reg2 version controlled

openproblems-bio · Aug 14, 2024 · 649e908 · 649e908
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commit 649e908
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Showing 9 changed files with 97 additions and 78 deletions.
diff --git a/params/celloracle_test.yaml b/params/celloracle_test.yaml
diff --git a/params/subsample_200_ridge.yaml b/params/subsample_200_ridge.yaml
@@ -6,7 +6,7 @@ param_list:
     method_id: celloracle
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
     prediction: s3://openproblems-data/resources/grn/grn_models/celloracle.csv
   - id: lognorm_celloracle
@@ -16,7 +16,7 @@ param_list:
     method_id: celloracle
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
     prediction: s3://openproblems-data/resources/grn/grn_models/celloracle.csv
   - id: scgen_pearson_celloracle
@@ -26,7 +26,7 @@ param_list:
     method_id: celloracle
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
     prediction: s3://openproblems-data/resources/grn/grn_models/celloracle.csv
   - id: scgen_lognorm_celloracle
@@ -36,7 +36,7 @@ param_list:
     method_id: celloracle
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
     prediction: s3://openproblems-data/resources/grn/grn_models/celloracle.csv
   - id: seurat_pearson_celloracle
@@ -46,7 +46,7 @@ param_list:
     method_id: celloracle
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
     prediction: s3://openproblems-data/resources/grn/grn_models/celloracle.csv
   - id: seurat_lognorm_celloracle
@@ -56,7 +56,7 @@ param_list:
     method_id: celloracle
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
     prediction: s3://openproblems-data/resources/grn/grn_models/celloracle.csv
   - id: pearson_scenicplus
@@ -66,7 +66,7 @@ param_list:
     method_id: scenicplus
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
     prediction: s3://openproblems-data/resources/grn/grn_models/scenicplus.csv
   - id: lognorm_scenicplus
@@ -76,7 +76,7 @@ param_list:
     method_id: scenicplus
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
     prediction: s3://openproblems-data/resources/grn/grn_models/scenicplus.csv
   - id: scgen_pearson_scenicplus
@@ -86,7 +86,7 @@ param_list:
     method_id: scenicplus
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
     prediction: s3://openproblems-data/resources/grn/grn_models/scenicplus.csv
   - id: scgen_lognorm_scenicplus
@@ -96,7 +96,7 @@ param_list:
     method_id: scenicplus
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
     prediction: s3://openproblems-data/resources/grn/grn_models/scenicplus.csv
   - id: seurat_pearson_scenicplus
@@ -106,7 +106,7 @@ param_list:
     method_id: scenicplus
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
     prediction: s3://openproblems-data/resources/grn/grn_models/scenicplus.csv
   - id: seurat_lognorm_scenicplus
@@ -116,7 +116,7 @@ param_list:
     method_id: scenicplus
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
     prediction: s3://openproblems-data/resources/grn/grn_models/scenicplus.csv
   - id: pearson_figr
@@ -126,7 +126,7 @@ param_list:
     method_id: figr
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
     prediction: s3://openproblems-data/resources/grn/grn_models/figr.csv
   - id: lognorm_figr
@@ -136,7 +136,7 @@ param_list:
     method_id: figr
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
     prediction: s3://openproblems-data/resources/grn/grn_models/figr.csv
   - id: scgen_pearson_figr
@@ -146,7 +146,7 @@ param_list:
     method_id: figr
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
     prediction: s3://openproblems-data/resources/grn/grn_models/figr.csv
   - id: scgen_lognorm_figr
@@ -156,7 +156,7 @@ param_list:
     method_id: figr
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
     prediction: s3://openproblems-data/resources/grn/grn_models/figr.csv
   - id: seurat_pearson_figr
@@ -166,7 +166,7 @@ param_list:
     method_id: figr
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
     prediction: s3://openproblems-data/resources/grn/grn_models/figr.csv
   - id: seurat_lognorm_figr
@@ -176,7 +176,7 @@ param_list:
     method_id: figr
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
     prediction: s3://openproblems-data/resources/grn/grn_models/figr.csv
   - id: pearson_granie
@@ -186,7 +186,7 @@ param_list:
     method_id: granie
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
     prediction: s3://openproblems-data/resources/grn/grn_models/granie.csv
   - id: lognorm_granie
@@ -196,7 +196,7 @@ param_list:
     method_id: granie
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
     prediction: s3://openproblems-data/resources/grn/grn_models/granie.csv
   - id: scgen_pearson_granie
@@ -206,7 +206,7 @@ param_list:
     method_id: granie
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
     prediction: s3://openproblems-data/resources/grn/grn_models/granie.csv
   - id: scgen_lognorm_granie
@@ -216,7 +216,7 @@ param_list:
     method_id: granie
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
     prediction: s3://openproblems-data/resources/grn/grn_models/granie.csv
   - id: seurat_pearson_granie
@@ -226,7 +226,7 @@ param_list:
     method_id: granie
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
     prediction: s3://openproblems-data/resources/grn/grn_models/granie.csv
   - id: seurat_lognorm_granie
@@ -236,7 +236,7 @@ param_list:
     method_id: granie
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
     prediction: s3://openproblems-data/resources/grn/grn_models/granie.csv
   - id: pearson_scglue
@@ -246,7 +246,7 @@ param_list:
     method_id: scglue
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
     prediction: s3://openproblems-data/resources/grn/grn_models/scglue.csv
   - id: lognorm_scglue
@@ -256,7 +256,7 @@ param_list:
     method_id: scglue
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
     prediction: s3://openproblems-data/resources/grn/grn_models/scglue.csv
   - id: scgen_pearson_scglue
@@ -266,7 +266,7 @@ param_list:
     method_id: scglue
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
     prediction: s3://openproblems-data/resources/grn/grn_models/scglue.csv
   - id: scgen_lognorm_scglue
@@ -276,7 +276,7 @@ param_list:
     method_id: scglue
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
     prediction: s3://openproblems-data/resources/grn/grn_models/scglue.csv
   - id: seurat_pearson_scglue
@@ -286,7 +286,7 @@ param_list:
     method_id: scglue
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
     prediction: s3://openproblems-data/resources/grn/grn_models/scglue.csv
   - id: seurat_lognorm_scglue
@@ -296,7 +296,7 @@ param_list:
     method_id: scglue
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
     prediction: s3://openproblems-data/resources/grn/grn_models/scglue.csv
   - id: seurat_lognorm_negative_control
@@ -306,7 +306,7 @@ param_list:
     method_id: negative_control
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
 
 
   - id: pearson_positive_control
@@ -316,7 +316,7 @@ param_list:
     method_id: positive_control
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     tf_all: s3://openproblems-data/resources/grn/prior/tf_all.csv
 
   - id: lognorm_positive_control
@@ -326,7 +326,7 @@ param_list:
     method_id: positive_control
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     tf_all: s3://openproblems-data/resources/grn/prior/tf_all.csv
 
   - id: scgen_pearson_positive_control
@@ -336,7 +336,7 @@ param_list:
     method_id: positive_control
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     tf_all: s3://openproblems-data/resources/grn/prior/tf_all.csv
 
   - id: scgen_lognorm_positive_control
@@ -346,7 +346,7 @@ param_list:
     method_id: positive_control
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     tf_all: s3://openproblems-data/resources/grn/prior/tf_all.csv
 
   - id: seurat_pearson_positive_control
@@ -356,7 +356,7 @@ param_list:
     method_id: positive_control
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     tf_all: s3://openproblems-data/resources/grn/prior/tf_all.csv
 
   - id: seurat_lognorm_positive_control
@@ -366,7 +366,7 @@ param_list:
     method_id: positive_control
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     tf_all: s3://openproblems-data/resources/grn/prior/tf_all.csv
 
 output_state: "state.yaml"

diff --git a/scripts/run_grn_evaluation_tw.sh b/scripts/run_grn_evaluation_tw.sh
@@ -38,7 +38,7 @@ append_entry() {
     method_id: $1
     subsample: $subsample
     max_workers: $max_workers
-    consensus: ${resources_dir}/prior/consensus.json
+    consensus: ${resources_dir}/prior/consensus-num-regulators.json
     ${2:+tf_all: ${resources_dir}/prior/tf_all.csv}
     ${3:+prediction: ${resources_dir}/grn_models/$1.csv}
 HERE
@@ -66,29 +66,21 @@ output_state: "state.yaml"
 publish_dir: "$publish_dir"
 HERE
 
-if [ "$submit" = true ]; then
-  nextflow run . \
-    -main-script  target/nextflow/workflows/run_grn_evaluation/main.nf \
-    -profile docker \
-    -with-trace \
-    -c src/common/nextflow_helpers/labels_ci.config \
-    -params-file ${param_file}
-
-  ./tw-windows-x86_64.exe launch `
-      https://github.com/openproblems-bio/task_grn_benchmark.git `
-      --revision build/main `
-      --pull-latest `
-      --main-script target/nextflow/workflows/run_grn_evaluation/main.nf `
-      --workspace 53907369739130 `
-      --compute-env 6TeIFgV5OY4pJCk8I0bfOh `
-      --params-file ./params/subsample_200_ridge.yaml `
-      --config src/common/nextflow_helpers/labels_tw.config
-
-fi
-
-
-if [ "$read_results" = true ]; then 
-    aws s3 sync s3://openproblems-data/resources/grn/results/${RUN_ID} ./resources/results/${RUN_ID} 
-fi
+# nextflow run . \
+#   -main-script  target/nextflow/workflows/run_grn_evaluation/main.nf \
+#   -profile docker \
+#   -with-trace \
+#   -c src/common/nextflow_helpers/labels_ci.config \
+#   -params-file ${param_file}
+
+./tw-windows-x86_64.exe launch `
+    https://github.com/openproblems-bio/task_grn_benchmark.git `
+    --revision build/main `
+    --pull-latest `
+    --main-script target/nextflow/workflows/run_grn_evaluation/main.nf `
+    --workspace 53907369739130 `
+    --compute-env 6TeIFgV5OY4pJCk8I0bfOh `
+    --params-file ./params/subsample_200_ridge.yaml `
+    --config src/common/nextflow_helpers/labels_tw.config