From 03f7ce80961bbb07093f94c73f41ca61458a89e8 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Sat, 7 Sep 2024 21:53:55 +0200 Subject: [PATCH] update scripts --- README.md | 6 +++--- notebooks/process_results.ipynb | 2 +- runs.ipynb | 4 ++-- scripts/render_readme.sh | 2 +- scripts/repo/run_grn_evaluation_all_layers.sh | 2 +- scripts/run_benchmark_single_omics.sh | 2 +- scripts/run_grn_evaluation.sh | 2 +- scripts/run_pc_vs_nc.sh | 2 +- scripts/run_process_perturbation_tw.sh | 2 +- src/api/task_info.yaml | 4 ++-- src/methods/multi_omics/celloracle_ns/run.sh | 4 ++-- src/methods/multi_omics/granie_ns/run.sh | 2 +- src/methods/multi_omics/scenicplus_ns/run.sh | 2 +- src/methods/multi_omics/scglue_ns/run.sh | 2 +- 14 files changed, 19 insertions(+), 19 deletions(-) diff --git a/README.md b/README.md index 77b8e42cc..f09552e96 100644 --- 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 git@github.com:openproblems-bio/task_grn_benchmark.git +git clone git@github.com: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 index e6345995d..402d643c3 100644 --- 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 index bb1f3e1a0..090a067f8 100644 --- 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 index 176978554..ce792e866 100644 --- 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 index b5e474f6c..f4435c94f 100644 --- 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 index 1860e9a35..fa7d88368 100644 --- 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 index 6cc7011cf..eeec944a1 100644 --- 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 index 055d43f98..cc2e0e5f5 100644 --- a/scripts/run_pc_vs_nc.sh +++ b/scripts/run_pc_vs_nc.sh @@ -72,7 +72,7 @@ HERE # -params-file ${param_file} # ./tw-windows-x86_64.exe launch ` -# https://github.com/openproblems-bio/task_grn_benchmark.git ` +# https://github.com/openproblems-bio/task_grn_inference.git ` # --revision build/main ` # --pull-latest ` # --main-script target/nextflow/workflows/run_grn_evaluation/main.nf ` diff --git a/scripts/run_process_perturbation_tw.sh b/scripts/run_process_perturbation_tw.sh index fe2d6e2ff..5f92d1631 100644 --- a/scripts/run_process_perturbation_tw.sh +++ b/scripts/run_process_perturbation_tw.sh @@ -14,7 +14,7 @@ publish_dir: "$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 index 700384fc8..32f23c6e5 100644 --- a/src/api/task_info.yaml +++ b/src/api/task_info.yaml @@ -19,9 +19,9 @@ readme: | ## Download resources ```bash - git clone git@github.com:openproblems-bio/task_grn_benchmark.git + git clone git@github.com: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 index 2af30c8ff..bd5b3160a 100644 --- 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 index c4abb32db..9ee2b676f 100644 --- 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 index 5edebabce..eef0d8c0a 100644 --- 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 index 4371b8197..6677eb0d3 100644 --- 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 `