Problems with installation of latest version of cobratoolbox 'binary' in .gitmodules

[Patrik]

Hi,

I am not a computer expert but have used older cobra toolbox versions fine for a while (also basing part of my teaching on it). However, when trying to implement FVA I was struck by recent changes to matlabpool. I was unsuccessful trying to solve this and therefore decided to install the latest version of cobra toolbox instead (on a Mac with MATLAB R2015a). Following instructions (https://opencobra.github.io/cobratoolbox/latest/installation.html), I downloaded the compressed archive as I did not have git installed. I subsequently installed git (2.15.1) using the Xcode terminals command line tools link. I deleted all the old cobra files from the Matlab path and set the new downloaded files and folders to the path. initCobraToolbox then gives me the following: 

 > Checking if git is installed ...  Done.

 > Checking if the repository is tracked using git ...  > Checking if curl is installed ...  Done.

 > Checking if remote can be reached ...  Done.

 Done.

 > Checking if curl is installed ...  Done.

 > Checking if remote can be reached ...  Done.

 > Initializing and updating submodules (this may take a while)...fatal: No url found for submodule path 'binary' in .gitmodules

Error using initCobraToolbox (line 196)

The submodules could not be initialized.

This is where I got stuck, searching for solutions yielded nothing, and would appreciate help to sort it out.

Thanks, Patrik

[Laurent Heirendt]

Hi Patrik,

Now as you have the command line tools installed, may you try installing the COBRA Toolbox by typing in the Terminal (not MATLAB):

$ git clone --depth=1 https://github.com/opencobra/cobratoolbox.git cobratoolbox

Then, restart MATLAB, and type:

>> restoredefaultpath; clear all;
>> cd cobratoolbox
>> initCobraToolbox

That should work. If all else fails, I recommend downloading the compressed archive as explained on the main website and re-run the MATLAB commands above. That .zip file includes all submodules, the one from Github does not.

Please let me know if this worked.

Best regards,

Laurent

[Patrik]

Hi Laurent,

It works, my pre-installed Gurobi solver was also recognized. Many thanks. I was just about to jump over to CobraPy..

Interestingly, just running a basic optimizeCbModel with older ecoli_core_model.xml models did not work but using the one that comes with the newly installed v.3.0 package did. 

Thank you, Patrik

[Koushik Garain]

Hi,

I am Koushik, facing the same problem. I am trying to build a community model in the COBRA toolbox. But, there are errors for initCobraToolbox. I am using Mac and Matlab 2015b. The error is 

Error in initCobraToolbox (line 212)
            if contains(result_gitSubmodule,'modified') ||
            contains(result_gitSubmodule,'Untracked files')

I don't know what to do. Please help me. After that, I want to use createCommModel for two specieses.

[Ronan M.T. Fleming]

contains is a function introduced in R2016b

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[Koushik Garain]

Thank you sir. Now, I am using Matlab R2020a and the Cobra toolbox is working properly. But, I need cplex solver. Is this freely available?

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[Ronan M.T. Fleming]

https://www.gurobi.com/academia/academic-program-and-licenses/

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