[WIP][ENH] add Dockerfile for python version og GLM single#46
Draft
Remi-Gau wants to merge 3 commits intocvnlab:mainfrom
Draft
[WIP][ENH] add Dockerfile for python version og GLM single#46Remi-Gau wants to merge 3 commits intocvnlab:mainfrom
Remi-Gau wants to merge 3 commits intocvnlab:mainfrom
Conversation
Remi-Gau
commented
Apr 11, 2022
Comment on lines
+1
to
+9
| # Generated by: Neurodocker version 0.7.0+0.gdc97516.dirty | ||
| # Latest release: Neurodocker version 0.8.0 | ||
| # Timestamp: 2022/04/11 12:55:39 UTC | ||
| # | ||
| # Thank you for using Neurodocker. If you discover any issues | ||
| # or ways to improve this software, please submit an issue or | ||
| # pull request on our GitHub repository: | ||
| # | ||
| # https://github.com/ReproNim/neurodocker |
Contributor
Author
There was a problem hiding this comment.
This file is automatically generated via the Makefile
Remi-Gau
commented
Apr 11, 2022
Comment on lines
+123
to
+134
| docker run --rm repronim/neurodocker:0.7.0 generate docker \ | ||
| --base python:3.9.12-slim-buster \ | ||
| --pkg-manager apt \ | ||
| --install "build-essential" \ | ||
| --copy glmsingle setup.py MANIFEST.in README.md requirements.txt /glmsingle/ \ | ||
| --workdir /glmsingle \ | ||
| --run "pip install ." \ | ||
| --run "pip install jupyterlab" \ | ||
| --expose 8888 \ | ||
| --user neuro \ | ||
| --workdir /home/neuro \ | ||
| --copy examples /home/neuro/examples > Dockerfile |
Contributor
Author
There was a problem hiding this comment.
This is the neurodocker command to build the Dockerfile for GLMsingle
Member
|
Hmm... I'm not sure what the action item is here. Perhaps earmark for a discussion soon. |
Remi-Gau
commented
Apr 27, 2022
Contributor
Author
There was a problem hiding this comment.
- add doc explaining how to build and run the docker image
- add singularity image
Current problem when building the singularity def file: neurodocker related.
Issue raised: ReproNim/neurodocker#447
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Will need to use a containerized version of glmsingle to build on top of so in case this is useful, here is how to do it for glmsingle alone.
Feel free to reject / close.
make Dockerfilewill create a Dockerfile for the python implementation using neurodockermake docker_buildwill run 1 and then create the docker imagemake docker_runwill run 2 and then run the docker image and open jupyter lab to use itOnce again this is based on the same initial commit as #43 and #44
TODO
Currently the examples notebook cannot run and throw this error and
pip listdoes showsGLMsingle 0.0.1