From 04b3fc82b5985257e7df657c9989dcaadf3205f0 Mon Sep 17 00:00:00 2001 From: matentzn Date: Mon, 6 Jan 2020 18:37:25 +0000 Subject: [PATCH 1/2] ebi config --- src/curation/upheno-config.yaml | 6 +++--- src/scripts/upheno_pipeline_singularity.sh | 9 +++++++++ 2 files changed, 12 insertions(+), 3 deletions(-) create mode 100755 src/scripts/upheno_pipeline_singularity.sh diff --git a/src/curation/upheno-config.yaml b/src/curation/upheno-config.yaml index 1a15739a..77853568 100644 --- a/src/curation/upheno-config.yaml +++ b/src/curation/upheno-config.yaml @@ -6,9 +6,9 @@ report_fail_on: none use_dosdps: TRUE dosdp_tools_options: "--obo-prefixes=true --restrict-axioms-to=logical" robot_opts: -vv -robot_java_args: -Xmx10G -timeout_external_processes: 36000 -working_directory: /work/src +robot_java_args: -Xmx50G +timeout_external_processes: 360000000 +working_directory: /nfs/production3/spot/sw/dev/monarch/data/upheno-dev/src overwrite_matches: False skip_pattern_download: True max_upheno_id: 9999999 diff --git a/src/scripts/upheno_pipeline_singularity.sh b/src/scripts/upheno_pipeline_singularity.sh new file mode 100755 index 00000000..cc70731e --- /dev/null +++ b/src/scripts/upheno_pipeline_singularity.sh @@ -0,0 +1,9 @@ +#!/usr/bin/env bash + +set -e +data=/nfs/production3/spot/sw/dev/monarch/data/upheno-dev/src/scripts + +cd $data +#singularity pull docker://obolibrary/odkfull +singularity shell --pwd $data docker://obolibrary/odkfull -c "python3 upheno_prepare.py ../curation/upheno-config.yaml" +singularity shell --pwd $data docker://obolibrary/odkfull -c "python3 upheno_create_profiles.py ../curation/upheno-config.yaml" \ No newline at end of file From 1719acbd21a469f2eedd89c23fdc5cf50a948140 Mon Sep 17 00:00:00 2001 From: matentzn Date: Wed, 8 Jan 2020 13:26:23 +0000 Subject: [PATCH 2/2] Update upheno_pipeline_singularity.sh --- src/scripts/upheno_pipeline_singularity.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/scripts/upheno_pipeline_singularity.sh b/src/scripts/upheno_pipeline_singularity.sh index cc70731e..7d8654d0 100755 --- a/src/scripts/upheno_pipeline_singularity.sh +++ b/src/scripts/upheno_pipeline_singularity.sh @@ -5,5 +5,5 @@ data=/nfs/production3/spot/sw/dev/monarch/data/upheno-dev/src/scripts cd $data #singularity pull docker://obolibrary/odkfull -singularity shell --pwd $data docker://obolibrary/odkfull -c "python3 upheno_prepare.py ../curation/upheno-config.yaml" -singularity shell --pwd $data docker://obolibrary/odkfull -c "python3 upheno_create_profiles.py ../curation/upheno-config.yaml" \ No newline at end of file +singularity exec --pwd $data docker://obolibrary/odkfull python3 upheno_prepare.py ../curation/upheno-config.yaml +singularity exec --pwd $data docker://obolibrary/odkfull python3 upheno_create_profiles.py ../curation/upheno-config.yaml \ No newline at end of file