I posted the thread
http://groups.google.com/group/spctools-discuss/browse_thread/thread/f21cbc8a677d6cca
back in January but didn't receive any responses so I am asking again
if anybody can assist.
When trying to use the TPP GUI the webserver error log is filled with
the following error
Start with the tpp_hostname: command not found message. The solution is a
combination of setting the PATH for the webserver user, and customizing your
tpp_gui_config.pl file to tell the GUI where you installed the various
executables.
Good luck,
Brian
On Tue, Mar 23, 2010 at 6:20 AM, Eliza
Hi All,
I thought of sharing my experience for making TPP - Apache to work with
network drive.
Here is my finding for trouble shooting Apache to recognize network drive.
a) Latest apache version available is 2.2.14 but apache does not start as a
service, and if we start apache from command
dear list,
i modified some of my mzXML files by removing ms2 spectra which did not
fulfill certain criteria.
afterwards i tried to analyze them via xtandem but got error messages like
might be a corrupted file.
to overcome this problem i used indexmzXML which corrected the index by
generating a
Hi Andreas,
You may need to re-number the indices so that the scans start at 1
have no gaps between subsequent ones, as well as adjust the total scan
count in the header of the file. Then apply the re-indexing.
Hope this helps,
--Luis
On Tue, Mar 23, 2010 at 9:46 AM, Andreas Quandt
hey luis,
nice to hear from you and many thanks for your fast answer!
unfortunately this does not do the trick :-(
i renumbered the scans starting from 1 (for ms1 and ms2 in ascending order),
ran indexmzXML on the file (successfully) and
tried 'MzXML2Search -mgf' afterwards.
and then
Does the file pass general XML validation? That is, did you possibly damage
it structurally?
It's hard to discuss these things without looking at the actual file, can
you upload to the group's files area?
Brian
On Tue, Mar 23, 2010 at 1:20 PM, Andreas Quandt quandt.andr...@gmail.comwrote:
hey brian,
nice to hear from you too and also thanks for picking up on this :-)
according to xmlwf the modified.mzXML is valid.
i uploaded both, original.mzXML and modified.mzXML to
ftp.systemsbiology.net/incoming.
it would be great if you guys could spare some time to help me with this as
i am
Andreas,
I don't believe Brian or any other helpful external person can access
the files when you place it in ISB's ftp site.
Anyways, the ramp parser is frail and finicky and expects an mzXML to
be formatted just the way it expects. Your modified mzXML has a lot
of formatting changes. The
Andreas,
When I modified your file get rid of all whitespace between the
peaks tags, the MzXML2Search program subsequently ran fine.
change:
peaks precision=32 byteOrder=network pairOrder=m/z-int
Q0BLmUBez4BDSRBhQQDRN0NN...w==
/peaks
to:
peaks precision=32
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