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https://forum.ugene.net/forum/YaBB.pl General Category >> Help and How-to >> Problems with external tool package in UGENE https://forum.ugene.net/forum/YaBB.pl?num=1533107576 Message started by hee on Aug 1^st, 2018 at 2:12pm

Title: Problems with external tool package in UGENE
Post by hee on Aug 1^st, 2018 at 2:12pm

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.

Title: Re: Problems with external tool package in UGENE
Post by Olga Golosova on Aug 1^st, 2018 at 7:04pm

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?

Title: Re: Problems with external tool package in UGENE
Post by hee on Aug 2^nd, 2018 at 6:39pm

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)

Title: Re: Problems with external tool package in UGENE
Post by Olga Golosova on Aug 3^rd, 2018 at 1:25pm

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?

Title: Re: Problems with external tool package in UGENE
Post by hee on Aug 7^th, 2018 at 2:20pm

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?

Title: Re: Problems with external tool package in UGENE
Post by Olga Golosova on Aug 7^th, 2018 at 2:33pm

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.

Title: Re: Problems with external tool package in UGENE
Post by hee on Aug 13^th, 2018 at 3:07pm

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.

Screenshot_from_2018-08-13_09-53-07.png (46 KB | 287 )

Screenshot_from_2018-08-13_09-53-46.png (96 KB | 278 )

Title: Re: Problems with external tool package in UGENE
Post by Olga Golosova on Aug 14^th, 2018 at 12:54pm

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.