WormBase / caltech-curation-services

Modular curation services for Caltech WormBase data
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Install get_nameserver_genes script with dependencies (needs Todd) #34

Closed valearna closed 1 year ago

valearna commented 1 year ago

This is the script from /home/postgres/work/pgpopulation/obo_oa_ontologies/geneace/get_nameserver_genes.sh

#!/bin/bash

export WB_DB_URI="datomic:ddb://us-east-1/WSNames/wormbase"
java -cp wb-names-export.jar clojure.main -m wormbase.names.export
gene genes.csv

It seems to require 

# install java8
#
# sudo apt-get install awscli
# aws configure
#   AWS Access Key ID [None]: 
#   AWS Secret Access Key [None]: 
# (goes into ~/.aws/config   could also have in ~/.aws/credentials)
#
# get the exporter :
# aws s3 ls s3://wormbase/names/exporter/
# aws s3 cp s3://wormbase/names/exporter/wb-names-export.jar
# wb-names-export.jar
valearna commented 1 year ago

I'll try to install the default java jdk on debian 10, which is probably different than java8, but should support older versions of java code. We'll need to test the script together @azurebrd as I'm not sure how if works.

azurebrd commented 1 year ago

Sounds good, thanks @valearna

valearna commented 1 year ago

WB AWS credentials were blocked. We are waiting for new credentials to test this script

azurebrd commented 1 year ago

Paulo set up something else, and that's working, so we don't need this