From ecbd4be0d92a59cad3a076afe761e2b911dde325 Mon Sep 17 00:00:00 2001
From: Kai Waldrant <kai@data-intuitive.com>
Date: Thu, 11 Jul 2024 21:51:28 +0200
Subject: [PATCH] add run_benchmark scripts

---
 scripts/run_benchmark.sh      | 23 +++++++++++++++++++++++
 scripts/run_benchmark_test.sh | 19 +++++++++++++++++++
 2 files changed, 42 insertions(+)
 create mode 100644 scripts/run_benchmark.sh
 create mode 100644 scripts/run_benchmark_test.sh

diff --git a/scripts/run_benchmark.sh b/scripts/run_benchmark.sh
new file mode 100644
index 0000000..cc4275e
--- /dev/null
+++ b/scripts/run_benchmark.sh
@@ -0,0 +1,23 @@
+#!/bin/bash
+
+RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)"
+publish_dir="s3://openproblems-data/resources/task_template/results/${RUN_ID}"
+
+# make sure only log_cp10k is used
+cat > /tmp/params.yaml << HERE
+input_states: s3://openproblems-data/resources/task_template/datasets/**/state.yaml
+rename_keys: 'input_train:output_train;input_test:output_test'
+output_state: "state.yaml"
+publish_dir: "$publish_dir"
+HERE
+
+tw launch https://github.com/openproblems-bio/task_template.git \
+  --revision build/main \
+  --pull-latest \
+  --main-script target/nextflow/workflows/run_benchmark/main.nf \
+  --workspace 53907369739130 \
+  --compute-env 6TeIFgV5OY4pJCk8I0bfOh \
+  --params-file /tmp/params.yaml \
+  --entry-name auto \
+  --config common/nextflow_helpers/labels_tw.config \
+  --labels task_template,full
\ No newline at end of file
diff --git a/scripts/run_benchmark_test.sh b/scripts/run_benchmark_test.sh
new file mode 100644
index 0000000..6c03d42
--- /dev/null
+++ b/scripts/run_benchmark_test.sh
@@ -0,0 +1,19 @@
+#!/bin/bash
+
+cat > /tmp/params.yaml << 'HERE'
+input_states: s3://openproblems-data/resources_test/task_template/**/state.yaml
+rename_keys: 'input_train:output_train;input_test:output_test'
+output_state: "state.yaml"
+publish_dir: s3://openproblems-nextflow/temp/task_template/
+HERE
+
+tw launch https://github.com/openproblems-bio/task_template.git \
+  --revision build/main \
+  --pull-latest \
+  --main-script target/nextflow/workflows/run_benchmark/main.nf \
+  --workspace 53907369739130 \
+  --compute-env 6TeIFgV5OY4pJCk8I0bfOh \
+  --params-file /tmp/params.yaml \
+  --entry-name auto \
+  --config common/nextflow_helpers/labels_tw.config \
+  --labels task_template,test
\ No newline at end of file