Re: [spctools-discuss] job end with error when following PTMprophet tutorial

['David Shteynberg' via spctools-discuss]

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 
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 <
> spctools-discuss@googlegroups.com> 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 <
>> david.shteynb...@isbscience.org> 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 
>>> 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 
> 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 spctools-discu...@googlegroups.com.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/spctools-discuss/5f678d66-9627-4064-9467-471d489eddd5n%40googlegroups.com
>> 
>> .
>>
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Re: [spctools-discuss] job end with error when following PTMprophet tutorial

[Panyue Chen]

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 <
spctools-discuss@googlegroups.com> 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 <
> david.shteynb...@isbscience.org> 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 
>> 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 
 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 spctools-discu...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/spctools-discuss/5f678d66-9627-4064-9467-471d489eddd5n%40googlegroups.com
> 
> .
>
 --
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>>>
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Re: [spctools-discuss] job end with error when following PTMprophet tutorial

['David Shteynberg' via spctools-discuss]

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 <
david.shteynb...@isbscience.org> 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 
> 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 
>>> 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 spctools-discu...@googlegroups.com.
 To view this discussion on the web visit
 https://groups.google.com/d/msgid/spctools-discuss/5f678d66-9627-4064-9467-471d489eddd5n%40googlegroups.com
 
 .

>>> --
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>> 
>> .
>>
>

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Re: [spctools-discuss] job end with error when following PTMprophet tutorial

['David Shteynberg' via spctools-discuss]

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  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  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 spctools-discu...@googlegroups.com.
>>> To view this discussion on the web visit
>>> https://groups.google.com/d/msgid/spctools-discuss/5f678d66-9627-4064-9467-471d489eddd5n%40googlegroups.com
>>> 
>>> .
>>>
>> --
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> 
> .
>

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Re: [spctools-discuss] job end with error when following PTMprophet tutorial

[Panyue Chen]

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  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 spctools-discu...@googlegroups.com.
>> To view this discussion on the web visit 
>> https://groups.google.com/d/msgid/spctools-discuss/5f678d66-9627-4064-9467-471d489eddd5n%40googlegroups.com
>>  
>> 
>> .
>>
>

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