Pipeline (TPP) software, release 4.7.0 (4.7 revision). The software is available for Windows as well as Linux (and unofficially) through OSX source fr

Re: [spctools-discuss] Validation of mzXML schema failed using XSD.EXE utility

Hi Josip, I checked and also noticed and agree that the files do exist, though they happen to be a fairly old version of the mzXML schema. This blog entry may be of help: http://blogs.msdn.com/b/mapo/archive/2008/02/20/xsd-exe-error-generating-classes-for-schema-myschema-xsd-the-element-http-sch

Re: [spctools-discuss] Re: TPP FDR Tutorial (How to use the decoy features)

3:30 PM, Brian Hampton wrote: > Hi Joe, > > I only see the Win binaries. Is the source available yet? > > Brian > > > > > On Wed, Feb 19, 2014 at 4:19 PM, Joseph Slagel < > joseph.sla...@systemsbiology.org> wrote: > >> You'll

Re: [spctools-discuss] Re: TPP FDR Tutorial (How to use the decoy features)

You'll find the latest release candidate (RC4) in: https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v0.0%20%28Development%29/ Since I don't expect any more changes this should be effectively 4.7. -Joe On Tue, Feb 18, 2014 at 10:28 PM, Robert Jones wr

Re: [spctools-discuss] combine FASTA files

Zeyu, If your on a Linux system, there's the "cat" command: http://en.wikipedia.org/wiki/Cat_%28Unix%29 http://www.thegeekstuff.com/2013/04/cat-command-examples/ http://linux.die.net/man/1/cat And while I've never tried it the "copy" command supposedly works: http://support.microsoft.com/KB/695

Re: [spctools-discuss] Re: TPP 4.6.2 installation problem Ubuntu 12.04 LTS virtual box

Anton, Can you take a look in your Apache httpd logs and see if there are any access or error messages occurring when you try to open TPP? -Joe On Wed, Feb 5, 2014 at 4:12 AM, Anton Gurkov wrote: > Hello! > > The same issue for me as well. I have changed "SetEnv WEBSERVER_ROOT > /usr/local/"

Re: [spctools-discuss] Re: xargs:cannot fork?

It sounds like a resource problem, you might be exceeding the capabilities of the system you are on. Do you have a lot of applications/processes running? How many spectrum files are in the directory Bladder-cancer-side-wall-BCa09 and what kind of run is this? And what version of Windows/TPP are

Re: [spctools-discuss] TPP on cluster - Petunia running remotely?

Gary/Josh, That's good to hear since we're using the last open source version of SGE and the commands should all be similar. Recently I've made to the Petunia web interface (tpp_gui.pl) that should also work for you. What I've done is made two simple modifications The first will prepend the "q

Re: [spctools-discuss] Re: error with installing TPP4.5.2

Hi Qiaojun, What version of perl are you using (perl -V)? -Joe On Mon, Nov 11, 2013 at 3:11 AM, chr12is wrote: > Hi Qiaojun, > > I had the same errors when installing the latest version of the TPP on my > CentOS cluster. For some reason it throws an error with the qw syntax in > the perl file

Re: [spctools-discuss] TPP on cluster - Petunia running remotely?

Josh, Its easily possible to run it as a remote process, not on the cluster. The trick of course is having it actually run jobs on the cluster. And I just recently did some work to make this a little easier. Which clustering software do you use? -Joe On Mon, Nov 11, 2013 at 8:07 AM, Joshua

Re: [spctools-discuss] Anyone running TPP on Mac 10.9 (Mavericks)?

I'd be very happy to put the changes in the trunk and test things out. On Thu, Oct 31, 2013 at 2:20 PM, Dave Trudgian < david.trudg...@utsouthwestern.edu> wrote: > I now seem to have TPP building boost 1.54 successfully on mavericks, > which is promising. It's working on CentOS 6 also, and the T

Re: [spctools-discuss] Anyone running TPP on Mac 10.9 (Mavericks)?

You might try trunk. I recently fixed a few issues found compiling with the more recent releases of gcc. -Joe On Mon, Oct 28, 2013 at 1:38 AM, Bjorn wrote: > Hi, > I tried to install the latest version of the TPP on a Mac 10.9, but I ran > into errors with Boost libraries not being built. >

Re: [spctools-discuss] Re: Problems building boost inside TPP

I'm working on fixing it on TPP's trunk now. -Joe On Mon, Oct 14, 2013 at 11:49 AM, Joseph Slagel < joseph.sla...@systemsbiology.org> wrote: > Actually we've been seeing some problems with the latest versions of gcc. > You might be running into some of the same is

Re: [spctools-discuss] Re: Problems building boost inside TPP

Actually we've been seeing some problems with the latest versions of gcc. You might be running into some of the same issues. -Joe On Mon, Oct 14, 2013 at 11:47 AM, Han Jo wrote: > I am using 4.5... good guess. I will give it a shot with a later version! > > > 2013/10

Re: [spctools-discuss] Re: Problems building boost inside TPP

What version of gcc are you using to do the build? -Joe On Mon, Oct 14, 2013 at 8:21 AM, Han Jo wrote: > Okay, after finding the line: > > "libs/regex/build/has_icu_test.cpp:12:30: fatal error: unicode/uversion.h: > No such file or directory". I tried to remove -q flag from the bjam command >

Re: [spctools-discuss] Running the TPP on an HPC through Command Line

Devesh, I would imagine your best bet then would be to download the TPP source, compile it on your Linux system then just copy the executable of the programs that you wish to use. The source is available at http://sourceforge.net/projects/sashimi/files/latest/download?source=files -Joe On Sun

Re: [spctools-discuss] Running the TPP on an HPC through Command Line

Robert, The bad news is that we haven't incorporated any logic in the Petunia web interface of TPP to interact with a cluster system. Most users at this level have been using the command line. Though we've been recently talking about developing this. The good news though is I have some scripts

Re: [spctools-discuss] Running the TPP on an HPC through Command Line

Hi Robert, I'm happy to help out as I've been managing the execution of TPP on our cluster here at ISB. How is your HPC setup? Are you using a batch job system such as Sun Grid Engine? And what Operating System are you using? Linux? -Joe On Thu, Aug 22, 2013 at 2:53 PM, Robert Jones wrote:

Re: [spctools-discuss] TPP: UNC paths are not supported when using Mascot2XML

Bao, The "//" at the beginning of the paths doesn't look correct. I would think that it would start with a '/'. -Joe On Thu, Aug 22, 2013 at 12:53 PM, wrote: > Hello everyone, > > I've been using Mascot-based Analysis Pipeline. However, converting mascot > DAT file to pepXML turns in an error

Re: [spctools-discuss] Protein Prophet - No data quitting

Rishika, Could you post the output you are seeing? Also please check your search results. Often times if the search parameters are incorrect you won't get enough good spectrum identifications for peptideprophet/proteinprophet. -Joe On Thu, Aug 15, 2013 at 1:55 PM, Rishika Bisaria wrote: > Hel

Re: [spctools-discuss] XTandem and k-score

Rishika, The TPP version of X!Tandem has some dependencies (such as mzParser) that are outside of the src_tpp directory. I hate to say it but the easiest thing to do is download and build all of TPP. -Joe On Fri, Jul 26, 2013 at 9:44 AM, Rishika Bisaria wrote: > Hi, > Thank you for the reply.

[spctools-discuss] TPP 4.6.3 Release is Available

Announcing the general availability of Trans-Proteomic Pipeline (TPP) "Occupy" 4.6.3. This is a maintenance update to the Trans-Proteomic Pipeline (TPP) software which addresses a number of issues identified with version 4.6.2. All TPPusers are advised to upgrade their installations to the latest

Re: [spctools-discuss] amztpp user for ssh

Ben, You've got the right username, ubuntu. You'll also have to make sure that the EC2 security group used for the instance allows ssh connections (which it sounds like you do). The last thing is that you'll have to create a EC2 key-pair and when you start the node make sure you tell AWS to use

Re: [spctools-discuss] X! TANDEM error

Kierstin, Try checking your input to X!Tandem. Make sure the database doesn't have any "bad" sequences in it. Often times special characters sneak into the file and can cause X!Tandem to crash. Also take a look at your spectrum -- can you see the input file in Pep3D? -Joe On Mon, Jul 22, 2013

Re: [spctools-discuss] X! TANDEM error

Kierstin, You might want to take a 2nd look at what parameters you are also using for X!Tandem. I find it pretty useful to use the API documentationas a guide. What platform are you running TPP on, Windows? and what version of TPP are you using? -Joe

Re: [spctools-discuss] TPP-4.6.2 on Ubuntu12.04-LTS

Sidney, How did you create the Apache configuration file? Meaning what editor did you use to cut and paste the text into? I only ask as Apache is complaining about invalid characters in the file. Also, while the instructions say tpp-x.y.z I think they mean to use the actual version of TPP, or t

Re: [spctools-discuss] Re: ProtXML viewer doesn't display iProphet results, another clue

Christine, Thanks for pointing this out and I'm glad to say this change is already in the trunk. Back in April I spent a little time running the pepxml files TPP produces through a XML validator to ensure that what we produced was valid XML and matched the pepXML schema. Needless to say we had

Re: [spctools-discuss] Re: TPP 4.6.2 installation problem Ubuntu 12.04 LTS virtual box

Glad you were able to figure it out. Just to followup on this thread and let everyone know, since the 4.4.1 release of TPP I've been maintaining prebuilt Amazon AMIs for TPP . (The latest 4.6.3 image is even built on Ubuntu 12.04 LTS). Details about these images are available at: http://tools.

Re: [spctools-discuss] Re: TPP 4.4.1 compile error on linux

s/Damian/Jonathan/ On Mon, May 13, 2013 at 2:13 PM, Joseph Slagel < joseph.sla...@systemsbiology.org> wrote: > Damian, > > Interesting find. Apparently I fixed this on the 4.6.2 branch and it > never made it into trunk. If you do an svn update you should get the change >

Re: [spctools-discuss] Re: TPP 4.4.1 compile error on linux

Damian, Interesting find. Apparently I fixed this on the 4.6.2 branch and it never made it into trunk. If you do an svn update you should get the change as I just merged it into the trunk and tested it out on Ubuntu 12.04. -Joe On Thu, May 9, 2013 at 8:59 PM, Jonathan Hilmer wrote: > I belie

Re: [spctools-discuss] X!tandem High Res K-score

Its the default to use K-score. If you are on Window's you'll find the defaults in the directory C:\Inetpub\wwwroot\ISB\data\parameters. -Joe On Sun, May 12, 2013 at 11:45 PM, 2kl...@gmail.com <2kl...@gmail.com> wrote: > Hi All, > Is the high-resolution X!Tandem k-score the default K-score p

Re: [spctools-discuss] Re: LibraPeptideParser takes FOREVER on linux

Just an FYI, I took a quick look at the difference between msconvert in TPP 4.5.2 and 4.6.2 and it looks as if the version in 4.5.2 doesn't support the sortByScanTime filter. I'm going to assume that this is a relatively new filter added by the ProteoWizard folks. Any chance you can provide the m

Re: [spctools-discuss] Instalation of TPP on Ubuntu 11.10 - make: /find_arch.sh: Command not found

word echo. On Thu, Apr 18, 2013 at 9:15 AM, Liam Bell wrote: > Where would the OBJ_ARCH directory be or how can I find it? > > > On 18 April 2013 16:34, Joseph Slagel wrote: > >> Liam, >> >> Try looking in the OBJ_ARCH directory and making sure things are built. &

Re: [spctools-discuss] Instalation of TPP on Ubuntu 11.10 - make: /find_arch.sh: Command not found

ion files to their location >> cp -f >> /usr/local/src/TPP-4.6.2/src/../build/Ubuntu-x86_64/ASAPRatioPeptideParser >> /usr/local/tpp/bin/ >> cp: cannot create regular file >> `/usr/local/tpp/bin/ASAPRatioPeptideParser': Permission denied >> make: *** [install-linu

Re: [spctools-discuss] Instalation of TPP on Ubuntu 11.10 - make: /find_arch.sh: Command not found

rd: > "make: *** /usr/local/src/TPP-4.6.2/src/: Is a directory. Stop." and > there was no compiling or anything happening. > > > > On 17 April 2013 23:45, Joseph Slagel wrote: > >> It could be that if you did have the PWD at the top that a few things got >&g

Re: [spctools-discuss] Instalation of TPP on Ubuntu 11.10 - make: /find_arch.sh: Command not found

It could be that if you did have the PWD at the top that a few things got built incorrectly. I'd do a make clean, make sure it isn't there then do the full make and make install. -Joe On Wed, Apr 17, 2013 at 2:36 PM, Brian Hampton wrote: > Did you remove the ($PWD) from the top of your make f

Re: [spctools-discuss] Instalation of TPP on Ubuntu 11.10 - make: /find_arch.sh: Command not found

Glad it worked. Just for the record you shouldn't have the $(PWD) in there if you are setting it explicitly. That's the root of the problem -- its blank so the actual path just turns into /usr/local/src/TPP-4.6.2/src/. If it were to suddenly have a value again then your Makefile would break. -J

Re: [spctools-discuss] Instalation of TPP on Ubuntu 11.10 - make: /find_arch.sh: Command not found

Liam, Typically make followed by make install should work. (This is pretty much the same as running make && make install). But we've seen now that for some newer installations that it doesn't propertly locate the current working directory. It could be a shell thing, or a Ubuntu version specific

Re: [spctools-discuss] Re: TPP 4.6: Cant convert RAW files, any help?

Marianne, Could you try executing the command from the Windows console/command shell? Just open up a new shell using Windows > Start and typing in cmd. They copy and paste the command: *c:\Inetpub\tpp-bin\msconvert c:/Inetpub/wwwroot/ISB/data/121119YEAST/2DYeast01.raw -v --mzML -o c:/Inetpub/www

Re: [spctools-discuss] Error in mzwiff when converting .wiff to mzXML

Have you looked at using msconvert from ProteoWizard to convert your files? Its bundled with TPP. There isn't much support for the older mzwiff program. -Joe On Fri, Mar 22, 2013 at 5:24 AM, wrote: > I encountered an error when I ran my command line to convert the .wiff to > mzXML. My comman

Re: [spctools-discuss] TPP 4.6.2 installation problem Ubuntu 12.04 LTS virtual box

Raj, It sounds as if you have an incorrect path somewhere in the configuration. What are the contents of your Makefile.config.inc file? And what did you use for paths in your /etc/apache2/sites-available/tpp-x.y.z file? -Joe On Thu, Mar 21, 2013 at 6:19 AM, raju wrote: > Hi, > I hope you ca

Re: [spctools-discuss] Error compiling TPP 4.6.2 on RHEL 6.3

Ah ok thanks! That explains the problem. I'll make sure we have a fix in the upcoming release. On Mon, Mar 18, 2013 at 10:59 AM, Damian wrote: > > On 03/18/2013 01:06 PM, Joseph Slagel wrote: > > Thanks for running the script. That is odd. Where are you running the > ma

Re: [spctools-discuss] The Problem in QualScore

You could try increasing your heap space as explained here: http://stackoverflow.com/questions/1596009/java-lang-outofmemoryerror-java-heap-space -Joe On Sun, Mar 17, 2013 at 9:55 AM, Jorey Dong wrote: > Dear all, > > When I run qualscore.jar (version 1.0_2), the following error occurred, as

Re: [spctools-discuss] Error compiling TPP 4.6.2 on RHEL 6.3

Damian, The reason for the funny error is because the build destination is a directory named -. In your case the operating system wasn't filled in hence the " -x86_64". Buried deep in the Makefile(s) for TPP is OBJ_ARCH, the destination used for the build directory. Its value is derived from th

Re: [spctools-discuss] Re: TPP 4.6 tandem2xml tutorial data error

I'll take a look at it. Before we released 4.6.2 I ran through the tutorial data, but I had started from the beginning and not from the already converted data. -Joe On Wed, Mar 6, 2013 at 1:52 AM, Ross wrote: > Bump. Has anyone else successfully used the tutorial data? It would help > to know

[spctools-discuss] TPP 4.6.2 Release is Available

Announcing the general availability of Trans-Proteomic Pipeline (TPP) "Occupy" 4.6.2 This is a maintenance update to the Trans-Proteomic Pipeline (TPP) software which addresses a number of issues identified with version 4.6.1. All TPPusers are urged to upgrade their installations to the latest ve

Re: [spctools-discuss] Re: Perl problem

Imp, I suspect that on Windows 8, perl is installed in a location other than where it use to be on Windows 7/Vista/XP and subsequently TPP doesn't see it. Would it be possible for you to send along the path were it resides on the hard drive? We typically expect it to be in C:\Perl. Thanks, Joe

Re: [spctools-discuss] Installation problem (perl?) - tpp 4.6.1

Pavel, >From the error message it appears as if you are missing a Perl dependency (IO::Compress::Zip). I suspect that the version of Perl that you have installed may not include this module by default but I wasn't able to check. You can try installing the module yourself, there are some good in

Re: [spctools-discuss] Mascot2XML buffer overflow

Thanks Phil! I just checked the fix into the upcoming 4.6.2. On Tue, Feb 12, 2013 at 8:05 AM, Phil Charles wrote: > Hi again, > > Not sure why I didn't catch this before, but the nextmods variable is also > vulnerable to the same overflow condition. A more complete fix is: > > *316:** *char ne

Re: [spctools-discuss] Hard coded paths in TPP result files

I feel your pain, I've been doing the same remapping myself all week. There's a utility in TPP called updateAllPaths.pl. But I've had some problems using this in the past. We were just discussing a need for a better more accurate and functional utility. So there should be a new implementation co

Re: [spctools-discuss] tpp ubuntu forbidden dir

I'm guessing FollowSymLinks wasn't set in Apache :) On Wed, Jan 16, 2013 at 3:44 PM, Brett Phinney wrote: > We fixed the problem, it had something to do with tpp/data being a > symlink I can find out the exact details if you are interested > > Cheers > > Brett > > > > On Wednesday, January 16

Re: [spctools-discuss] Edit privileges for SPC Wiki

Brian, You should be getting an email shortly with the details. -Joe On Wed, Jan 16, 2013 at 3:09 PM, Brian Hampton wrote: > Hello, > > I would like to help edit the very useful wiki pages for installing TPP on > linux. Whom do I contact? > > Thanks in advance, > > Brian > > Brian Hampton >

Re: [spctools-discuss] tpp ubuntu forbidden dir

What are the permissions set to in your topdir? ls -al /opt/tpp/data On Wed, Jan 16, 2013 at 12:42 PM, Brett Phinney wrote: > Hi everyone, we have the tpp up and running (I thought anyway) on ubuntu > and are having an issue accessing subdir's in our /opt/tpp/data dir, We can > create subfolders

Re: [spctools-discuss] Re: TPP 4.6.1 Amazon Machine Image is now available

up right on my Ubuntu install. FYI, I port my result > files over to a Win7 install of TPP and it all works fine. So its not the > data. > > Thanks in advance! > > Brian > > > > On Fri, Jan 11, 2013 at 2:17 PM, Joseph Slagel < > joseph.sla...@systemsbiology.org>

Re: [spctools-discuss] Re: TPP 4.6.1 Amazon Machine Image is now available

Here's a post with some instructions that might work: http://linux.blogs.com.np/2010/04/05/how-to-move-a-virtual-machine-from-ec2-to-virtualbox-or-kvm/ though it might be easier though to start with a standard Ubuntu image and just run the scripts that I run to setup the AMI images. Here's a sho

Re: [spctools-discuss] Re: TPP 4.6.1 Amazon Machine Image is now available

Hi Brett, Amazon machine images can't necessarily be downloaded, they are really for use only on Amazons EC2 cloud product. Though I have heard of ways of making snapshots into a open machine format and possibly getting this to run in another virtual machine environment. What virtual platform ar

Re: [spctools-discuss] TPP architecture

Pretty much the only documentation on the architecture is on the wiki site at http://tools.proteomecenter.org/wiki/index.php?title=Main_Page. Specifically the out-of-date developer documentation. Beyond that there's the code :( On Sat, Dec 29, 2012 at 7:42 AM, Cobistu wrote: > Hi all, > Is the

Re: [spctools-discuss] Strange file name re-writing by "Generate Pep3D"

Brian, Eric, I just checked into the TPP trunk a fix that corrects the issue. It turned out to be an invalid use of strcpy() which doesn't seem to manifest itself on older versions of glibc/gcc and the platforms we regularly use. I can provide a patch for your source if you need it or you can ge

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