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Added solanaceae bundle
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holegar committed Jul 8, 2024
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38 changes: 38 additions & 0 deletions rres-endpoints/config/datasets/solanaceae-58-cfg.sh
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# /home/data/knetminer/etl-test/solanaceae/58/generic/knowledge-network.oxl

# Unfortunately, there isn't consistence, so we can use KETL_DATASET_ID here
oxl_home="$KNET_HOME/etl-test/solanaceae/$KETL_DATASET_VERSION"

export KETL_SRC_OXL="$oxl_home/generic/knowledge-network.oxl"

export KETL_OUT="$KETL_OUT_HOME/$KETL_DATASET_ID/$KETL_DATASET_VERSION"

## Neo 
#
export KETL_HAS_NEO4J=true
export KETL_NEO_VERSION='5.20.0'
export NEO4J_HOME="$KNET_SOFTWARE/neo4j-community-$KETL_NEO_VERSION-etl"

## Knet Initialiser
#
# The name within the code base, which identifies the config dir to be
# used for the KnetMiner initialiser
export KNET_INIT_DATASET_ID="solanaceae"


##### Values for server-sync.sh
#

## RRes Neo server
export [email protected]
export KNET_NEO_DATA=/opt/data


## RRes Test instances for Knetminer
#

# Test servers like babvs73
export KNET_TESTINST_DATA_PATH=/opt/data/knetminer-datasets/solanaceae
# babvs73: based on old Traverser, available at knetminer.com/ci-test
# babvs72: based on Neo4j+OXL Traverser, available at knetminer.com/ci-test-cypher
export KNET_TESTINST_SSH="[email protected] [email protected]"
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# These files are passed to the Ondex Metadata descriptor tool.
# https://github.com/Rothamsted/knetbuilder/tree/master/ondex-knet-builder/modules/rdf-export-2
#
datasetId = solanaceae
datasetAccession = KnetMiner:Solanaceae
datasetTitle = Knetminer's knowledge graph about solanaceae
datasetDescription = \
Knetminer is a gene discovery platform, which allows for exploring knwoledge graphs computed \
from common plant biology data, such as ENSEMBL, UniProt, TAIR, PUBMED and more.\n\
The solanaceae dataset contains information about the 5 gramineae species, which is also linked \
to embedded data about the Arabidopsis model organism.\n\
This edition includes Arabidopsis, Asparagus officinalis, Arabidopsis thaliana, Beta vulgaris, Capsicum annuum, Cucumis sativus, Daucus carota, Lactuca sativa, Nicotiana attenuata, Solanum lycopersicum, Solanum tuberosum.
datasetVersion = 58
# TODO: better URLs
datasetURL = https://knetminer.com/about
datasetNeo4jBrowserURL = <http://knetminer-wheat.cyverseuk.org:7474>
datasetNeo4jBOLTURL = <bolt://knetminer-neo4j.cyverseuk.org:7687>

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