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cannin / enhance_nlp_interaction_network_gsoc2020

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Add Documentation/Tests/Dockerfile to Reactome Failed Search Code #12

Open cannin opened 4 years ago

cannin commented 4 years ago

To improve reuse please add:

PritiShaw commented 4 years ago

Docker Repository : https://hub.docker.com/r/pritishaw/reactome-query-processing

cannin commented 4 years ago

This is connected to #15 #13

rocker/shiny-verse:3.6.3

next, we'll start to install R packages for my R code

https://mybinder.org/

repo2docker to test locally: https://github.com/jupyter/repo2docker

You can still use Google Colab to run if you prefer.

https://github.com/nteract/papermill

example: https://mybinder.org/v2/gh/mwouts/papermill_jupytext/master?filepath=README.md (don't use jupytext unless necessary)

postpone #14 until the above with papermill is done to see how it might connect with .env

cannin commented 4 years ago

A Binder example to try out: https://mybinder.org/v2/gh/binder-examples/r/master?filepath=index.ipynb

PritiShaw commented 4 years ago
  • Can you use this image as the base: rocker/shiny-verse:3.6.3

I have done this, can you provide me with the R packages to be installed

Should I shift all my python notebooks to a single repository? This repository can also be used but the blog will have to be shifted to gh-pages branch in settings

cannin commented 4 years ago
  • Can you use this image as the base: rocker/shiny-verse:3.6.3

I have done this, can you provide me with the R packages to be installed

Check the HTML I sent Guanming. Look for library(NAME) for the names.

Try installing using this: https://gist.github.com/cannin/6b8c68e7db19c4902459

Example R Code (but copy the R file into the container (or use a specific revision). 

source("https://gist.githubusercontent.com/cannin/6b8c68e7db19c4902459/raw/installPackages.R")
installPackages("r-requirements.dcf")

Set mran-date: 2020-07-27

Should I shift all my python notebooks to a single repository? This repository can also be used but the blog will have to be shifted to gh-pages branch in settings

Yes, use this repository and write a README.md and shift the blog.

cannin commented 4 years ago

You need commands in Docker like this: 

RUN R -e 'source("installPackage.R")'

Test my notebook like this: 

R -e "rmarkdown::render('script.Rmd', output_file='output.html')"

See emails to Guanming for Rmd. Don't include the Rmd in the notebook, yet.

PritiShaw commented 4 years ago

Python Notebook

I have made the changes, the notebook is parameterized using papermill and is compatible with binder, (added links in README)

Docker Container

At present I am mounting the Rmd file when Docker is run, I have tested using the Rmd in email

Also I have shifted the blog to gh-pages branch, so the repository(cannin/enhance_nlp_interaction_network_gsoc2020) settings needs to be changed. Thanks

cannin commented 4 years ago

Can you deploy on https://mybinder.org/ and let me know when ready? Deploy here means submit the form on mybinder.org and it will build the Docker container.

Manually upload the needed input files (do not include in the container) and test out as you have done. Let me know when ready and I will also test.

cannin commented 4 years ago

Also, I don't see how you installed and ran all the R code?

You need to do something like this: https://mybinder.readthedocs.io/en/latest/tutorials/dockerfile.html

with the Dockerfile and then I think you know how to get all the R and Java dependencies you need. Remember to use "rocker/shiny-verse:3.6.3" as the base. Here is an example:

https://github.com/binder-examples/dockerfile-rstudio/blob/master/Dockerfile

cannin commented 4 years ago

Sorry a correction use: rocker/binder:3.6.3 otherwise important things will be missing

PritiShaw commented 4 years ago

Thanks for the material, I was able to deploy the container, link. When I manually uploaded the Rmd file, it is showing as following image image

Is this the way you want? I am searching how can run both Python and R notebook(RStudio) using same Dockerfile

Thanks

PritiShaw commented 4 years ago

I am searching how can run both Python and R notebook(RStudio) using same Dockerfile

I was able to run RStudio and Python notebook, but both of them are at different url

Python Notebook: https://mybinder.org/v2/gh/cannin/enhance_nlp_interaction_network_gsoc2020/master?filepath=Reactome_Failed_Query_Analysis.ipynb RStudio: https://mybinder.org/v2/gh/cannin/enhance_nlp_interaction_network_gsoc2020/master?urlpath=rstudio

I have checked that files are shared among these links. Can you please say if I am doing it the right way?

Thanks

cannin commented 4 years ago

There is something wrong with the links. Please provide them like:

https://mybinder.org/v2/gh/cannin/enhance_nlp_interaction_network_gsoc2020/master?filepath=Reactome_Failed_Query_Analysis.ipynb

the hub.gke links are not reusable.

I am searching how can run both Python and R notebook(RStudio) using same Dockerfile

I was able to run RStudio and Python notebook, but both of them are at different url

Python Notebook: https://hub.gke.mybinder.org/user/cannin-enhance_-etwork_gsoc2020-clraz0qz/notebooks/Reactome_Failed_Query_Analysis.ipynb

RStudio: https://hub.gke.mybinder.org/user/cannin-enhance_-etwork_gsoc2020-clraz0qz/rstudio/

I have checked that files are shared among these links. Can you please say if I am doing it the right way?

Thanks