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. 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