https://github.com/greenelab/bioconductor-scraper
A scraper which tries to generate conda recipes for bioconductor and other needed R packages.
https://github.com/greenelab/bioconductor-scraper
bioconductor scraper script tool
Last synced: 11 months ago
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A scraper which tries to generate conda recipes for bioconductor and other needed R packages.
- Host: GitHub
- URL: https://github.com/greenelab/bioconductor-scraper
- Owner: greenelab
- License: bsd-3-clause
- Created: 2017-05-22T14:50:11.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2017-06-05T17:50:39.000Z (over 8 years ago)
- Last Synced: 2025-01-13T00:42:45.480Z (about 1 year ago)
- Topics: bioconductor, scraper, script, tool
- Language: Python
- Homepage:
- Size: 23.4 KB
- Stars: 1
- Watchers: 5
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# biconductor-scraper
A scraper which tries to generate conda recipes for bioconductor and other needed R packages.
## Getting Started
You should make sure you have MongoDB installed and running. You should also create
a virtual environment and run `pip install -r requirements.txt` within it.
Before anything else will work, running `python generate_annotation_recipes.py`
is required. This will populate a mongo collection with metadata about packages.
Tracking all this metadata in a database allows `build_all_recipes.py` to be
stopped and restarted without losing work. Once you've done that you can either run:
```
python build_all_recipes.py
```
to build all the packages on bioconductor.org, or
```
python create_recipe.py -n
```
to just build one package by name.
Note that this repo adheres to PEP8 standards with a 100 character line limit.