Open cannin opened 4 years ago
Docker Repository : https://hub.docker.com/r/pritishaw/reactome-query-processing
This is connected to #15 #13
rocker/shiny-verse:3.6.3
next, we'll start to install R packages for my R code
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
A Binder example to try out: https://mybinder.org/v2/gh/binder-examples/r/master?filepath=index.ipynb
- 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
- Can you make a git repository compatible with https://mybinder.org/
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
- 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
- Can you make a git repository compatible with https://mybinder.org/
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 settingsYes, use this repository and write a README.md and shift the blog.
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.
I have made the changes, the notebook is parameterized using papermill and is compatible with binder, (added links in README)
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
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.
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
Sorry a correction use: rocker/binder:3.6.3 otherwise important things will be missing
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
Is this the way you want? I am searching how can run both Python and R notebook(RStudio) using same Dockerfile
Thanks
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
There is something wrong with the links. Please provide them like:
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
To improve reuse please add: