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Problems with external tool package in UGENE (Read 732 times)
Aug 1st, 2018 at 2:12pm

hee   Offline
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Hi Olga

I exported the external tool package for UGENE in order to use python scripts. I set the path in settings to the external tool file (buttons at the right site are red) but don't get the python nodes in elements after a restart. I also set the path to the python executable file and installed the necessary packages (numpy, django).

Thanks in advance.
 
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Reply #1 - Aug 1st, 2018 at 7:04pm

Olga Golosova   Offline
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Hi!
  • What is your operating system?
  • Is it 32 or 64 bit?
  • Which UGENE package do you use?
  • Which external tools package do you use?
 
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Reply #2 - Aug 2nd, 2018 at 6:39pm

hee   Offline
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I'm working with archlinux, 64 bit.

UGENE version: 1.30.0

and i got the external tool package from ugene.net -> Downloads -> External Tools (filename: ext_tools_linux_64-bit)
 
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Reply #3 - Aug 3rd, 2018 at 1:25pm

Olga Golosova   Offline
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Note that numpy and django modules are required for ChIP-Seq data analysis only (they are necessary for SeqPos tool). So, to use python for other tools in UGENE you may use a common Python2 version without the modules.

Please try to specify these standard python executables in the UGENE Application Settings (install Python2, if you don't currently have it). Does this work for you?
 
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Reply #4 - Aug 7th, 2018 at 2:20pm

hee   Offline
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Hi Olga

I'm working with python2.7 (also python 3.6) and i've tried it without the modules but it's still not working. (Is there really a difference between working with installed modules or without?)

I got the executable path to python with the terminal command 'whereis python' and checked the properties of this file.

Can i create a 'element with script' or something like that to use python?
 
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Reply #5 - Aug 7th, 2018 at 2:33pm

Olga Golosova   Offline
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Quote:
I'm working with python2.7

What output do you get in the terminal when you run "python --version"?

Quote:
Is there really a difference between working with installed modules or without?

No in general case.
This is important only if you run Cistrome workflow. But it is not your case, as I understand.

Quote:
Can i create a 'element with script' or something like that to use python?

You can create/use an element with command line tool. In this case you don't even need to set up python in the UGENE Application Settings.
 
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Reply #6 - Aug 13th, 2018 at 3:07pm

hee   Offline
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Actually i would prefer to use python directly in ugene but i think to create an element with command line tools will also work if we cannot fix the problem.
 
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Reply #7 - Aug 14th, 2018 at 12:54pm

Olga Golosova   Offline
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There is currently no integration between python external tool and elements with command line tools. So, you'll have to run python directly in the current UGENE version.

As for the tool validation in the Application Settings, from the screenshot it seems everything is correct now.
 
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