Reproducible Installation from source only?

drieslab / Giotto

Spatial omics analysis toolbox

https://drieslab.github.io/Giotto_website/

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Reproducible Installation from source only? #107

Closed serverhorror closed 3 years ago

serverhorror commented 3 years ago

Hello,

We'd like to try your method. We are running into a few challenges:

http://spatialgiotto.rc.fas.harvard.edu/giotto.install.2.html — this talks about a Docker image but we cannot find a Dockerfile to reliably create the image in our system and we were unable to find it on hub.docker.com.

Is it possible to add this so that we can rebuild the image internally?
There's quite a bit of Python code and we're having trouble finding a requirements.txt file to rebuild a virtualenv with the package versions you've been using.

Is it possible to add these so that a pip install -r requirements.txt works?

(Of course if you prefer pipenv or poetry that's perfectly fine too)

ndelrossi7 commented 3 years ago

Hi @serverhorror, thanks for reaching out! We have recently set up a new Docker image and I have pushed those changes today. I will be adding instructions to our site, but I will also add them here:

docker pull delron01/giotto:latest
docker run --rm -p 8787:8787 -e PASSWORD=mypassword delron01/giotto:latest (note that you can use whatever port you want as long as it's available and any password you choose to set for yourself)
Open your browser > localhost:8787 (or localhost:yourport)
username: rstudio, password: mypassword

This will open an RStudio session and you'll be able to work with Giotto from there. Please let me know if you have any issues with this.

Currently we have the function installGiottoEnvironment() which will create the environment with the necessary Python packages. I'll be working on creating a requirements.txt file with the same information - thank you for the feedback!

ndelrossi7 commented 3 years ago

I am closing this issue but please don't hesitate to reach out with any questions in the future!

serverhorror commented 3 years ago

Thanks!

installGiottoEnvironment is a nice starting point. I'll try and see if I can pinpoint to exact versions of the Python packages.

Will you be adding a Dockerfile and requirements.txt (or similiar), I find conda to be quite cumbersome to use. My clients are not able to use conda without licensing and it is quite hard to integrate something so far out of the typical software development ecosystem.

ndelrossi7 commented 3 years ago

Hi @serverhorror, you can find the Dockerfile here as well as the instructions for Docker usage here. Thanks again for the feedback regarding a requirements.txt file! We are looking into this. I would be happy to update you when it's complete. Thanks!

RubD commented 3 years ago

I would also like to add that installGiottoEnvironment will install miniconda and will use that to install all python modules. So while it is the easiest option for most users, it might not be compatible with your clients licensing policy. I'm unfortunately not familiar with this part of software development.