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Unable to run BioNetGen from command line (old version?) #5

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TorkelE opened this issue Feb 10, 2022 · 0 comments
Open

Unable to run BioNetGen from command line (old version?) #5

TorkelE opened this issue Feb 10, 2022 · 0 comments

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@TorkelE
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TorkelE commented Feb 10, 2022

Hello,
I have a .bngl file that I can run from VSCode, but I want to run it from the command line. If I understand it right, I cannot run the .bngl file directly, but need to create an OMEX archive. To try this out I download this one: https://run.biosimulations.org/simulations/61fea499f499ccf25faafc6b#tab=files

However, when I try I get an error:

~/Downloads$ bionetgen -i archive.omex 
usage: bionetgen [-h] [-d] [-q] [-v] [-req REQUIRE]
                 {atomize,graphdiff,info,notebook,plot,run,visualize} ...
bionetgen: error: argument command: invalid choice: 'archive.omex' (choose from 'atomize', 'graphdiff', 'info', 'notebook', 'plot', 'run', 'visualize')

it seems that my bionetgen do not have access to the -i option, I try:

~/Downloads$ bionetgen -h
usage: bionetgen [-h] [-d] [-q] [-v] [-req REQUIRE]
                 {atomize,graphdiff,info,notebook,plot,run,visualize} ...

optional arguments:
  -h, --help            show this help message and exit
  -d, --debug           full application debug mode
  -q, --quiet           suppress all console output
  -v, --version         show program's version number and exit
  -req REQUIRE, --require REQUIRE

sub-commands:
  {atomize,graphdiff,info,notebook,plot,run,visualize}
    atomize             SBML to BNGL translator
    graphdiff           A subcommand to compare two contact maps made by
                        BioNetGen. The default mode is "matrix" mode and will
                        generate 4 graphs, two for each individual input
                        recolored, one for input 1 - input 2 and one for input
                        2 - input 1. This can be used to find differences and
                        communalities between two BNGL models of the same
                        process.
    info                Provides version information for BNG and dependencies
    notebook            Starts a Jupyter notebook to help run and analyze
                        bionetgen models
    plot                Rudimentary plotting of gdat/cdat/scan files
    run                 Runs a given model using BNG2.pl
    visualize           Provides a simple way to get various visualizations of
                        the model.

Maybe I have the wrong version, however, I did install it yesterday. I try:

~/Downloads$ bionetgen -v
BioNetGen simple command line interface 0.6.2
BioNetGen version: BioNetGen-2.7.1
Cement Framework 3.0.6
Python 3.7.4
Platform Linux-5.4.0-99-generic-x86_64-with-debian-bullseye-sid

but I cannot actually find anywhere which is the latest version, so cannot tell if 2.7.1 is the latest version.

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