portia max link added

scripts/run_benchmark_single_omics.sh

@@ -1,20 +1,19 @@
 #!/bin/bash
 
 # RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)"
-RUN_ID="single_omics_inference"
-resources_dir="./resources_test/"
-# resources_dir="s3://openproblems-data/resources/grn"
+RUN_ID="benchmark_donor_0_default"
+# resources_dir="./resources_test/"
+resources_dir="s3://openproblems-data/resources/grn"
 publish_dir="${resources_dir}/results/${RUN_ID}"
 
-
 reg_type=ridge
 subsample=-2
 max_workers=10
 layer='scgen_pearson'
-metric_ids="[regression_1]"
-cell_type_specific=true #for controls
+metric_ids="[regression_1, regression_2]"
+cell_type_specific=false #for controls
 # method_ids="[tigress, ennet, scsgl, pidc]"
-method_ids="[pearson_corr, pearson_causal, positive_control]"
+method_ids="[pearson_corr, pearson_causal, positive_control, portia, grnboost2]"
 
 param_file="./params/${RUN_ID}.yaml"
 
@@ -25,8 +24,8 @@ param_list:
     metric_ids: $metric_ids
     method_ids: $method_ids
     perturbation_data: ${resources_dir}/grn-benchmark/perturbation_data.h5ad
-    multiomics_rna: ${resources_dir}/grn-benchmark/multiomics_rna.h5ad
-    multiomics_atac: ${resources_dir}/grn-benchmark/multiomics_atac.h5ad
+    multiomics_rna: ${resources_dir}/grn-benchmark/multiomics_rna_0.h5ad
+    multiomics_atac: ${resources_dir}/grn-benchmark/multiomics_atac_0.h5ad
     reg_type: $reg_type
     subsample: $subsample
     max_workers: $max_workers
@@ -39,27 +38,27 @@ output_state: "state.yaml"
 publish_dir: "$publish_dir"
 HERE
 
-nextflow run . \
-  -main-script  target/nextflow/workflows/run_benchmark_single_omics/main.nf \
-  -profile docker \
-  -with-trace \
-  -c src/common/nextflow_helpers/labels_ci.config \
-  -params-file ${param_file}
+# nextflow run . \
+#   -main-script  target/nextflow/workflows/run_benchmark/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_inference.git `
-#     --revision build/main `
-#     --pull-latest `
-#     --main-script target/nextflow/workflows/run_benchmark_single_omics/main.nf `
-#     --workspace 53907369739130 `
-#     --compute-env 6TeIFgV5OY4pJCk8I0bfOh `
-#     --params-file ./params/single_omics_inference.yaml `
-#     --config src/common/nextflow_helpers/labels_tw.config
+./tw-windows-x86_64.exe launch `
+    https://github.com/openproblems-bio/task_grn_inference.git `
+    --revision build/main `
+    --pull-latest `
+    --main-script target/nextflow/workflows/run_benchmark/main.nf `
+    --workspace 53907369739130 `
+    --compute-env 6TeIFgV5OY4pJCk8I0bfOh `
+    --params-file ./params/benchmark_donor_0_default.yaml `
+    --config src/common/nextflow_helpers/labels_tw.config
 
 # ./tw launch https://github.com/openproblems-bio/task_grn_inference \
 #   --revision build/main \
 #   --pull-latest \
-#   --main-script target/nextflow/workflows/run_benchmark_single_omics/main.nf \
+#   --main-script target/nextflow/workflows/run_benchmark/main.nf \
 #   --workspace 53907369739130 \
 #   --compute-env 6TeIFgV5OY4pJCk8I0bfOh \
 #   --params-file ${param_file} \

src/methods/multi_omics/scenicplus/config.vsh.yaml

@@ -1,4 +1,4 @@
-__merge__: ../../../api/comp_method_mo.yaml
+__merge__: ../../../api/comp_method.yaml
 
 
 functionality:
@@ -39,10 +39,12 @@ functionality:
 
 platforms:
   - type: docker
-    image: apassemi/scenicplus:1.0.1
-    setup:
-      - type: python
-        packages: [ flatbuffers ]
+    # image: apassemi/scenicplus:1.0.1
+    # image: vanallenlab/scenicplus_x86_64:initial
+    image: aertslab/pyscenic:0.12.1
+    # setup:
+    #   - type: python
+    #     packages: [ flatbuffers ]
   - type: native
   - type: nextflow
     directives:

src/methods/multi_omics/scenicplus/script.py

@@ -1,17 +1,17 @@
 import os
-import sys
-import yaml
-import pickle
-import tempfile
-import contextlib
-import hashlib
-import shutil
-import requests
-import traceback
-import subprocess
-import gc
-import gzip
-import tarfile
+# import sys
+# import yaml
+# import pickle
+# import tempfile
+# import contextlib
+# import hashlib
+# import shutil
+# import requests
+# import traceback
+# import subprocess
+# import gc
+# import gzip
+# import tarfile
 # from urllib.request import urlretrieve
 
 # import numpy as np
@@ -59,8 +59,10 @@
 # setattr(pycisTopic.loom, 'TSNE', TSNE)
 # os.environ['MALLET_MEMORY'] = '200G'
 
-atac_dir = f"output/scenicplus/atac/"
-os.makedirs(atac_dir)
+atac_dir = f"output/gulack/"
+print(atac_dir)
+os.makedirs(atac_dir, exist_ok=True)
+os.makedirs(f'{atac_dir}/atac', exist_ok=True)
 raise ValueError('here')
 
 # Get list of samples (e.g., donors)

src/methods/single_omics/portia/script.py

@@ -41,9 +41,10 @@ def infer_grn(X, gene_names):
   dataset = pt.GeneExpressionDataset()
   for exp_id, data in enumerate(X):
       dataset.add(pt.Experiment(exp_id, data))
+
   M_bar = pt.run(dataset, method='no-transform')
-
-  ranked_scores = pt.rank_scores(M_bar, gene_names)
+  limit = min([10000000, X.size])
+  ranked_scores = pt.rank_scores(M_bar, gene_names, limit=limit)
   sources, targets, weights = zip(*[(gene_a, gene_b, score) for gene_a, gene_b, score in ranked_scores])
 
   grn = pd.DataFrame({'source':sources, 'target':targets, 'weight':weights})

src/methods/single_omics/portia/test.sh

@@ -1 +1,4 @@
-viash run src/methods/single_omics/portia/config.vsh.yaml -- --multiomics_rna resources/grn-benchmark/multiomics_rna_0.h5ad --tf_all resources/prior/tf_all.csv --prediction output/portia/prediction.csv
+viash run src/methods/single_omics/portia/config.vsh.yaml -- --multiomics_rna resources_test/grn-benchmark/multiomics_rna.h5ad \
+    --tf_all resources/prior/tf_all.csv \
+    --prediction output/portia/prediction.csv \
+    --cell_type_specific false

src/methods/single_omics/scenic/config.vsh.yaml

@@ -30,8 +30,7 @@ functionality:
 
 platforms:
   - type: docker
-    # image: aertslab/pyscenic:0.12.1
-    image: janursa/scenicplus:19-08-2024
+    image: aertslab/pyscenic:0.12.1
     setup:
     #   - type: docker
     #     run: |