Cobra toolbox installation problem‏

[mahtab barany]

Hello friends
I was installing a Cobra toolbox when I encountered a problem. Please help me. I do not know what to do.
very Thanks  

 > Checking if git is installed ...  Done (version: 2.30.1).
 > Checking if the repository is tracked using git ...  Done.
 > Checking if curl is installed ...  Done.
 > Checking if remote can be reached ...  Done.
 > Initializing and updating submodules (this may take a while)...Submodule 'binary' (https://github.com/opencobra/COBRA.binary.git) registered for path 'binary'
Submodule 'CnaCobraInterface' (https://github.com/SteffKlamt/CnaCobraInterface.git) registered for path 'external/analysis/CnaCobraInterface'
Submodule 'Volume-and-Sampling' (https://github.com/Bounciness/Volume-and-Sampling.git) registered for path 'external/analysis/Volume-and-Sampling'
Submodule 'gaimc' (https://github.com/dgleich/gaimc.git) registered for path 'external/analysis/gaimc'
Submodule 'octave-networks-toolbox' (https://github.com/aeolianine/octave-networks-toolbox.git) registered for path 'external/analysis/octave-networks-toolbox'
Submodule 'looplessFluxSampler' (https://github.com/rmtfleming/looplessFluxSampler) registered for path 'external/base/samplers/looplessFluxSampler'
Submodule 'lusol' (https://github.com/nwh/lusol.git) registered for path 'external/base/solvers/lusol'
Submodule 'pdco' (https://github.com/mxsaunders/pdco.git) registered for path 'external/base/solvers/pdco'
Submodule 'Smith-Decomposition' (https://github.com/nbfigueroa/Smith-Decomposition.git) registered for path 'external/base/utilities/Smith-Decomposition'
Submodule 'papers' (https://github.com/opencobra/COBRA.papers.git) registered for path 'papers'
Submodule 'models' (https://github.com/opencobra/COBRA.models) registered for path 'test/models'
Submodule 'tutorials' (https://github.com/opencobra/COBRA.tutorials.git) registered for path 'tutorials'
Cloning into 'C:/Users/kralsystem/cobratoolbox/binary'...
error: RPC failed; curl 56 OpenSSL SSL_read: Connection was reset, errno 10054
error: 5642 bytes of body are still expected
fetch-pack: unexpected disconnect while reading sideband packet
fatal: early EOF
fatal: index-pack failed
fatal: clone of 'https://github.com/opencobra/COBRA.binary.git' into submodule path 'C:/Users/kralsystem/cobratoolbox/binary' failed
Failed to clone 'binary'. Retry scheduled
Cloning into 'C:/Users/kralsystem/cobratoolbox/external/analysis/CnaCobraInterface'...
Cloning into 'C:/Users/kralsystem/cobratoolbox/external/analysis/Volume-and-Sampling'...
Cloning into 'C:/Users/kralsystem/cobratoolbox/external/analysis/gaimc'...
Cloning into 'C:/Users/kralsystem/cobratoolbox/external/analysis/octave-networks-toolbox'...
Cloning into 'C:/Users/kralsystem/cobratoolbox/external/base/samplers/looplessFluxSampler'...
Cloning into 'C:/Users/kralsystem/cobratoolbox/external/base/solvers/lusol'...
Cloning into 'C:/Users/kralsystem/cobratoolbox/external/base/solvers/pdco'...
Cloning into 'C:/Users/kralsystem/cobratoolbox/external/base/utilities/Smith-Decomposition'...
Cloning into 'C:/Users/kralsystem/cobratoolbox/papers'...
Cloning into 'C:/Users/kralsystem/cobratoolbox/test/models'...
Cloning into 'C:/Users/kralsystem/cobratoolbox/tutorials'...
fatal: not a git repository: C:/Users/kralsystem/cobratoolbox/binary/../.git/modules/binary
Failed to clone 'binary' a second time, aborting
Error using initCobraToolbox (line 225)
The submodules could not be initialized.

[Ronan M.T. Fleming]

Hi Mahtab,

it seems like the issue might be an unstable internet connection
because it says "unexpected disconnect while reading sideband packet".

Cloning into 'C:/Users/kralsystem/cobratoolbox/binary'...
error: RPC failed; curl 56 OpenSSL SSL_read: Connection was reset, errno 10054
error: 5642 bytes of body are still expected
fetch-pack: unexpected disconnect while reading sideband packet
fatal: early EOF
fatal: index-pack failed
fatal: clone of 'https://github.com/opencobra/COBRA.binary.git' into
submodule path 'C:/Users/kralsystem/cobratoolbox/binary' failed

Regards,

Ronan


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[mahtab barany]

Hello to all
I have a lot of questions, please help.
I want to do a simulation of the Escherichia coli metabolic network to produce butane triol, but I do not know which database model is suitable for this? I do not know where to start? Also, after doing the simulation, I have to find the antisense algorithm. Thank you for your help. I am a beginner, I do not know exactly what to do.
Thank you very much

‫‪Ronan M.T. Fleming‬‏ <‪ronan.mt...@gmail.com‬‏> در تاریخ جمعه ۱۹ فوریهٔ ۲۰۲۱ ساعت ۱۶:۴۳ نوشت:‬

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