[IMP-dev] Re: installing IMP on google colab

[Ben Webb <>]

On 1/18/23 5:27 AM, Barak Raveh wrote:
> This shell snippet used to work for installing IMP on google colab, but 
> it seems to have stopped working:
> 
> !echo "deb https://integrativemodeling.org/latest/download/ $(lsb_release -cs)/" 
>  > /etc/apt/sources.list.d/salilab.list
> !apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 22A3BF2B
> !apt update
> !apt install imp

See https://integrativemodeling.org/download-linux.html
We had to change the signing key for this release because the old key 
used SHA1, which is no longer supported by recent operating systems such 
as RedHat Enterprise 9.

I believe "apt-key adv" is deprecated. The officially supported way to 
add a key now is to put it in /etc/apt/trusted.gpg.d/. See that URL 
above or one of the tutorials at 
https://integrativemodeling.org/tutorials/ that use Colab, e.g. the 
deposition tutorial at 
https://colab.research.google.com/github/salilab/imp_deposition_tutorial/blob/main/rnapolii/modeling/deposition-colab.ipynb

As Riccardo mentioned, an alternative is to replace Google's Python with 
conda using the condacolab package. That works too[*] and is certainly 
helpful if you also want to install conda packages. I find it takes a 
lot longer to run than installing the Debian package though, since it 
also has to install all of IMP's dependencies, most of which are already 
there for the Debian package. Plus, since it replaces Python, it 
restarts the kernel which some users may find confusing.

[*] However, you don't need to use the "salilab" conda channel any more. 
IMP is part of conda-forge now.

	Ben
-- 
                      https://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
	- Sir Arthur Conan Doyle