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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
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:
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:
it seems that my bionetgen do not have access to the
-i
option, I try:Maybe I have the wrong version, however, I did install it yesterday. I try:
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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