Let the installGiottoEnvironment() function accept a specified conda path.

[IMJoeyZhu]

Dear Giotto group,

Many thanks for developing this powerful and comprensive tool.

I noticed that installGiottoEnvironment() function does not accept a specified conda path, even though I assigned the conda_path to my own conda directory like this:

conda_path <- "/path/to/my/Anaconda3"

I checked the script (python_environment.R) and found out that installGiottoEnvironment() function keep redirecting the conda_path to a miniconda_path generated by reticulate::miniconda_path().

So, I made a few changes to the script. All these codes in the scripts:

conda_path = reticulate::miniconda_path()

were replaced by:

if (!dir.exists(conda_path)) {
  conda_path = reticulate::miniconda_path()
}

Then I specify my own conda directory before conducting installGiottoEnvironment() function:

conda_path <- "/path/to/my/Anaconda3"
installGiottoEnvironment()

Finally, I got these messages, shown below, which illustrate that I successfully install the Giotto Environment to the specified conda path:

# To activate this environment, use
#
#     $ conda activate /path/to/my/Anaconda3/envs/giotto_env
#
# To deactivate an active environment, use
#
#     $ conda deactivate

I hope this idea could provide some clue for other people facing the same problem as me.

Best regards,
Jiacheng Zhu

[RubD]

Hi Jiacheng Zhu,

Thanks for the suggestion and I agree that this would provide additional flexibility.

I hope you know we already do provide a solution to use your own python path / conda environment, although in this case you would have to install everything yourself. And then you would simply have to provide the python path you want to use to createGiottoInstructions using the python_path parameter.

The miniconda was created to make it as easy as possible for everyone not familiar with conda environments and/or python paths. However, as mentioned earlier, providing your own conda environment would be an interesting intermediate solution.

I think @mattobny has already been looking into that.

Best,
Ruben

[IMJoeyZhu]

Dear Prof. Ruben,

Thank you for your email and kind reminder! I appreciate your feedback.
I have realized that the Giotto Master Branch is indeed capable of handling the task I was previously inquiring about.
It's great to hear that the Giotto Suite will also be able to do so in the future. Thank you for developing such a powerful tool!
I am really looking forward to your update and utilizing it soon.

Best regards,
Jiacheng Zhu

[mattobny]

@IMJoeyZhu Hello! PR #549 on our development branch allows this behavior. This will be merged into Suite shortly.

[IMJoeyZhu]

Thanks a lot! Looking forward to utilizing it soon. 😄