Thanks, Luis!
Sure. TPP is the gold standard for MS-based proteomics and a long-going
community project.
Finally I had some other problems on FreeBSD (otherwise an excellent
platform) and moved back to a Debionid system.
I hate boost.
Robert
On Saturday 29 June 2024 at 04:01:09 UTC-6 Luis
of . between user:group)
And in the the test recipie:
- Login with guest and password
the password is 'guest' .
Best, Robert
--
You received this message because you are subscribed to the Google Groups
"spctools-discuss" group.
To unsubscribe from this group and stop receiving e
$(CXX)
-dumpmachine. Stop.
~~~
manually invoking `gcc -dumpmachine` gives `x86_64-portbld-freebsd14.0`
Is there an elegant way for convincing TPP to build?
Best, Robert
--
You received this message because you are subscribed to the Google Groups
"spctools-discuss" group.
To unsubscribe
Shteynberg' via spctools-discuss wrote:Hi Robert,The fact that the css is not loading is an strong indication that the apache configuration is not correct.I just built a 7.0.0 TPP instance on a fresh ubuntu 22.04.4 "jammy" node in the Azure "cloud", using ins
to modify this file, perhaps only for testing. Is the css stylesheet loading for you on the login screen? Can you provide a screenshot? Are you serving any other sites from this server?Thanks!On Mon, Apr 15, 2024, 11:50 PM Robert Willows <rwillow...@gmail.com> wrote:one more piece of puzz
an additional tpp/cgi-bin/ to the path after login as guest.
Is this a webserver config issue or a tpp issue?
On Tuesday, April 16, 2024 at 1:14:03 PM UTC+10 Robert Willows wrote:
> Hi David,
>
> I've changed the site.mk and recompiled.
> Deleted the old install in the /usr/local/t
output before headers:
tpp_gui_config.pl
On Tuesday, April 16, 2024 at 11:02:17 AM UTC+10 David Shteynberg wrote:
> Hi Robert,
>
> I think I see the problem. TPP_BASEURL and TPP_DATAURL should be
> relative, no start with '/', try changing your site.mk to :
>
> INSTALL_DI
r/local/tpp
On Tuesday, April 16, 2024 at 12:01:17 AM UTC+10 David Shteynberg wrote:
Hi Robert,
Thanks for trying to install and use TPP on Ubuntu. It seems the webserver
is somewhat misconfigured for tpp on your system. Can you share the site.mk
file that you are using for this build as this f
I just finished building and installing TPP 7.0 under Ubuntu. All appears
well until I go to http://localhost:10401/tpp/cgi-bin/tpp_gui.pl
The login appears:
ISB/SPC Trans Proteomic Pipeline ::
.
TPP v7.0.0 Arafel, Build 202404151216-exported (Linux-x86_64)
But after entering guest as
Hi, which operating system are you using?
The conversion of raw files needs the windows libraries.
On Linux, you can use the docker image with msconvert, wine and these
libraries.
Quoting felipe velasquez (2021-04-24 16:00:30)
> hi, it seems I have the same problem. were you able to find a
Hi, e.g. I used X!Tandem in the past when searching for point mutations
in proteins. For most tasks, I would use Comet, because it is easy to
set-up and extremely fast.
Excerpts from vipulb...@gmail.com's message of 2020-10-01 22:46:58 -0700:
> Hello Robert,
>
> Thanks for replying
For LFQ and sample comparison, you also could try ProtyQuant, which uses
TPP pepXML (PeptideProphet validated) as input.
https://www.sciencedirect.com/science/article/pii/S1874391920303535
Best, Robert
Excerpts from 'Luis Mendoza' via spctools-discuss's message of 2020-10-02
13:07:24 -0700
Hi, congratulations for using TPP!
>From my experience, comet is much more performant, I only would use
X!Tandem if you need special features of it.
Best, Robert
Excerpts from vipulb...@gmail.com's message of 2020-09-29 22:43:24 -0700:
> Hello,
>
> I am a novice using TPP v5.2.0 F
some scripts ;-).
"ProtyQuant: Comparing label-free shotgun proteomics datasets using
accumulated peptide probabilities"
https://doi.org/10.1016/j.jprot.2020.103985
Have fun, Robert
--
You received this message because you are subscribed to the Google Groups
"spctools
/protyquant/
Feedback and questions are welcome (the manuscript is currently under review).
Best regards, Robert
Excerpts from Mehar Un Nissa's message of 2020-08-25 14:47:34 +0530:
> Dear Sir/Madam,
> Which tool in TPP is used to get the abundance value or is there any other
> way to measure th
e CLI
session, but not with Petunia.
Someone (docker, apache, .. ??) seems to have missing privileges, even if I
started the container as user root.
Best, Robert
Am Sonntag, 9. Dezember 2018 19:12:18 UTC+1 schrieb Eric Deutsch:
>
> Hi Robert, I think you just need to go here:
>
73727a87cff0 8 days ago 2.86 GB
Best, Robert
On Dec 3 2018, at 6:29 pm, Eric Deutsch wrote:
> Hi Robert, when you get an error like this:
>
>
> Bind for 0.0.0.0:10401
> (https://link.getmailspring.com/link/1544163446.local-95947193-1da1-v1.5.3-420ce...@getmailspring.com/0
Up 11 hours 0.0.0.0:10401->10401/tcp dazzling_mahavira
Am Donnerstag, 29. November 2018 01:32:55 UTC+1 schrieb Eric Deutsch:
>
> Hi Robert, thanks for testing. Based on our testing, we now changed the
> calling sequence for starting Petunia to this:
>
>
>
&g
Hi, I just started the new TPP image 16899d782bad, running on Win 10.
Before, I was normal biodocker user, now I am root.
Is this intended?
--
You received this message because you are subscribed to the Google Groups
"spctools-discuss" group.
To unsubscribe from this group and stop receiving
Sure, Eric! Could you please give me the recommended command line
parameters for running TPP Petunia on both systems (Linux and Windows 10)?
Any precautions concerning the ownership etc. of the host system?
Am Donnerstag, 22. November 2018 19:47:25 UTC+1 schrieb Eric Deutsch:
>
> Hi
Hi, a simple text editor (e.g. vi(m) and/or nano) would make the life much
more convenient for running the TPP in a headless (well, referring to
'without graphical interface' ;-)) mode.
E.g. for editing comet.params, writing little scripts etc.
Best, Robert
--
You received this message because
i
-action ExportExcel; done
Leave TPP docker session by exit and enjoy your results.
Conclusion
The TPP docker image ebf55696681a (version 5.2) runs on both, Linux and
Windows 10 host, in the CLI mode as expected.
Am Freitag, 16. November 2018 16:39:06 UTC+1 schrieb Robert:
>
tsplusdos.fasta uni50plantsplus.fasta
dos2unix: converting file uni50plantsplusdos.fasta to file
uni50plantsplus.fasta in Unix format...
No error message.
Conclusion
sed -i 's/\x0//g' uni50plantsplusdos.fasta
Am Mittwoch, 21. November 2018 09:10:34 UTC+1 schrieb Robert:
>
> Thanks
Thanks David, you are right, this was a WinLin problem!
Am Dienstag, 20. November 2018 17:04:35 UTC+1 schrieb David Shteynberg:
>
> Could this be windows line endings? Have you tried to run dos2unix
> command on your fasta file?
>
> Thanks,
> -David
>
> On Tue, Nov 20
This is what I try to find out at the moment. head and tail look fine. The DB
consists of 3 individual DBs. 2 of them look fine. The UniRef50 could be the
problem but I cannot check it manually. Information about the "strange" output
would help.
Robert Winkler
E // r
-residue:
WARNING: Trying to compute mass of non-residue:
WARNING: Trying to compute mass of non-residue:
WARNING: Trying to compute mass of non-residue:
Any idea how to track down the error (I suppose a strange symbol??)?
Best, Robert
--
You received this message because you are subscribed
d/DATA/UPS48_yeast_centroided/:/data
spctools/tpp``
- **Open GUI** with Firefox at
<http://localhost:10401/tpp/cgi-bin/tpp_gui.pl>
GUI and guest:guest login works!
However: Problems with accessing the directory structure/ uploading files.
Am Montag, 22. Oktober 2018 14:49:30 UTC+2 schrieb Robe
, Robert
--
You received this message because you are subscribed to the Google Groups
"spctools-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to spctools-discuss+unsubscr...@googlegroups.com.
To post to this group, send email to spctoo
Hi, I just run the TPP docker Prophet scripts.
However, the EXCELxx option for exporting the protein results into a
tabular format seems not to work (in contrast, EXCELPEPS works).
I also tried perl propxml2html.pl, but it complains: pepxml2html.pl: cannot
open xsl file : No such file or
Hi Eric,
Thanks, I am using the TPP Docker container on Fedora/Win10, but especially for
courses/trying tools/.. a GUI would be very useful.
Definitely, I would like to participate as a tester of TPP 5.2.0.
Best, Robert
On Oct 22 2018, at 7:22 pm, Eric Deutsch wrote:
>
> Hi
Dear TPP friends,
has anyone tried (or even solved) to run the TPP/Petunia GUI from a Docker
container/image?
Best, Robert
--
You received this message because you are subscribed to the Google Groups
"spctools-discuss" group.
To unsubscribe from this group and stop receiving e
P_5.0.0-src/build/linux-x86_64/'
make: *** No rule to make target
'/home/massypup64-downloads/TPP_5.0.0-src/extern/ProteoWizard/pwiz-msi/',
needed by '/home/massypup64-downloads/TPP_5.0.0-src/build/linux-x86_64/'.
Stop.
Any clue? Robert
--
You received this message because you are subscribed t
Hi, have you tried to convert the files after PeptideProphet validation?
Best Regards,
Robert
On 16/01/17 15:44, Francesca Barry wrote:
I would like to convert the .pep.xml files I am obtaining from Comet
in the TPP into mzid files. However the converter module in the TPP
only converts
oteomeXChange. Is there a trick?
Best Regards, Robert
On 27/07/16 17:00, Luis Mendoza wrote:
This has been fixed in the new schema (pepXML_V120.xsd), which is
already on our code repository, and scheduled to be released with TPP
5.0 soon.
Cheers,
--Luis
On Thu, Mar 3, 2016 at 9:37 AM, Dav
, Robert
On 18/11/15 11:23, Eric Deutsch wrote:
Dear Robert, thank you for sharing this with everyone, this looks like a
great resource. The maintenance of a resource like this is important, and it
is really great that you've been maintaining and updating this for quite a
long time now!
Regards,
Eric
of Java
programming!) as comet. At the end of the day, a question of ability and
taste. I tested also Galaxy-P, but taverna has many advantages.
Best, Robert
Am Donnerstag, 19. November 2015 10:14:04 UTC-6 schrieb
magnus@gmail.com:
>
> Dear Robert,
>
> Nice work - thanks for the
y is well known from Market Basket algorithms ("maybe you also
want to buy Parry Hotter 2-8?") and Social Networks ("do you know Peter,
Paul and Marry?") ..
Any comments are welcome!
Best regards, Robert
--
Este mensaje ha sido analizado por MailScanner
en busca de virus y otr
. This causes confusion, because the -x86.. can
be interpreted as an option during compilation. Suggestion: e.g. Replacing
the - for an _, or performing a check/ implementing a function, which
secures that ARCH_DISTRO is not empty .
Now, everything compiles happily without error.
Have fun, Robert
Hi Jimmy, Thanks for the quick reply. David and me re-compiled the
libpng and subsequently the libgd (obviously with png support). The
error is persistent.
Best Regards,
Robert
On 06/02/2015 07:06 PM, Jimmy Eng wrote:
Based on googling , my best guess would be your libgd was compiled
Hi Jana,
Did you try already the ProteoWizard (msconvert) for conversion? It has
an option for TPP compatibility.
Best, Robert
On 03.09.2014 02:29, Jana Horáková wrote:
Hi,
I would like to use TPP with Tandem to generate pepXML. I have
encountered a problem when trying to do the database
?
Best, Robert
On Mo 23 Jun 2014 19:57:26 CDT, Joseph Slagel wrote:
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
output with PRIDE Converter, but the
conversion failed.
Any hints for a workflow that produces standard conform output?
Best, Robert
--
You received this message because you are subscribed to the Google Groups
spctools-discuss group.
To unsubscribe from this group and stop receiving emails from
Dear Joe,
great. I could test the patched version and give feedback on the
outcome (re-submission ProteomeXchange).
Best Regards,
Robert
On Mo 23 Jun 2014 13:11:35 CDT, Joseph Slagel wrote:
Hi Robert,
I've prepared a patch containing changes made by Steven Lewis to
Proteowizard's
Hi, same here. I compiled and installed the boost libraries 1.55.0 on
Ubuntu 14.04.
The compilation of TPP 4.7.1 stops with
[ERROR] Boost libary build failed (missing
/home/rob/Downloads/tpp_4.7.1/src/../build/Ubuntu-x86_64/boost/lib/libboost_thread.a),
please report the results of manually
(today's
upload 140528), TPP/Petunia now can be started by a simple click,
directly after starting the Web Browser.
Have fun with the portable TPP,
Robert
Am Montag, 19. Mai 2014 09:33:43 UTC-5 schrieb Robert:
Dear Luis,
I just uploaded a new release of MASSyPup, with TPP v4.7, Petunia
Dear Luis,
I just uploaded a new release of MASSyPup, with TPP v4.7, Petunia GUI,
X!Tandem workflow and Comet 14.01.rev0 working.
Any comments are welcome.
Best Regards,
Robert
On 14.05.2014 15:38, Luis Mendoza wrote:
That's great, Robert! Thanks for including TPP in MASSyPup.
Does
) ?
Anything else needed?
Best regards, Robert
Am Donnerstag, 15. Mai 2014 04:38:30 UTC+8 schrieb Luis:
That's great, Robert! Thanks for including TPP in MASSyPup.
Does that mean that you are also including the Comet search engine, since
we bundle it with TPP?
Let us know if we can help
Congratulations to the TPP team! We are very grateful for your great
work and especially we want the thank Eric and Luis for coming down to
Mexico and giving a course! Let us know, if we can somehow contribute to
the future success of the TPP.
Best Regards, Robert
CINVESTAV Unidad Irapuato
,
group (I had to edit them manually for adding the www-data user) and the
apache2 directory (which contains the Apache and TPP configuration).
Please share your experiences (also pleasant ones) and bug fixes!
Have fun, Robert
--
You received this message because you are subscribed to the Google
Dear Joe,
Is the release considered to be stable?
I would like to include it into the next MASSyPup
(http://www.lababi.bioprocess.org/index.php/lababi-software/78-massypup)
release.
Best Regards,
Robert
On 05.03.2014 10:28, Joseph Slagel wrote:
Lorenz,
That's a good question -- I
is that it is
synonymous with unique spectra but I realize that the wording does leave a
little room for interpretation. Thanks so much for your help everyone!
Best,
Robert M Jones
--
You received this message because you are subscribed to the Google Groups
spctools-discuss group.
To unsubscribe
PM UTC-7, Robert Jones wrote:
Hello again all,
I was hoping someone might be able to clarify exactly how the data in the
proteinprophet column titled total indep spectra which I take to mean
total independent spectra is arrived at. I'm preferably looking for a
strict definition and any
Bjorn,
Thank you so very much that was extremely helpful! I'll be well on my way
to finishing my analysis.
-Robert M Jones
On Tuesday, February 18, 2014 6:45:24 AM UTC-7, Bjorn wrote:
Hi,
As far as I understand it, the TPP uses a mixture model-based approach to
determine posterior
comparison. Has anyone
had great success utilizing the FDR functions in the TPP or is there a
tutorial out there I could look into. Thank you very much for your
assistance!
Best,
Robert M Jones
--
You received this message because you are subscribed to the Google Groups
spctools-discuss group
might consider to use X!Tandem instead.
Best regards, Robert
On 12/05/2013 10:59 PM, srihari sharma wrote:
Hello,
I am a very new student of OMSSA database search. I have my .mgf files
with me. I am intending to do an OMSSA search. Could anyone please
give me a lead through the steps.
Thanks
. Thanks so
much!
Best,
Robert M Jones
--
You received this message because you are subscribed to the Google Groups
spctools-discuss group.
To unsubscribe from this group and stop receiving emails from it, send an email
to spctools-discuss+unsubscr...@googlegroups.com.
To post to this group
Dave,
As far as I know the HPC does not have Galazy installed.
Best
Robert M Jones
On Tuesday, August 27, 2013 1:38:03 PM UTC-7, Dave Trudgian wrote:
Robert,
Do you know if any of the HPC systems have Galaxy installed? If they do
then maybe you could try to persuade sysadmins to install
line
tutorial to help get me started. Also, I'm curious if there is a way in
which I could use the local TPP GUI on my computer but have the processing
exported to the HPC. Thank you so much for any information you can give,
I'm looking forward to using this software!
Best,
Robert M Jones
Pilot compared with the Libra values. I think the filtering of outliers done by
Libra using a group comparison method is quite valid given how an iTRAQ
experiment is actually set up and what we expect to see in regards the pattern
of intensities.
I hope this helps.
Regards
Robert
On 16/05
Hi Ulrich,
Thank you.
I was missing the
SetEnv WEBSERVER_TMP /tmp/
from the httpd.conf file.
This has been added and after restarting it all works now.
Cheers
Robert
On 08/05/2012, at 6:55 PM, Ulrich auf dem Keller wrote:
Hi Robert,
from this I would guess WEBSERVER_ROOT is not correctly
is not an environment variable in a bash terminal.
If this is the problem I'm not sure how to fix it since I'm not that familiar
with C++.
Regards
Robert
On 08/05/2012, at 4:03 AM, Luis Mendoza wrote:
Hi Ulrich,
Thanks for reporting the bug in Petunia. It will be fixed as of the
next upcoming
with xinteract also all work and the files are
generated as expected and can be viewed through the web interface.
I'm not sure where InteractParser is trying to write the tmp file but maybe
this is the problem?
Regards
Robert
--
You received this message because you are subscribed to the Google Groups
wrote:
Dear Robert,
You can try to follow these guidelines. Maybe the answer to your
problems is there somewhere.
http://tools.proteomecenter.org/wiki/index.php?title=TPP:Installing_the_Trans-Proteomic_Pipeline_%28TPP%29_4.4.0_on_Mac_OS_X_10.6.4
Cheers,
Bjorn
--
You received
charge would be desirable.
Any suggestions, how the charge could be added to mzXML?
Best, Robert
--
You received this message because you are subscribed to the Google Groups
spctools-discuss group.
To post to this group, send email to spctools-discuss@googlegroups.com.
To unsubscribe from
.. only and the
raw data are stored/distributed on my laptop/ the mass spec/
collaborators PC ...
Discussion/ solutions are welcome,
Robert
--
You received this message because you are subscribed to the Google Groups
spctools-discuss group.
To post to this group, send email to spctools-discuss
is not
recommended.
So, may I publish the identifications or will there be an update
regarding the discriminant function?
Best, Robert
http://groups.google.com/group/spctools-discuss/browse_thread/thread/f5f944d983ce9699/99c661635800bce2?lnk=gstq=omssavalidation#99c661635800bce2
--
You received
proteins before the SDS-PAGE, search the MS/MS
spectra with OMSSA and evaluate the OMSSA hits with
Peptide/ProteinProphet. The results are compatible with TPP and PRIDE.
Best regards, Robert
On 20/05/2010 04:01 p.m., Luis Mendoza wrote:
This upcoming week, the SPC software tools team will be hosting
the linking to the spectrum data is causing trouble.
I really would appreciate your comments. I think the combination OMSSA/
TPP really would be exciting, if everything works finally (viewing,
PRIDE etc.).
Thanks and greetings, Robert
--
You received this message because you are subscribed to the Google
MzXML2Search -mgf -ACID -M2-2 -P5 -I0.01 -B10 -T5000.0
%I
converts all *.mzXML files to OMSSA compatible *.mgf
Saludos, Robert
On Feb 11, 1:04 pm, Matt Chambers matthew.chamb...@vanderbilt.edu
wrote:
As Natalie suggested, Analysis.yep indicates the Bruker/Agilent YEP
format which ProteoWizard reads
coverage.
Now also the peptides assigned to a protein by OMSSA are included
Regards, Robert
--~--~-~--~~~---~--~~
You received this message because you are subscribed to the Google Groups
spctools-discuss group.
To post to this group, send email to spctools-discuss
70 matches
Mail list logo
