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| -rw-r--r-- | README.md | 16 |
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diff --git a/README.md b/README.md index 2088fc9..1897704 100644 --- a/README.md +++ b/README.md @@ -39,28 +39,28 @@ Note that the build includes minipubmed and punkt for testing! ## Install local mirror of PubMed -- Following the instruction provided by NCBI: https://www.nlm.nih.gov/dataguide/edirect/archive.html +Following the instruction provided by NCBI: https://www.nlm.nih.gov/dataguide/edirect/archive.html unpack the data in, for example, /export/PubMed/ -Point environment variables to this dir: +Point environment variables to this dir and run in the local source tree: ``` -env EDIRECT_PUBMED_MASTER=/export3/PubMed GEMINI_API_KEY="AIzaSy**" `guix build -L . genecup-gemini`/server.py --port 4201 +env EDIRECT_PUBMED_MASTER=/export GEMINI_API_KEY="AIzaSy**" `guix build -L . genecup-gemini`/server.py --port 4201 ``` You can run from a proper container: ``` -guix shell -L . -C -N -F genecup-gemini coreutils -- env GEMINI_API_KEY="AIzaSy**" genecup --port 4201 +guix shell -L . -C -N -F genecup-gemini -- env GEMINI_API_KEY="AIzaSy**" genecup --port 4201 ``` Environment variables used: ``` -EDIRECT_PUBMED_MASTER: PubMed datadir +EDIRECT_PUBMED_MASTER: PubMed datadir (defaults to ./minipubmed) GEMINI_API_KEY: LLM access key -GENECUP_DATADIR: SQLITE DB directory -NLTK_DATA: punkt directory -TMPDIR +GENECUP_DATADIR: SQLITE DB directory (default .) +NLTK_DATA: punkt directory (defaults to ./minipubmed/tokenizer) +TMPDIR (default /tmp) ``` # Development |