Dear friends,
I am installing TPP. Unfortunately, after reboot, the check_env.pl
reports as follows:
--12:19:49-- http://localhost/tpp-bin/check_env.pl
(try: 8) = `test.txt'
Connecting to localhost[127.0.0.1]:80... failed: Bad file descriptor.
Retrying.
--12:19:50--
Has there been any thought about packaging up TPP for Ubuntu/Debian
and possibly RedHat/CentOS?
I went through the exercise of installing it from scratch, following
the directions on the wiki page, and I can imagine that this would be
quite daunting for a non-programmer.
Just off the top of my
Hi Mike,
As Matt says, it's mostly a matter of somebody deciding they want to take
that on. It's unlikely to be any current TPP developer, we're already
hands-full.
The working assumption is that windows user are almost certainly not
programmers, but linux users are probably at least able to
If TPP would link to boost statically it wouldn't be an issue. But IIRC
there has been a thread on this topic before and it wasn't deemed worth
the effort of maintaining...unless you're volunteering? ;)
-Matt
Mike Coleman wrote:
Has there been any thought about packaging up TPP for
Hi Jimmy:
Here I pasted the error for the search and you may have a look.
Thank you for your help
Eileen
...skipping 39 lines of output...
running: C:/Inetpub/tpp-bin/DatabaseParser interact.pep.xml
command
Eileen,
Can you paste the output including the 39 skipped lines?
The fact that one of the tools, RefreshParser, is looking to open
combo_human_both.fasta.hdr indicates that changing the database back
to the non-indexed version wasn't successful for whatever reason.
On Tue, Sep 8, 2009 at 9:04
Hi Eileen,
Apparently after PeptideProphet analysis the dataset given doesn't
contain any peptides with probability above 0.05 . See relevant
message pasted below.
. . . reading in
c:/Inetpub/wwwroot/ISB/data/eileen/a549/EROLDSETTING/interact.pep.xml.
. .
. . . read in 0 1+, 0 2+, 0 3+, 0 4+,
That 742.5391 precursor mass is the monoisotopic m/z mass recorded in
the scan header of the raw file itself. readw just grabs this value,
if present, via the thermo interface. No way to turn this off in
readw (besides a relatively simple edit of the code and rebuilding the
binary).
Without
Yeah, I'd like to see the isolation window from the triggering survey
scan because it seems unlikely that the monoisotopic m/z would be less
accurate than the filter's isolation m/z (except it might pick the a+1
peak, but that's almost certainly still better than the isolation m/z).
-Matt
Version 1.39 of Boost isn't in Ubuntu currently, so there's nothing to
link to that way. I assume you mean doing something like folding
Boost into the TPP/extern directory and handling Boost as libexpat is
handled, for example. I'm not completely unsympathetic to this idea,
but on the whole I'm
Dear Jimmy,
the problem is that Thermo software is not especially intelligent by
assigning the monoisotopic mass when a complex sample is analyzed. I
actually would like to have the converter not making this decision.
For that we have developed our own software.
Can I somehow switch that
Hi Eileen,
It appears that your changes to the sequest.params file didn't take
effect and are not reflected in the pepXML file.
When you reconverted your data using Out2XML did you specify the
sequest.params file?
Can you double check the database path written in the file you
specified? It is
Dear all:
May I check one question? I am doing SILAC analysis with LCQ OR LTQ.
After I load the data to run the peptide analysis in TPP, I select the running
protein probability, asap xpress ratio. I am wondering whether the software
kicks out all the duplicated peptides (the peptide come from
Sounds like your apache webserver is not firing up correctly. Please
check your apache weblogs for any clues.
On Tue, Sep 8, 2009 at 3:49 AM, rhodearho...@gmail.com wrote:
Dear friends,
I am installing TPP. Unfortunately, after reboot, the check_env.pl
reports as follows:
--12:19:49--
Windows actually remains the most important thing to package, if for no
other reason than that's where the converters have to live. And, I think,
if you look at the traffic on the list it's at least half the TPP user base
(that's not very scientific though, I grant you).
Again, we already do
Hi Mike,
Thanks for your efforts with helping Eliza, and for your good thoughts
and comments. I'd like to respond to a few things:
1) Boost in the TPP: I'd like to clarify how we've set things up. The
included Boost under tpp/extern is compiled and used without any
system interactions
An other thing. Did you remember to install ActivePerl? This is free
and required by the TPP.
-David
On Tue, Sep 8, 2009 at 12:06 PM, David
Shteynbergdshteynb...@systemsbiology.org wrote:
Sounds like your apache webserver is not firing up correctly. Please
check your apache weblogs for any
Hello Dominik, Jimmy,
Besides my recommendation to try msconvert, which is the program with
more developer focus at this point, there is already a command-line
option in the 4.3 series ReAdW program. I'd added this feature
because Thermo's software did not understand which scan to report
My ideas somewhat differ on this, but you guys are doing the work, and
it would hardly do for me to be disagreeable. I'm glad to hear that
you're working on build scripts--this should improve the situation,
and is a step towards packaging later, if you decide it's worthwhile.
Mike
On Sep 8,
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