Hi Joe, thanks a lot for your help. I wasn't sure whether the copying of the PTMProphetParser file was the reason for its behavior, so I added the missing line in the makefile and installed it again. Unfortunately the behavior of PTMPropeht to remove phosphopeptides is still the same. I hope David can shed some light on what might be going wrong.
Maik On Thursday, 23 August 2012 01:19:41 UTC+2, jsl...@systemsbiology.org wrote: > > Maik, > > PTMProphet should be available on both Linux and Windows. It appears that > we left out a line in the makefile for installing the executable under > Llinux. I'll make sure this gets corrected in 4.6.1. In the meantime you > can just copy the executable from the build into your bin directory. As to > the removal of the peptides I'll let David S. take a stab at answering that. > > -Joe > > > On Wed, Aug 22, 2012 at 7:05 AM, Maik Boehmer > <maik.b...@gmail.com<javascript:> > > wrote: > >> Hi, >> >> I installed TPP 4.6.0 on Ubuntu 10.04 for a Labkey server we are running >> on that machine. As requested in the Labkey installation instructions for >> TPP, I added XML_ONLY=1 to the TPP MAKEFILE.incl. >> >> I was hoping that the new release of the TPP would give us PTMProphet >> support also on Linux. So far it was only working on our windows machines. >> Unfortunately PTMProphetParser is not available in the TPP root directory >> after install. There is a PTMProphetParser available in the /build folder >> that seems to work but it acts quite peculiar. It recognizes petides with >> phosphorylations but then removes these peptides from the pep.xml file >> instead of adding probabilities to them. >> >> So my questions is: Should PTMProphet be available also on Linux or is it >> only available on Windows machines? or Did I miss something that would >> explain the peculiar behavior of PTMProphetParser on our machine? >> >> Thanks >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To view this discussion on the web visit >> https://groups.google.com/d/msg/spctools-discuss/-/TISCBRJtmXkJ. >> To post to this group, send email to >> spctools...@googlegroups.com<javascript:> >> . >> To unsubscribe from this group, send email to >> spctools-discu...@googlegroups.com <javascript:>. >> For more options, visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. >> > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To view this discussion on the web visit https://groups.google.com/d/msg/spctools-discuss/-/DEjyYXgNFg0J. To post to this group, send email to spctools-discuss@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
