Not able to install on Mac

[YMVio]

Hello there,

I'm new to programming but want to self-learn CellModeller. However it seems it didn't install successfully in my terminal. It looks like this:

1. Installing CellModeller and dependencies via Anaconda...

Collecting package metadata (current_repodata.json): done Solving environment: done

Package Plan

environment location: /Applications/anaconda3/envs/cellmodeller

Preparing transaction: done Verifying transaction: done Executing transaction: done #

To activate this environment, use

#

$ conda activate cellmodeller

#

To deactivate an active environment, use

#

$ conda deactivate

Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: \ Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError:

usage: dirname path

2. Setting up user environment in /Users/YM/cellmodeller...

cp: /PackageFiles/Scripts: No such file or directory cp: /Users/YM/Pictures: unable to copy extended attributes to 1/cellmodeller/YM/Pictures: Permission denied cp: /Users/YM/Pictures: Permission denied cp: /Users/YM/Library: unable to copy extended attributes to 1/cellmodeller/YM/Library: Permission denied cp: /Users/YM/Library: Permission denied cp: /PackageFiles/Doc: No such file or directory cp: /Users/YM/Pictures: unable to copy extended attributes to 1/cellmodeller/YM/Pictures: Permission denied cp: /Users/YM/Pictures: Permission denied cp: /Users/YM/Library: unable to copy extended attributes to 1/cellmodeller/YM/Library: Permission denied cp: /Users/YM/Library: Permission denied cp: /PackageFiles/Examples: No such file or directory cp: /Users/YM/Pictures: unable to copy extended attributes to 1/cellmodeller/YM/Pictures: Permission denied cp: /Users/YM/Pictures: Permission denied cp: /Users/YM/Library: unable to copy extended attributes to 1/cellmodeller/YM/Library: Permission denied cp: /Users/YM/Library: Permission denied cp: /PackageFiles/cmgui: No such file or directory cp: /Users/YM is a directory (not copied). cp: /PackageFiles/cmpython: No such file or directory cp: /Users/YM is a directory (not copied).

3. Adding paths to bash_profile

touch: /Users/YM: Permission denied touch: /Users/YM: Permission denied /Users/YM 1/Downloads/InstallCellModeller-v4.3-OSX/InstallCellModeller: line 73: $HOME/.bash_profile: ambiguous redirect /Users/YM 1/Downloads/InstallCellModeller-v4.3-OSX/InstallCellModeller: line 74: $HOME/.bash_profile: ambiguous redirect /Users/YM 1/Downloads/InstallCellModeller-v4.3-OSX/InstallCellModeller: line 75: $HOME/.bashrc: ambiguous redirect /Users/YM 1/Downloads/InstallCellModeller-v4.3-OSX/InstallCellModeller: line 76: $HOME/.bashrc: ambiguous redirect logout Saving session... ...copying shared history... ...saving history...truncating history files... ...completed.

[Process completed]

And then command "cmgui" cannot be found.

Looking forward to your response.

[avimanyu786]

Hi @YMVio,

You are getting "Permission denied" errors since the CellModeller OSX installer shell script perhaps does not have executable permissions on your user account. It seems to be located under /Users/YM 1/Downloads/. Try placing it within the YM folder instead of YM 1. Please check this link for more details and workarounds on the error.

You can also try this container image with Docker on Mac. Since you're on Mac, the appropriate modifications as per this reference would be necessary as the documentation provided with the image is for Linux. However, on Docker for Mac, you would still require connecting to a Linux host for GPU support .

[timrudge]

Hi - the installer is out of date and needs to be updated. I recommend that you switch to our python 3 version which is currently on a development branch awaiting release soon. In the meantime, here are instructions to set it up (make sure you are using python 3).

1. Clone the repo: git clone https://github.com/HaseloffLab/CellModeller.git
2. cd CellModeller
3. Switch to new branch: git checkout python3
4. pip install -e .

Now you can run the GUI as “python Scripts/CellModellerGUI.py"

Let me know any problems.

Tim

On 18-08-2020, at 02:34, Avimanyu Bandyopadhyay notifications@github.com wrote:

Hi @YMVio,

You are getting "Permission denied" errors since the CellModeller OSX installer shell script perhaps does not have executable permissions on your user account. It seems to be located under /Users/YM 1/Downloads/. Try placing it within the YM folder instead of YM 1. Please check this link for more details and workarounds on the error.

You can also try this container image with Docker on Mac. Since you're on Mac, the appropriate modifications as per this reference would be necessary as the documentation provided with the image is for Linux. However, on Docker for Mac, you would still require connecting to a Linux host for GPU support .

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[Gonza10V]

Newest versions of MacOS does not support OpenCL as they opted for Metal. https://appleinsider.com/articles/18/06/28/why-macos-mojave-requires-metal----and-deprecates-opengl

We are working in a solution for this but in the meantime I suggest you to use a Linux partition or virtual machine to run CellModeller.