update scripts

openproblems-bio · Jul 16, 2024 · d9f62f7 · d9f62f7
1 parent 02def51
commit d9f62f7
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Showing 3 changed files with 6 additions and 9 deletions.
diff --git a/scripts/datasets/neurips-2023-data.sh b/scripts/datasets/neurips-2023-data.sh
@@ -45,10 +45,7 @@ viash run src/metrics/mean_rowwise_error/config.vsh.yaml -- \
   --output "$OUT/score.h5ad"
 
 echo ">> Uploading results to S3"
-# aws s3 sync --profile op2 \
-#   --include "*" \
-#   --exclude "neurips-2023-raw/*" \
-#   --exclude "neurips-2023-public/*" \
-#   "resources" \
-#   "s3://openproblems-bio/public/neurips-2023-competition/workflow-resources/" \
+# aws s3 sync --profile op \
+#   "resources/datasets" \
+#   "s3://openproblems-data/resources/perturbation_prediction/datasets/" \
 #   --delete --dryrun
diff --git a/scripts/run_benchmark_test.sh b/scripts/run_benchmark_test.sh
@@ -25,4 +25,4 @@ nextflow run . \
   -main-script target/nextflow/workflows/run_benchmark/main.nf \
   -profile docker \
   -resume \
-  -params-file /tmp/params.yaml
+  -params-file /tmp/params.yaml
diff --git a/scripts/run_benchmark_tw.sh b/scripts/run_benchmark_tw.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)"
-resources_dir="s3://openproblems-bio/public/neurips-2023-competition/workflow-resources"
+resources_dir="s3://openproblems-data/resources/perturbation_prediction/datasets/"
 publish_dir="s3://openproblems-data/resources/perturbation_prediction/results/${RUN_ID}"
 
 cat > /tmp/params.yaml << HERE
@@ -20,7 +20,7 @@ output_state: "state.yaml"
 publish_dir: "$publish_dir"
 HERE
 
-tw launch https://github.com/openproblems-bio/task_perturbation_prediction.git \
+tw launch openproblems-bio/task_perturbation_prediction \
   --revision main_build \
   --pull-latest \
   --main-script target/nextflow/workflows/run_benchmark/main.nf \