Run arpeggio from external app

Question

Run arpeggio from external app

eusebiu opened this issue 4 years ago · comments

Hi,
I am trying to run arpeggio after installing it using miniconda but I get an error:

(base) C:>arpeggio -h
'arpeggio' is not recognized as an internal or external command,
operable program or batch file.

(base) C:>conda list
.# packages in environment at C:\ProgramData\Miniconda3:
.#
.# Name Version Build Channel
arpeggio 1.4.1 pypi_0 pypi
biopython 1.77 pypi_0 pypi
bzip2 1.0.8 he774522_0

How can I run arpeggio? I am interested in executing it from an external application.

Thanks!

Lukas Pravda · Answer 1 · Sat Jul 11 2020 02:03:34 GMT+0800 (China Standard Time)

Hi @eusebiu , thank you for getting touch with us.

I assume that you are using Windows. Apparently python packages works a bit differently on windows, I have improved the setup script and tested it on windows server, if you pip install it like this:

pip install git+https://github.com/PDBeurope/arpeggio.git@master#egg=arpeggio

arpeggio -h

correctly displays what is supposed to be displayed, please let me know if this works for you.

Lukas Pravda · Answer 2 · Sat Jul 11 2020 02:06:45 GMT+0800 (China Standard Time)

Question out of curiosity, is the other application written in python 3.6+? If so I could put together a short snippet how you can run the main functions and get the result in memory so that you can work with it.

Eusebiu Marcu · Answer 3 · Sat Jul 11 2020 04:36:47 GMT+0800 (China Standard Time)

Hey @lpravda ,

Thank you for the quick reply!
After installing the openbabel from here https://www.lfd.uci.edu/~gohlke/pythonlibs/#openbabel and installing the arpeggio with your command, I was able to run arpeggio -h from command line.

The other app is a dotnet core app and I plan to execute arpeggio similar to the command line approach.

Thank you!