https://github.com/greenelab/iscb-diversity
Analyzing diversity of ISCB keynote speakers & fellows compared to the field of bioinformatics
https://github.com/greenelab/iscb-diversity
bioinformatics computational-biology diversity iscb ismb keynotes pubmed
Last synced: 6 months ago
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Analyzing diversity of ISCB keynote speakers & fellows compared to the field of bioinformatics
- Host: GitHub
- URL: https://github.com/greenelab/iscb-diversity
- Owner: greenelab
- License: other
- Created: 2019-09-11T13:03:02.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2021-09-09T19:38:31.000Z (over 3 years ago)
- Last Synced: 2024-05-02T06:00:22.509Z (12 months ago)
- Topics: bioinformatics, computational-biology, diversity, iscb, ismb, keynotes, pubmed
- Language: Jupyter Notebook
- Homepage: https://greenelab.github.io/iscb-diversity
- Size: 168 MB
- Stars: 7
- Watchers: 6
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: readme.md
- License: license-code.md
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README
# Diversity of ISCB Honorees
This is a data analysis repository for the study at .
## Datasets
Datasets are stored in the [`data`](data) directory.
This repository uses [Git LFS](https://git-lfs.github.com/) to store large / binary datasets.
Make sure to have Git LFS installed locally before cloning the repository,
if you'd like to download the datasets.
You can also download datasets directly from the GitHub website by clicking "Raw".
The source code saves large files using [XZ](https://tukaani.org/xz/) compression (denoted by an `.xz` extension).
Since not all users are familiar with XZ-compression,
we have also created gzip exports of all XZ-compressed files
(with the [`convert-xz-to-gzip.bash`](utils/convert-xz-to-gzip.bash) script).
These files are placed alongside their XZ source in the `data` directory.
The source code pipelines use XZ compression since gzip encodes a timestamp causing non-deterministic output files.
## Development
This repository has a corresponding Docker image with the required dependencies.
See [`environment`](environment) for the Docker image specification.
Note that the following Docker commands have a `--mount` argument to give the Docker container access to files in this repository.
Therefore, any changes to the repository content created while running the Docker container will persist in this directory after the container is stopped.
The Docker image is automatically built and published by a GitHub Action.
Even though this repository is public, GitHub [requires](https://github.community/t5/GitHub-Actions/docker-pull-from-public-GitHub-Package-Registry-fail-with-quot/td-p/32782) authentication to download from its package registry.
Therefore, you will need a GitHub account to pull the image.
Use the following steps to [authenticate](https://help.github.com/en/packages/using-github-packages-with-your-projects-ecosystem/configuring-docker-for-use-with-github-packages#authenticating-to-github-packages) your local docker with your GitHub.
Go to and create a new personal access token, selecting only the `read:packages` scope.
You can name the token anything, for example "docker login read-only token".
Then run the following command, substituting your username and token from above:
```shell
docker login --username USERNAME --password TOKEN docker.pkg.github.com
```
### Interactive
For interactive development in Python notebooks, run the following command:
```shell
# This command must be run with the repository root as your working directory.
# Requires docker version >= 17.06.
docker run \
--name iscb-diversity \
--detach --rm \
--env JUPYTER_TOKEN=ksbegpqzrurktbkikyo \
--publish 8899:8888 \
--mount type=bind,source="$(pwd)",target=/user/jupyter \
docker.pkg.github.com/greenelab/iscb-diversity/iscb-diversity
```
Then navigate to the following URL in your browser:
You should see a Jupyter Notebook landing page where you can open, edit, and run any of the notebooks.
When you are done, you shutdown the Jupyter notebook server and remove the Docker container by running ```docker stop iscb-diversity``` in a new terminal.
Similarly, for the R notebooks:
```shell
# This command must be run with the repository root as your working directory.
# Requires docker version >= 17.06.
docker run \
--name iscb-diversity-r \
--detach --rm \
--publish 8787:8787 \
--env DISABLE_AUTH=true \
--mount type=bind,source="$(pwd)",target=/home/rstudio/repo \
docker.pkg.github.com/greenelab/iscb-diversity/iscb-diversity-r
```
Navigate to and you should be logged into RStudio as the rstudio user.
When you are done, shutdown the RStudio server and remove the Docker container by running ```docker stop iscb-diversity-r```.
## GitHub Pages
The [`docs`](docs) directory is used as the GitHub Pages source for .
To regenerate outputs in the `docs` directory, run the following command
```shell
python utils/prepare_docs.py --nbviewer --readme
```
Edit [`utils/prepare_docs.py`](utils/prepare_docs.py) to change the template for `docs/readme.md`.
## License
The entire repository is released under the CC BY 4.0 License available in [`license.md`](license.md).
All code files and snippets are additionally released under the BSD 3-Clause License available in [`license-code.md`](license-code.md).