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move materialised queries to top of repo
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jamesamcl committed Dec 22, 2024
1 parent 46d2509 commit deda89f
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Showing 6 changed files with 8 additions and 2 deletions.
4 changes: 2 additions & 2 deletions dataload/08_run_queries/run_queries.slurm.py
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Expand Up @@ -35,7 +35,7 @@ def main():
'--bind ' + shlex.quote(neo_data_path) + ':/data',
'--bind ' + shlex.quote(neo_logs_path) + ':/logs',
'--bind ' + os.path.abspath(os.path.join(os.environ['GREBI_DATALOAD_HOME'], '08_run_queries/run_queries.dockerpy')) + ':/run_queries.py',
'--bind ' + os.path.abspath(os.path.join(os.environ['GREBI_DATALOAD_HOME'], 'materialised_queries', os.environ['GREBI_SUBGRAPH'] )) + ':/materialised_queries',
'--bind ' + os.path.abspath(os.environ['QUERY_YAMLS_PATH']) + ':/materialised_queries',
'--bind ' + os.path.abspath(args.out_sqlites_path) + ':/out',
'--writable-tmpfs',
'--network=none',
Expand All @@ -50,7 +50,7 @@ def main():
'-v ' + shlex.quote(neo_data_path) + ':/data',
'-v ' + shlex.quote(neo_logs_path) + ':/logs',
'-v ' + os.path.abspath(os.path.join(os.environ['GREBI_DATALOAD_HOME'], '08_run_queries/run_queries.dockerpy')) + ':/run_queries.py',
'-v ' + os.path.abspath(os.path.join(os.environ['GREBI_DATALOAD_HOME'], 'materialised_queries', os.environ['GREBI_SUBGRAPH'] )) + ':/materialised_queries',
'-v ' + os.path.abspath(os.environ['QUERY_YAMLS_PATH']) + ':/materialised_queries',
'-v ' + os.path.abspath(args.out_sqlites_path) + ':/out',
'-e NEO4J_AUTH=none',
'ghcr.io/ebispot/grebi_neo4j_with_extras:5.18.0',
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1 change: 1 addition & 0 deletions dataload/scripts/dataload_codon.sh
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@@ -1,5 +1,6 @@
#!/bin/bash
export GREBI_DATALOAD_HOME=/nfs/production/parkinso/spot/grebi/dataload
export GREBI_QUERY_YAMLS_PATH=/nfs/production/parkinso/spot/grebi/materialised_queries
export GREBI_TMP=/hps/nobackup/parkinso/spot/grebi/tmp
export GREBI_CONFIG=ebi
export GREBI_IS_EBI=true
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1 change: 1 addition & 0 deletions dataload/scripts/dataload_local.sh
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@@ -1,5 +1,6 @@
#!/bin/bash
export GREBI_DATALOAD_HOME=~/grebi/dataload
export GREBI_QUERY_YAMLS_PATH=~/grebi/materialised_queries
export GREBI_TMP=$(pwd)
export GREBI_CONFIG=ebi
export GREBI_IS_EBI=false
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1 change: 1 addition & 0 deletions dataload/scripts/dataload_saturos.sh
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@@ -1,5 +1,6 @@
#!/bin/bash
export GREBI_DATALOAD_HOME=/home/james/grebi/dataload
export GREBI_QUERY_YAMLS_PATH=/home/james/grebi/materialised_queries
export GREBI_TMP=/data/grebi_tmp
export GREBI_CONFIG=ebi
export GREBI_IS_EBI=false
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@@ -1,5 +1,8 @@
title: Human GWAS variants to mouse models in IMPC
description: Connects human GWAS variants to mouse models in IMPC using multiple different graph paths through phenotype and disease ontologies
subgraphs:
- ebi_monarch_xspecies
- impc_x_gwas
uses_datasources:
- IMPC
- GWAS
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