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Diffstat (limited to 'README.md')
| -rw-r--r-- | README.md | 18 |
1 files changed, 5 insertions, 13 deletions
diff --git a/README.md b/README.md index 04677c7..ce7d2e3 100644 --- a/README.md +++ b/README.md @@ -26,23 +26,19 @@ Live searches are conducted through PubMed to get relevant PMIDs, which are then * [local copy of PubMed](https://dataguide.nlm.nih.gov/edirect/archive.html) * python == 3.8 -* see requirements.txt for list of packages and versions +* see requirements.txt and guix.scm for list of packages and versions ## Deploy with GNU Guix -The main genecup.org service is deployed deterministically (and self contained) using GNU Guix. See https://issues.genenetwork.org/topics/deploy/genecup and https://git.genenetwork.org/guix-bioinformatics/ +The main genecup.org service is deployed deterministically (and self contained) using GNU Guix. + +See also https://issues.genenetwork.org/topics/deploy/genecup. ## Development The source code and data are in a git repository: https://git.genenetwork.org/genecup/ -Unpack minipubmed and punkt (see below). And run, for example, using GNU Guix: - -```sh -guix shell -C -N -F python python-flask coreutils-minimal python-bcrypt python-nltk python-numpy python-pandas python-regex python-flask-sqlalchemy edirect inetutils python-keras tensorflow sed -- env EDIRECT_PUBMED_MASTER=minipubmed/ NLTK_DATA=`pwd`/minipubmed ./server.py -``` - -and the service should be listening on port 4200. +Unpack minipubmed and punkt (see below). And run, for example ## Mini PubMed for testing @@ -69,10 +65,6 @@ wget https://raw.githubusercontent.com/nltk/nltk_data/gh-pages/packages/tokenize unzip punkt.zip ``` -## Source code - -https://git.genenetwork.org/genecup/ - ## Support E-mail [Pjotr Prins](https://thebird.nl) or [Hao Chen](https://www.uthsc.edu/neuroscience-institute/about/faculty/chen.php). |