update scripts

openproblems-bio · Sep 7, 2024 · 03f7ce8 · 03f7ce8
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Showing 14 changed files with 19 additions and 19 deletions.
diff --git a/README.md b/README.md
@@ -9,7 +9,7 @@ Do not edit this file directly.
 Benchmarking GRN inference methods
 
 Path to source:
-[`src`](https://github.com/openproblems-bio/task_grn_benchmark/tree/main/src)
+[`src`](https://github.com/openproblems-bio/task_grn_inference/tree/main/src)
 
 ## README
 
@@ -22,9 +22,9 @@ to install the required dependencies.
 ## Download resources
 
 ``` bash
-git clone [email protected]:openproblems-bio/task_grn_benchmark.git
+git clone [email protected]:openproblems-bio/task_grn_inference.git
 
-cd task_grn_benchmark
+cd task_grn_inference
 
 # download resources
 scripts/download_resources.sh

diff --git a/notebooks/process_results.ipynb b/notebooks/process_results.ipynb
@@ -51,7 +51,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "base_folder = '../../task_grn_benchmark/resources/results/subsample_200_gb/'"
+    "base_folder = '../../task_grn_inference/resources/results/subsample_200_gb/'"
    ]
   },
   {

diff --git a/runs.ipynb b/runs.ipynb
@@ -32,7 +32,7 @@
       "temporaryFolder: /tmp/viash_hub_repo10489538114835231235 uri: https://github.com/openproblems-bio/openproblems-v2.git\n",
       "Cloning into '.'...\n",
       "checkout out: List(git, checkout, origin/main_build, --, .) 0 \n",
-      "\u001b[37mExporting run_grn_evaluation (workflows) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/workflows/run_grn_evaluation\u001b[0m\n",
+      "\u001b[37mExporting run_grn_evaluation (workflows) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_inference/target/nextflow/workflows/run_grn_evaluation\u001b[0m\n",
       "\u001b[33mNot all configs built successfully\u001b[0m\n",
       "\u001b[33m  39 configs were disabled\u001b[0m\n",
       "\u001b[32m  1/1 configs built successfully\u001b[0m\n"
@@ -90,7 +90,7 @@
       "temporaryFolder: /tmp/viash_hub_repo10268443552668753296 uri: https://github.com/openproblems-bio/openproblems-v2.git\n",
       "Cloning into '.'...\n",
       "checkout out: List(git, checkout, origin/main_build, --, .) 0 \n",
-      "\u001b[37mExporting run_robustness_analysis (workflows) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/workflows/run_robustness_analysis\u001b[0m\n",
+      "\u001b[37mExporting run_robustness_analysis (workflows) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_inference/target/nextflow/workflows/run_robustness_analysis\u001b[0m\n",
       "\u001b[33mNot all configs built successfully\u001b[0m\n",
       "\u001b[33m  39 configs were disabled\u001b[0m\n",
       "\u001b[32m  1/1 configs built successfully\u001b[0m\n"

diff --git a/scripts/render_readme.sh b/scripts/render_readme.sh
@@ -7,5 +7,5 @@ set -e
 ../openproblems-v2/bin/create_task_readme \
   --task "grn_benchmark" \
   --task_dir "src" \
-  --github_url "https://github.com/openproblems-bio/task_grn_benchmark/tree/main/" \
+  --github_url "https://github.com/openproblems-bio/task_grn_inference/tree/main/" \
   --output "README.md"
diff --git a/scripts/repo/run_grn_evaluation_all_layers.sh b/scripts/repo/run_grn_evaluation_all_layers.sh
@@ -77,7 +77,7 @@ HERE
 #   -params-file ${param_file}
 
 # ./tw-windows-x86_64.exe launch `
-#     https://github.com/openproblems-bio/task_grn_benchmark.git `
+#     https://github.com/openproblems-bio/task_grn_inference.git `
 #     --revision build/main `
 #     --pull-latest `
 #     --main-script target/nextflow/workflows/run_grn_evaluation/main.nf `

diff --git a/scripts/run_benchmark_single_omics.sh b/scripts/run_benchmark_single_omics.sh
@@ -39,7 +39,7 @@ HERE
 #   -params-file ${param_file}
 
 # ./tw-windows-x86_64.exe launch `
-#     https://github.com/openproblems-bio/task_grn_benchmark.git `
+#     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 `

diff --git a/scripts/run_grn_evaluation.sh b/scripts/run_grn_evaluation.sh
@@ -86,7 +86,7 @@ nextflow run . \
   -params-file ${param_file}
 
 # ./tw-windows-x86_64.exe launch `
-#     https://github.com/openproblems-bio/task_grn_benchmark.git `
+#     https://github.com/openproblems-bio/task_grn_inference.git `
 #     --revision build/main `
 #     --pull-latest `
 #     --main-script target/nextflow/workflows/run_grn_evaluation/main.nf `

diff --git a/scripts/run_pc_vs_nc.sh b/scripts/run_pc_vs_nc.sh
@@ -72,7 +72,7 @@ HERE
 #   -params-file ${param_file}
 
 # ./tw-windows-x86_64.exe launch `
-#     https://github.com/openproblems-bio/task_grn_benchmark.git `
+#     https://github.com/openproblems-bio/task_grn_inference.git `
 #     --revision build/main `
 #     --pull-latest `
 #     --main-script target/nextflow/workflows/run_grn_evaluation/main.nf `

diff --git a/scripts/run_process_perturbation_tw.sh b/scripts/run_process_perturbation_tw.sh
@@ -14,7 +14,7 @@ publish_dir: "$publish_dir"
 HERE
 
 
-  ./tw-windows-x86_64.exe launch  https://github.com/openproblems-bio/task_grn_benchmark.git `
+  ./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/process_perturbation/main.nf `
      --workspace 53907369739130 --compute-env 6TeIFgV5OY4pJCk8I0bfOh `

diff --git a/src/api/task_info.yaml b/src/api/task_info.yaml
@@ -19,9 +19,9 @@ readme: |
 
   ## Download resources
   ```bash
-  git clone [email protected]:openproblems-bio/task_grn_benchmark.git
+  git clone [email protected]:openproblems-bio/task_grn_inference.git
 
-  cd task_grn_benchmark
+  cd task_grn_inference
   
   # download resources
   scripts/download_resources.sh

diff --git a/src/methods/multi_omics/celloracle_ns/run.sh b/src/methods/multi_omics/celloracle_ns/run.sh
@@ -33,7 +33,7 @@ if [ "$submit" = true ]; then
 
 
   ./tw-windows-x86_64.exe launch `
-        https://github.com/openproblems-bio/task_grn_benchmark.git `
+        https://github.com/openproblems-bio/task_grn_inference.git `
         --revision build/main `
         --pull-latest `
         --main-script target/nextflow/workflows/run_grn_inference/main.nf `
@@ -51,7 +51,7 @@ fi
 
 
 ./tw-windows-x86_64.exe launch `
-       https://github.com/openproblems-bio/task_grn_benchmark.git `
+       https://github.com/openproblems-bio/task_grn_inference.git `
        --revision build/main `
        --pull-latest `
        --main-script target/nextflow/workflows/grn_inference_celloracle/main.nf `

diff --git a/src/methods/multi_omics/granie_ns/run.sh b/src/methods/multi_omics/granie_ns/run.sh
@@ -25,7 +25,7 @@ HERE
 
 
 ./tw-windows-x86_64.exe launch `
-       https://github.com/openproblems-bio/task_grn_benchmark.git `
+       https://github.com/openproblems-bio/task_grn_inference.git `
        --revision build/main `
        --pull-latest `
        --main-script target/nextflow/workflows/grn_inference_scglue/main.nf `

diff --git a/src/methods/multi_omics/scenicplus_ns/run.sh b/src/methods/multi_omics/scenicplus_ns/run.sh
@@ -32,7 +32,7 @@ nextflow run . \
 
 
 # ./tw-windows-x86_64.exe launch `
-#       https://github.com/openproblems-bio/task_grn_benchmark.git `
+#       https://github.com/openproblems-bio/task_grn_inference.git `
 #       --revision build/main `
 #       --pull-latest `
 #       --main-script target/nextflow/workflows/grn_inference_scenicplus/main.nf `

diff --git a/src/methods/multi_omics/scglue_ns/run.sh b/src/methods/multi_omics/scglue_ns/run.sh
@@ -24,7 +24,7 @@ HERE
 
 
 # ./tw-windows-x86_64.exe launch `
-#        https://github.com/openproblems-bio/task_grn_benchmark.git `
+#        https://github.com/openproblems-bio/task_grn_inference.git `
 #        --revision build/main `
 #        --pull-latest `
 #        --main-script target/nextflow/workflows/grn_inference_scglue/main.nf `