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ga4gh / ga4gh-server

Reference implementation of the APIs defined in ga4gh-schemas. RETIRED 2018-01-24
http://ga4gh.org
Apache License 2.0
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Update configuration.rst with g2p #1445

Open bwalsh opened 7 years ago

bwalsh commented 7 years ago

Create appropriate directory

$cd   /run/shm/1000Genomes/cgd

Download CGD reference data

$ wget https://github.com/ohsu-computational-biology/ohsu-server-util/raw/master/cgd-08-09-2016.ttl

Navigate to server directory

$ cd /srv/ga4gh0_6_0a8pre
$ python repo_dev.py add-featureset /srv/ga4gh0_6_0a8pre/repo.db 1kgenomes /run/shm/1000Genomes/cgd/  -R NCBI37 -O so-xp  -C ga4gh.datamodel.genotype_phenotype_featureset.PhenotypeAssociationFeatureSet
$ python repo_dev.py add-phenotypeassociationset /srv/ga4gh0_6_0a8pre/repo.db 1kgenomes /run/shm/1000Genomes/cgd/ -n cgd

Then restart server

$ sudo service apache2 restart
david4096 commented 7 years ago

https://github.com/ga4gh/server/blob/master/docs/configuration.rst has a cookbook for setting up a server. These directions should be modified and added there.

https://github.com/ga4gh/server/issues/1431