Hello Vidya, Unfortunately, I don't have that release easily available. You will have to build the tools on your system.
Thanks, -David On Thu, Jul 12, 2018 at 10:14 PM, Vidya Venkatraman <[email protected] > wrote: > I am using CentOS release 6.3 > > Regards > Vidya > > On Tue, Jul 10, 2018 at 4:57 PM, David Shteynberg <David.Shteynberg@ > systemsbiology.org> wrote: > >> 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 < >>> [email protected]> 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/grou >>>>>>>>>>>>> ps/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/grou >>>>>>>>>>>>> ps/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 spctools-discuss@googlegroups. >>>>>>> com. >>>>>>> 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 spctools-discuss@googlegroups. >>>>>> com. >>>>>> 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 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.
