Hi Panyue, Thanks for confirming that it works. I think after you run that code from the commandline allowing perl interpreter to process it, at least on my system it registered the file and allowed me to run it through Petunia the next time I tried it. Maybe updatePaths.pl will work for you from Petunia going forward? If not it should work the next time you install a TPP update.
Cheers, -David On Wed, Mar 10, 2021 at 10:28 AM Panyue Chen <[email protected]> wrote: > Hi David, > > Thank you so much! It works for me. > Just in case other people are in the same situation. I want to > provide more detail here. I ran the Petunia command line (as in the image) > in the command prompt of Windows system: > cd d:/TPP/data/tutorials/Ferries2017/com_tan_HCDOT && d: && D:/TPP/bin/ > updatepaths.pl -v > d:/TPP/data/tutorials/Ferries2017/com_tan_HCDOT/interact.ipro.pep.xml > > [image: command.png] > > Best, > Panyue > > On Wed, Mar 10, 2021 at 12:54 AM 'David Shteynberg' via spctools-discuss < > [email protected]> wrote: > >> Hello again, >> >> I downloaded the code from sourceforge and replaced my version to test >> and at first it hung, like it did for you. I think this is because it >> wasn't installed by the installer. Here is how I got around the issue: >> >> 1. Open cmd prompt >> >> 2. Copy entire updatePaths.pl commandline generated by Petunia >> updatePaths page to the command line and run it. Windows should ask you >> for permission to run perl interpreter on this file, allow it! >> >> 3. updatePaths.pl should now run to completion and you should be able to >> use Petunia to run it also >> >> This worked for me, let me know if it does or doesn't work for you. >> >> Thanks! >> -David >> >> On Tue, Mar 9, 2021 at 9:33 PM David Shteynberg < >> [email protected]> wrote: >> >>> It should only take a few minutes to run the code. Perhaps there is a >>> permissions issue to execute that file on your computer. Normally the >>> installer makes sure the permissions are setup correctly. Can you check >>> the permissions for this file under properties -> security? >>> >>> On Tue, Mar 9, 2021, 8:47 PM Panyue Chen <[email protected]> >>> wrote: >>> >>>> Hi David, >>>> >>>> Thanks for your fast reply and your help! >>>> >>>> I downloaded the code you provided and replaced the old updatepaths.pl >>>> file in the bin folder. >>>> While I updated the paths by updatedPaths utility in the Pentunia, the >>>> job was not finished after around 40min. How long should I expect to get >>>> the job done? Or could it because the web fails to connect? >>>> >>>> For your information I posted an image of what I selected on the >>>> updatePaths utility page and an image of the job submitted. >>>> >>>> Best, >>>> Panyue >>>> [image: Updatepaths.png][image: JobRun.png] >>>> >>>> On Tuesday, March 9, 2021 at 4:34:01 PM UTC-5 David Shteynberg wrote: >>>> >>>>> Hello Panyue, >>>>> >>>>> I test the updatePaths.pl and found some problems with it correcting >>>>> paths to directories on other drives on windows. I have committed a fix >>>>> to >>>>> this script which you can download here: >>>>> https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/trans_proteomic_pipeline/perl/bin/updatepaths.pl >>>>> >>>>> Please replace your existing file in C:\TPP\bin (or where you >>>>> installed the TPP) with the code at the link above. >>>>> >>>>> Cheers, >>>>> -David >>>>> >>>>> On Tue, Mar 9, 2021 at 9:02 AM Panyue Chen <[email protected]> >>>>> wrote: >>>>> >>>>>> Hi there, >>>>>> >>>>>> I was trying to follow the PTPprophet tutorial v0.4.0 to analyze a >>>>>> subset of data from Ferries et al. (2017, JPR, 16, 3448). I have download >>>>>> the tutorial data into the "tutorials" folder and checked all the files >>>>>> and >>>>>> directories I should have. >>>>>> But when I ran the PTM prophet, the job ends with an error as shown >>>>>> in the picture. >>>>>> >>>>>> Please let me know if I missed any thing and how should I fix the >>>>>> error. Thanks! >>>>>> >>>>>> -- >>>>>> >>>>>> Panyue Chen >>>>>> Graduate student >>>>>> Dr. Hazbun group >>>>>> Purdue University >>>>>> [image: error.png] >>>>>> >>>>>> -- >>>>>> >>>>> 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 view this discussion on the web visit >>>>>> https://groups.google.com/d/msgid/spctools-discuss/5f678d66-9627-4064-9467-471d489eddd5n%40googlegroups.com >>>>>> <https://groups.google.com/d/msgid/spctools-discuss/5f678d66-9627-4064-9467-471d489eddd5n%40googlegroups.com?utm_medium=email&utm_source=footer> >>>>>> . >>>>>> >>>>> -- >>>> 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 view this discussion on the web visit >>>> https://groups.google.com/d/msgid/spctools-discuss/8e2e44ad-b9a3-41c2-badb-dbf955c5eb37n%40googlegroups.com >>>> <https://groups.google.com/d/msgid/spctools-discuss/8e2e44ad-b9a3-41c2-badb-dbf955c5eb37n%40googlegroups.com?utm_medium=email&utm_source=footer> >>>> . >>>> >>> -- >> 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/topic/spctools-discuss/-ELC5rtcIx0/unsubscribe >> . >> To unsubscribe from this group and all its topics, send an email to >> [email protected]. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D_wTX8ZaEtk60wTeJcNTHsibz7oLj60V0AAS-HzWvktQA%40mail.gmail.com >> <https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D_wTX8ZaEtk60wTeJcNTHsibz7oLj60V0AAS-HzWvktQA%40mail.gmail.com?utm_medium=email&utm_source=footer> >> . >> > -- > 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 view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/CAMzCNru7FHnQjW9PQAcJYZtxqLkHMR0pMbNQn_f-68eY1bghbQ%40mail.gmail.com > <https://groups.google.com/d/msgid/spctools-discuss/CAMzCNru7FHnQjW9PQAcJYZtxqLkHMR0pMbNQn_f-68eY1bghbQ%40mail.gmail.com?utm_medium=email&utm_source=footer> > . > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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