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update scripts and submodule
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rcannood committed Sep 24, 2024
1 parent c76ae47 commit ea97606
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Showing 5 changed files with 6 additions and 29 deletions.
1 change: 1 addition & 0 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -436,3 +436,4 @@ Data structure:
| `uns["metric_values"]` | `double` | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. |

</div>

2 changes: 1 addition & 1 deletion common
10 changes: 1 addition & 9 deletions scripts/run_benchmark/run_full_local.sh
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Expand Up @@ -11,14 +11,6 @@ cd "$REPO_ROOT"
# please refer to the nextflow information for more details:
# https://www.nextflow.io/docs/latest/

# remove this when you have implemented the script
echo "TODO: once the 'run_benchmark' workflow has been implemented, update this script to use it."
echo " Step 1: replace 'task_batch_integration' with the name of the task in the following command."
echo " Step 2: replace the rename keys parameters to fit your run_benchmark inputs"
echo " Step 3: replace the settings parameter to fit your run_benchmark outputs"
echo " Step 4: remove this message"
exit 1

set -e

echo "Running benchmark on test data"
Expand All @@ -31,7 +23,7 @@ publish_dir="resources/results/${RUN_ID}"
# write the parameters to file
cat > /tmp/params.yaml << HERE
input_states: resources/datasets/**/state.yaml
rename_keys: 'input_train:output_train;input_test:output_test;input_solution:output_solution'
rename_keys: 'input_dataset:output_dataset;input_solution:output_solution'
output_state: "state.yaml"
publish_dir: "$publish_dir"
HERE
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12 changes: 2 additions & 10 deletions scripts/run_benchmark/run_full_seqeracloud.sh
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Expand Up @@ -6,14 +6,6 @@ REPO_ROOT=$(git rev-parse --show-toplevel)
# ensure that the command below is run from the root of the repository
cd "$REPO_ROOT"

# remove this when you have implemented the script
echo "TODO: once the 'run_benchmark' workflow has been implemented, update this script to use it."
echo " Step 1: replace 'task_batch_integration' with the name of the task in the following command."
echo " Step 2: replace the rename keys parameters to fit your run_benchmark inputs"
echo " Step 3: replace the settings parameter to fit your run_benchmark outputs"
echo " Step 4: remove this message"
exit 1

set -e

# generate a unique id
Expand All @@ -23,7 +15,7 @@ publish_dir="s3://openproblems-data/resources/task_batch_integration/results/${R
# write the parameters to file
cat > /tmp/params.yaml << HERE
input_states: s3://openproblems-data/resources/task_batch_integration/datasets/**/state.yaml
rename_keys: 'input_train:output_train;input_test:output_test;input_solution:output_solution'
rename_keys: 'input_dataset:output_dataset;input_solution:output_solution'
output_state: "state.yaml"
publish_dir: "$publish_dir"
HERE
Expand All @@ -37,4 +29,4 @@ tw launch https://github.com/openproblems-bio/task_batch_integration.git \
--params-file /tmp/params.yaml \
--entry-name auto \
--config common/nextflow_helpers/labels_tw.config \
--labels task_batch_integration,full
--labels task_batch_integration,full
10 changes: 1 addition & 9 deletions scripts/run_benchmark/run_test_seqeracloud.sh
Original file line number Diff line number Diff line change
Expand Up @@ -6,20 +6,12 @@ REPO_ROOT=$(git rev-parse --show-toplevel)
# ensure that the command below is run from the root of the repository
cd "$REPO_ROOT"

# remove this when you have implemented the script
echo "TODO: once the 'run_benchmark' workflow has been implemented, update this script to use it."
echo " Step 1: replace 'task_batch_integration' with the name of the task in the following command."
echo " Step 2: replace the rename keys parameters to fit your run_benchmark inputs"
echo " Step 3: replace the settings parameter to fit your run_benchmark outputs"
echo " Step 4: remove this message"
exit 1

set -e

# write the parameters to file
cat > /tmp/params.yaml << 'HERE'
input_states: s3://openproblems-data/resources_test/task_batch_integration/**/state.yaml
rename_keys: 'input_train:output_train;input_test:output_test;input_solution:output_solution'
rename_keys: 'input_dataset:output_dataset;input_solution:output_solution'
output_state: "state.yaml"
publish_dir: s3://openproblems-nextflow/temp/task_batch_integration/
HERE
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