From e935f356e228e920243902b1a666d3081d1e43e5 Mon Sep 17 00:00:00 2001 From: matin Date: Wed, 24 Jul 2024 20:38:55 +0100 Subject: [PATCH] scglue: test-2 --- scripts/download_resources_test.sh | 12 +++++++ src/api/file_multiomics_atac_h5ad.yaml | 2 +- src/api/file_multiomics_rna_h5ad.yaml | 2 +- .../{config.vsh.yaml => config.novsh.yaml} | 0 .../{config.vsh.yaml => config.novsh.yaml} | 0 .../{scglue => dummy}/config.novsh.yaml | 20 ++++++------ src/methods/{dummy => scglue}/config.vsh.yaml | 31 +++++++++---------- .../{config.vsh.yaml => config.novsh.yaml} | 0 8 files changed, 38 insertions(+), 29 deletions(-) create mode 100644 scripts/download_resources_test.sh rename src/control_methods/negative_control/{config.vsh.yaml => config.novsh.yaml} (100%) rename src/control_methods/positive_control/{config.vsh.yaml => config.novsh.yaml} (100%) rename src/methods/{scglue => dummy}/config.novsh.yaml (80%) rename src/methods/{dummy => scglue}/config.vsh.yaml (72%) rename src/metrics/regression_1/{config.vsh.yaml => config.novsh.yaml} (100%) diff --git a/scripts/download_resources_test.sh b/scripts/download_resources_test.sh new file mode 100644 index 000000000..b4fc33e4d --- /dev/null +++ b/scripts/download_resources_test.sh @@ -0,0 +1,12 @@ +#!/bin/bash + +set -e + +echo ">> Downloading resources" + +viash run src/common/sync_test_resources/config.vsh.yaml -- \ + --input "s3://openproblems-data/resources_test/grn/" \ + --output "resources_test" \ + --delete + + diff --git a/src/api/file_multiomics_atac_h5ad.yaml b/src/api/file_multiomics_atac_h5ad.yaml index 3acf53026..de891bf67 100644 --- a/src/api/file_multiomics_atac_h5ad.yaml +++ b/src/api/file_multiomics_atac_h5ad.yaml @@ -1,5 +1,5 @@ type: file -example: resources_test/grn-benchmark/multiomics_atac.h5ad +example: resources/grn-benchmark/multiomics_atac.h5ad info: label: multiomics atac summary: "Peak data for multiomics data." diff --git a/src/api/file_multiomics_rna_h5ad.yaml b/src/api/file_multiomics_rna_h5ad.yaml index 8197a74bf..061601e15 100644 --- a/src/api/file_multiomics_rna_h5ad.yaml +++ b/src/api/file_multiomics_rna_h5ad.yaml @@ -1,5 +1,5 @@ type: file -example: resources_test/grn-benchmark/multiomics_rna.h5ad +example: resources/grn-benchmark/multiomics_rna.h5ad info: label: multiomics rna summary: "RNA expression for multiomics data." diff --git a/src/control_methods/negative_control/config.vsh.yaml b/src/control_methods/negative_control/config.novsh.yaml similarity index 100% rename from src/control_methods/negative_control/config.vsh.yaml rename to src/control_methods/negative_control/config.novsh.yaml diff --git a/src/control_methods/positive_control/config.vsh.yaml b/src/control_methods/positive_control/config.novsh.yaml similarity index 100% rename from src/control_methods/positive_control/config.vsh.yaml rename to src/control_methods/positive_control/config.novsh.yaml diff --git a/src/methods/scglue/config.novsh.yaml b/src/methods/dummy/config.novsh.yaml similarity index 80% rename from src/methods/scglue/config.novsh.yaml rename to src/methods/dummy/config.novsh.yaml index be1addca1..0ce454812 100644 --- a/src/methods/scglue/config.novsh.yaml +++ b/src/methods/dummy/config.novsh.yaml @@ -1,13 +1,14 @@ __merge__: ../../api/comp_method.yaml functionality: - name: scglue + name: dummy info: - label: scglue - summary: "GRN inference using scglue" + label: dummy + summary: "FILL IN: A one sentence summary of this method." description: | - GRN inference using scglue. - documentation_url: https://scglue.readthedocs.io/ + A dummy method that contains the format of a real GRN inference method. + documentation_url: https://url.to/the/documentation + repository_url: https://github.com/organisation/repository arguments: - name: --multiomics_rna __merge__: ../../api/file_multiomics_rna_h5ad.yaml @@ -62,20 +63,17 @@ functionality: type: integer direction: input default: 4 - + resources: - type: python_script path: script.py - - path: main.py platforms: - type: docker - image: nvcr.io/nvidia/pytorch:24.06-py3 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python - packages: [ scglue==0.3.2, pyscenic==0.12.1, numpy==1.23.4, scanpy, networkx, pyarrow, cytoolz, scikit-misc, cuda-python] - - type: apt - packages: [bedtools] + packages: [ ] - type: native - type: nextflow diff --git a/src/methods/dummy/config.vsh.yaml b/src/methods/scglue/config.vsh.yaml similarity index 72% rename from src/methods/dummy/config.vsh.yaml rename to src/methods/scglue/config.vsh.yaml index 109110b24..50fa3c45d 100644 --- a/src/methods/dummy/config.vsh.yaml +++ b/src/methods/scglue/config.vsh.yaml @@ -1,14 +1,13 @@ -# __merge__: ../../api/comp_method.yaml +__merge__: ../../api/comp_method.yaml functionality: - name: dummy + name: scglue info: - label: dummy - summary: "FILL IN: A one sentence summary of this method." + label: scglue + summary: "GRN inference using scglue" description: | - A dummy method that contains the format of a real GRN inference method. - documentation_url: https://url.to/the/documentation - repository_url: https://github.com/organisation/repository + GRN inference using scglue. + documentation_url: https://scglue.readthedocs.io/ arguments: - name: --multiomics_rna __merge__: ../../api/file_multiomics_rna_h5ad.yaml @@ -63,21 +62,21 @@ functionality: type: integer direction: input default: 4 - test_resources: - - type: python_script - path: /src/common/component_tests/run_and_check_output.py - - path: /resources/grn-benchmark - dest: resources/grn-benchmark + resources: - type: python_script path: script.py + - path: main.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 - setup: - - type: python - packages: [ ] + image: janursa/scglue:19-08-2024: + # image: nvcr.io/nvidia/pytorch:24.06-py3 + # setup: + # - type: python + # packages: [ scglue==0.3.2, pyscenic==0.12.1, numpy==1.23.4, scanpy, networkx, pyarrow, cytoolz, scikit-misc, cuda-python] + # - type: apt + # packages: [bedtools] - type: native - type: nextflow diff --git a/src/metrics/regression_1/config.vsh.yaml b/src/metrics/regression_1/config.novsh.yaml similarity index 100% rename from src/metrics/regression_1/config.vsh.yaml rename to src/metrics/regression_1/config.novsh.yaml