diff options
| author | Pjotr Prins | 2026-03-29 11:02:35 +0200 |
|---|---|---|
| committer | Pjotr Prins | 2026-03-29 11:02:35 +0200 |
| commit | 6e4c8a7685ed3073c91bec7c5695e2916bfba928 (patch) | |
| tree | fe62ddb60b49bff1788b668676b5c4ebdc1f4567 /README.md | |
| parent | 1562c45827c7d98d4a23bd424b6cc88968d83dba (diff) | |
| download | genecup-6e4c8a7685ed3073c91bec7c5695e2916bfba928.tar.gz | |
Update README
Diffstat (limited to 'README.md')
| -rw-r--r-- | README.md | 29 |
1 files changed, 15 insertions, 14 deletions
diff --git a/README.md b/README.md index 7c09004..0df4841 100644 --- a/README.md +++ b/README.md @@ -35,16 +35,6 @@ You can use the [guix.scm](./guix.scm) container to run genecup: Note that the build includes minipubmed and punkt for testing! -## Gemini API credentials - -For stress classification via Gemini, create a credentials file: - -```sh -mkdir -p ~/.config/gemini -echo "YOUR_API_KEY_HERE" > ~/.config/gemini/credentials -``` - -The server reads the API key from `~/.config/gemini/credentials` on startup. # Run a production server @@ -73,6 +63,17 @@ NLTK_DATA: punkt_tab directory (defaults to built-in nltk-punkt) TMPDIR (default /tmp) ``` +## Gemini API credentials + +For stress classification via Gemini, create a credentials file: + +```sh +mkdir -p ~/.config/gemini +echo "YOUR_API_KEY_HERE" > ~/.config/gemini/credentials +``` + +The server reads the API key from `~/.config/gemini/credentials` on startup. + # Development @@ -99,7 +100,7 @@ You also need to fetch punkt.zip from https://www.nltk.org/nltk_data/ cd minipubmed mkdir tokenizers cd tokenizers -wget https://raw.githubusercontent.com/nltk/nltk_data/gh-pages/packages/tokenizers/punkt.zip +wget https://raw.githubusercontent.com/nltk/nltk_data/gh-pages/packages/tokenizers/punkt_tab.zip unzip punkt.zip ``` @@ -107,15 +108,15 @@ unzip punkt.zip The source code and data are in a git repository: https://git.genenetwork.org/genecup/ -## Support +# Support E-mail [Pjotr Prins](https://thebird.nl) or [Hao Chen](https://www.uthsc.edu/neuroscience-institute/about/faculty/chen.php). -## License +# License GeneCup source code is published under the liberal free software MIT licence (aka expat license) -## Cite +# Cite [GeneCup: mining PubMed and GWAS catalog for gene-keyword relationships](https://academic.oup.com/g3journal/article/12/5/jkac059/6548160) by Gunturkun MH, Flashner E, Wang T, Mulligan MK, Williams RW, Prins P, and Chen H. |