Which version of linux are you using? I may be able to provide a binary for you. Or you can recompile from source.
Cheers, -David On Tue, Jul 10, 2018 at 4:50 PM, Vidya Venkatraman <[email protected]> wrote: > I am using Linux. Do i need to compile it again? > > Regards > > On Tue, Jul 10, 2018 at 12:07 PM, David Shteynberg <David.Shteynberg@ > systemsbiology.org> wrote: > >> Hello Vidya, >> >> I have added the support of Morpheus into the TPP codebase. Please let >> me know which OS (windows or linux) you are processing on so I can provide >> you with an executable that you should be able to use. >> >> Thanks, >> -David >> >> On Mon, Jun 25, 2018 at 1:09 PM, Vidya Venkatraman < >> [email protected]> wrote: >> >>> I just shared a box folder with you which contains mzML, fasta and the >>> pepxml file. >>> >>> https://cedars.app.box.com/folder/50657299852 >>> >>> Regards >>> Vidya >>> >>> On Mon, Jun 25, 2018 at 9:41 AM, David Shteynberg < >>> [email protected]> wrote: >>> >>>> Hello Vidya, >>>> >>>> Currently, there is no support for Morpheus in the TPP. If you are >>>> able to place you search results in a shared drive and send me a link for >>>> testing, I should be able to add the Morpheus support back in. >>>> >>>> Thanks, >>>> -Davod >>>> >>>> On Sat, Jun 23, 2018 at 3:25 PM, Vidya Venkatraman < >>>> [email protected]> wrote: >>>> >>>>> Hi David, >>>>> >>>>> I am using TPP v5.1.0 and when i try to run xinteract on the Morpheus >>>>> pep.xml, I get the following error that engine Morpheus not recognized. >>>>> Any >>>>> ideas if I am missing something? >>>>> >>>>> xinteract (TPP v5.1.0 Syzygy, Build 201806211802-exported >>>>> (Linux-x86_64)) >>>>> >>>>> running: "/hpc/apps/TPP/5.1.0/bin/InteractParser >>>>> 'interact.morpheus.pep.xml' '2017-12-4_ABRF_200_DDA1.pep.xml' -L'7'" >>>>> file 1: 2017-12-4_ABRF_200_DDA1.pep.xml >>>>> processed altogether 72135 results >>>>> command completed in 9 sec >>>>> >>>>> running: "/hpc/apps/TPP/5.1.0/bin/DatabaseParser >>>>> 'interact.morpheus.pep.xml'" >>>>> command completed in 1 sec >>>>> >>>>> running: "/hpc/apps/TPP/5.1.0/bin/RefreshParser >>>>> 'interact.morpheus.pep.xml' '/common/venkatramanv/Data/Pra >>>>> tik/Thermo/DDA/raw/PRG2016_DECOY.fasta'" >>>>> >>>>> - Searching the tree... >>>>> - Linking duplicate entries... >>>>> - Printing results... >>>>> >>>>> command completed in 15 sec >>>>> >>>>> running: "/hpc/apps/TPP/5.1.0/bin/PeptideProphetParser >>>>> 'interact.morpheus.pep.xml' ACCMASS RT NONPARAM DECOYPROBS DECOY=DECOY_" >>>>> using Accurate Mass Bins >>>>> using RT >>>>> Using Decoy Label "DECOY_". >>>>> Decoy Probabilities will be reported. >>>>> Using non-parametric distributions >>>>> (Morpheus) >>>>> error: engine Morpheus not recognized >>>>> >>>>> command "/hpc/apps/TPP/5.1.0/bin/PeptideProphetParser >>>>> 'interact.morpheus.pep.xml' ACCMASS RT NONPARAM DECOYPROBS DECOY=DECOY_" >>>>> exited with non-zero exit code: 256 >>>>> QUIT - the job is incomplete >>>>> >>>>> Thanks >>>>> Vidya >>>>> >>>>> On Friday, February 7, 2014 at 12:22:54 PM UTC-8, David Shteynberg >>>>> wrote: >>>>>> >>>>>> I was able to make a first stab attempt at it and I was successful >>>>>> after minor modification to the way spectrum_names are encoded in >>>>>> spectrum_query tags in the morpheus pepXML files. After running a simple >>>>>> sed to replace the names with something that wouldn't overlap with anoth >>>>>> file when combined by using the each run's basename I was able to >>>>>> generate >>>>>> results. >>>>>> >>>>>> >>>>>> My PeptideProphet processed analysis for these two searches can be >>>>>> downloaded here: >>>>>> >>>>>> https://www.dropbox.com/s/f5r8j5yj2p2r3b8/morpheus_interact.tgz >>>>>> >>>>>> >>>>>> Here are my sed commands, but I hope this could be fixed within >>>>>> morpheus. >>>>>> >>>>>> sed -i 's/controllerType=0 controllerNumber=1 >>>>>> scan=[0-9]*/OR20080317_S_SILAC-LH_1-1_01/g' >>>>>> OR20080317_S_SILAC-LH_1-1_01.pep.xml >>>>>> >>>>>> >>>>>> sed -i 's/controllerType=0 controllerNumber=1 >>>>>> scan=[0-9]*/OR20080320_S_SILAC-LH_1-1_11/g' >>>>>> OR20080320_S_SILAC-LH_1-1_11.pep.xml >>>>>> >>>>>> >>>>>> >>>>>> Cheers, >>>>>> -David >>>>>> >>>>>> >>>>>> P.S. I expect to merge this into the SVN codebase sooner than later. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On Fri, Feb 7, 2014 at 8:35 AM, Dave Trudgian < >>>>>> [email protected]> wrote: >>>>>> >>>>>>> David, >>>>>>> >>>>>>> That's the same data. I've made PepXML and the other Morpheus output >>>>>>> available at: >>>>>>> >>>>>>> https://proteomics.swmed.edu/data/morpheus_tpp/ >>>>>>> >>>>>>> DT >>>>>>> >>>>>>> >>>>>>> On Thursday, February 6, 2014 5:36:35 PM UTC-6, David Shteynberg >>>>>>> wrote: >>>>>>> >>>>>>>> I was referring to this data: >>>>>>>> >>>>>>>> http://tools.proteomecenter.org/wiki/index.php?title=TPP_Tut >>>>>>>> orial_v2 >>>>>>>> >>>>>>>> However, this is not high res MS/MS either. This would be a good >>>>>>>> starting point. The decoys and targets don't have to separate by score >>>>>>>> alone, PeptideProphet should be able to model the plots you show in >>>>>>>> either >>>>>>>> case. >>>>>>>> >>>>>>>> Cheers, >>>>>>>> -David >>>>>>>> >>>>>>>> >>>>>>>> On Thu, Feb 6, 2014 at 3:13 PM, Dave Trudgian <david.t...@ >>>>>>>> utsouthwestern.edu> wrote: >>>>>>>> >>>>>>>>> Hi David, >>>>>>>>> >>>>>>>>> Am happy to generate some pepXMLs from the tutorial data, but >>>>>>>>> assuming you mean the stuff at: >>>>>>>>> >>>>>>>>> ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/TPP_D >>>>>>>>> emo2009/ >>>>>>>>> >>>>>>>>> ... I'm not sure that's the best to work with for Morpheus. It's >>>>>>>>> CID Ion-trap MS/MS, which is not Morpheus' target. Morpheus doesn't >>>>>>>>> work as >>>>>>>>> well as other algorithms on low-res MS/MS so I'm not sure if anyone >>>>>>>>> would >>>>>>>>> want to use it like that. >>>>>>>>> >>>>>>>>> I grabbed two of the result sets from the Coon lab site - Yeast >>>>>>>>> analysis with FT HCD or IT CID. The distributions of Morpheus scores >>>>>>>>> are >>>>>>>>> very different. The CID data doesn't even look like target and decoy >>>>>>>>> matches are separable, so I think high-res MS/MS is a must. See >>>>>>>>> attached. >>>>>>>>> >>>>>>>>> DT >>>>>>>>> >>>>>>>>> >>>>>>>>> On Thursday, February 6, 2014 3:44:08 PM UTC-6, David Shteynberg >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>>> I was dabbling in this, but running into some issues with >>>>>>>>>> morpheus slowing my machine to a point where I was unable to do any >>>>>>>>>> other >>>>>>>>>> work so I moved to another project. However, I am certainly still >>>>>>>>>> interested in this, but I know that pepXML coming out of morpheus >>>>>>>>>> may need >>>>>>>>>> some work. If you'd be willing to generate some pepXML's from the >>>>>>>>>> tutorial >>>>>>>>>> data and work with me to correct the pepXML issues I should be able >>>>>>>>>> to >>>>>>>>>> model the results quite quickly with PeptideProphet. Please let me >>>>>>>>>> know if >>>>>>>>>> that sounds good to you. >>>>>>>>>> >>>>>>>>>> Cheers, >>>>>>>>>> -David >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Thu, Feb 6, 2014 at 12:08 PM, Eric Deutsch < >>>>>>>>>> [email protected]> wrote: >>>>>>>>>> >>>>>>>>>>> Hi Dave, at ISB we are not planning this, so please go ahead and >>>>>>>>>>> let us know how it goes! >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Regards, >>>>>>>>>>> >>>>>>>>>>> Eric >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> *From:* [email protected] [mailto:spctools...@ >>>>>>>>>>> googlegroups.com] *On Behalf Of *Dave Trudgian >>>>>>>>>>> >>>>>>>>>>> *Sent:* Thursday, February 06, 2014 12:02 PM >>>>>>>>>>> *To:* [email protected] >>>>>>>>>>> >>>>>>>>>>> *Subject:* [spctools-discuss] Re: support for Morpheus search >>>>>>>>>>> algorithm in TPP >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Craig, just wondering if you or anyone else is working on this? >>>>>>>>>>> If not I was thinking I would have a go at putting in a Morpheus >>>>>>>>>>> model for >>>>>>>>>>> PeptideProphet towards the end of next week. >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Dave Trudgian >>>>>>>>>>> >>>>>>>>>>> On Saturday, November 30, 2013 4:37:30 PM UTC-6, Craig Wenger >>>>>>>>>>> wrote: >>>>>>>>>>> >>>>>>>>>>> Is there a mechanism for adding support for a new search >>>>>>>>>>> algorithm to the various TPP tools? A few users have requested TPP >>>>>>>>>>> compatibility for the Morpheus >>>>>>>>>>> <http://morpheus-ms.sourceforge.net/> search algorithm. It >>>>>>>>>>> already outputs pepXML. >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -Craig >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> 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 [email protected]. >>>>>>>>>>> To post to this group, send email to spctools...@googlegroups. >>>>>>>>>>> com. >>>>>>>>>>> >>>>>>>>>>> Visit this group at http://groups.google.com/group >>>>>>>>>>> /spctools-discuss. >>>>>>>>>>> For more options, visit https://groups.google.com/groups/opt_out >>>>>>>>>>> . >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> 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 [email protected]. >>>>>>>>>>> To post to this group, send email to spctools...@googlegroups. >>>>>>>>>>> com. >>>>>>>>>>> >>>>>>>>>>> Visit this group at http://groups.google.com/group >>>>>>>>>>> /spctools-discuss. >>>>>>>>>>> For more options, visit https://groups.google.com/groups/opt_out >>>>>>>>>>> . >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>> 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 [email protected]. >>>>>>>>> To post to this group, send email to [email protected]. >>>>>>>>> Visit this group at http://groups.google.com/group >>>>>>>>> /spctools-discuss. >>>>>>>>> For more options, visit https://groups.google.com/groups/opt_out. >>>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>> 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 [email protected]. >>>>>>> To post to this group, send email to [email protected]. >>>>>>> Visit this group at http://groups.google.com/group/spctools-discuss. >>>>>>> For more options, visit https://groups.google.com/groups/opt_out. >>>>>>> >>>>>> >>>>>> -- >>>>> 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 [email protected]. >>>>> To post to this group, send email to [email protected] >>>>> . >>>>> Visit this group at https://groups.google.com/group/spctools-discuss. >>>>> For more options, visit https://groups.google.com/d/optout. >>>>> >>>> >>>> -- >>>> You received this message because you are subscribed to a topic in the >>>> Google Groups "spctools-discuss" group. >>>> To unsubscribe from this topic, visit https://groups.google.com/d/to >>>> pic/spctools-discuss/qdmov2KGlJE/unsubscribe. >>>> To unsubscribe from this group and all its topics, send an email to >>>> [email protected]. >>>> To post to this group, send email to [email protected]. >>>> Visit this group at https://groups.google.com/group/spctools-discuss. >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> >>> -- >>> 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 [email protected]. >>> To post to this group, send email to [email protected]. >>> Visit this group at https://groups.google.com/group/spctools-discuss. >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> > -- 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 [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
