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opencobra / COBRA.tutorials

Repository of tutorials for The COBRA Toolbox
https://git.io/COBRA.tutorials
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Submodules could no be initialized #167

Closed DanelOlaverri closed 2 years ago

DanelOlaverri commented 2 years ago

Good morning, I am trying to work with the latest upload of the cobratoolbox (downloaded from gitbash using: git clone --depth=1 https://github.com/opencobra/cobratoolbox.git cobratoolbox), and, when executing the initCobraToolbox line in Matlab R2019b, the following message appears:

initCobraToolbox

  _____   _____   _____   _____     _____     |
 /  ___| /  _  \ |  _  \ |  _  \   / ___ \    |   COnstraint-Based Reconstruction and Analysis
 | |     | | | | | |_| | | |_| |  | |___| |   |   The COBRA Toolbox - 2021
 | |     | | | | |  _  { |  _  /  |  ___  |   |
 | |___  | |_| | | |_| | | | \ \  | |   | |   |   Documentation:
 \_____| \_____/ |_____/ |_|  \_\ |_|   |_|   |   http://opencobra.github.io/cobratoolbox
                                              |

Checking if git is installed ... Done (version: 2.33.1). 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)...Entering 'binary' Your branch is up to date with 'origin/master'. Already on 'master' Entering 'external/analysis/CnaCobraInterface' Your branch is up to date with 'origin/master'. Already on 'master' Entering 'external/analysis/GeoCalcLib' Your branch is up to date with 'origin/master'. Already on 'master' Entering 'external/analysis/PolytopeSamplerMatlab' Your branch is up to date with 'origin/master'. Already on 'master' Entering 'external/analysis/Volume-and-Sampling' Your branch is up to date with 'origin/master'. Already on 'master' Entering 'external/analysis/gaimc' Your branch is up to date with 'origin/master'. Already on 'master' Entering 'external/analysis/octave-networks-toolbox' Your branch is up to date with 'origin/master'. Already on 'master' Entering 'external/base/samplers/looplessFluxSampler' Your branch is up to date with 'origin/master'. Already on 'master' Entering 'external/base/solvers/lusol' Your branch is up to date with 'origin/master'. Already on 'master' Entering 'external/base/solvers/pdco' Your branch is up to date with 'origin/master'. Already on 'master' Entering 'external/base/utilities/Smith-Decomposition' Your branch is up to date with 'origin/master'. Already on 'master' Entering 'external/base/utilities/condalab' Your branch is up to date with 'origin/master'. Already on 'master' Entering 'papers' Your branch is up to date with 'origin/master'. Already on 'master' Entering 'test/models' Your branch is up to date with 'origin/master'. Already on 'master' Entering 'tutorials' error: invalid path 'dataIntegration/metaboAnnotator/data/ctf-main\mets\molFiles/10zhepta.mol' error: invalid path 'dataIntegration/metaboAnnotator/data/ctf-main\mets\molFiles/_apine.mol' error: invalid path 'dataIntegration/metaboAnnotator/data/ctf-main\mets\molFiles/dopa.mol' fatal: run_command returned non-zero status for tutorials . Error using initCobraToolbox (line 233) The submodules could not be initialized.

I have been looking into it, and I suspect it could be the latest upload done into tutorials/dataIntegration/metaboAnnotator/data is not properly defined, because when I enter in the github, the folder named: "ctf-main\mets\molFiles" is the one that is giving me problems. imagen

edit: formatting

DanelOlaverri commented 2 years ago

Looks like cloning the tutorials repo from opencobra/tutorials in its respective folder solves the issue.

rmtfleming commented 2 years ago

Hi Daniel, I made changes last night so that should not be a problem if you do a fresh clone. Please can you try it? Regards, Ronan

On Thu, 2 Dec 2021 at 08:02, Danel Olaverri @.***> wrote:

Looks like cloning the tutorials repo from opencobra/tutorials in its respective folder solves the issue.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/opencobra/COBRA.tutorials/issues/167#issuecomment-984379659, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAQMEOSEHQCRXCREIA4KFZDUO4R23ANCNFSM5JEMAAVA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Associate Professor, School of Medicine, National University of Ireland, Galway. & Assistant Professor, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University. https://www.universiteitleiden.nl/en/staffmembers/ronan-fleming & H2020 Project Coordinator, Systems Medicine of Mitochondrial Parkinson’s Disease, http://sysmedpd.eu

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DanelOlaverri commented 2 years ago

Hello! Thanks for your response, I just cloned the repository and ran the initCobraToolbox and I had no problem whatsoever. Thank you, Danel

rmtfleming commented 2 years ago

Hi Daniel, thanks for the feedback. Regards, Ronan

On Thu, 2 Dec 2021 at 11:41, Danel Olaverri @.***> wrote:

Hello! Thanks for your response, I just cloned the repository and ran the initCobraToolbox and I had no problem whatsoever. Thank you, Danel

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/opencobra/COBRA.tutorials/issues/167#issuecomment-984549908, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAQMEOSIVIIX6MIIC6EXG6DUO5LOVANCNFSM5JEMAAVA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

--

Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Associate Professor, School of Medicine, National University of Ireland, Galway. & Assistant Professor, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University. https://www.universiteitleiden.nl/en/staffmembers/ronan-fleming & H2020 Project Coordinator, Systems Medicine of Mitochondrial Parkinson’s Disease, http://sysmedpd.eu

Peer-reviewed publications: https://goo.gl/FZPG23 Mobile: +353 852 109 806 Skype: ronan.fleming

(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)