diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index 1610dca..f422c04 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -57,10 +57,9 @@ jobs: - name: Run Snakemake workflow for DMMMs shell: bash --login {0} run: snakemake --cores 4 --configfile configs/dmmm.yaml --show-failed-logs -s spras/Snakefile - # TODO: re-enable PRAs once RN/synthetic data PRs are merged. - # - name: Run Snakemake workflow for PRAs - # shell: bash --login {0} - # run: snakemake --cores 1 --configfile configs/pra.yaml --show-failed-logs -s spras/Snakefile + - name: Run Snakemake workflow for PRAs + shell: bash --login {0} + run: snakemake --cores 1 --configfile configs/pra.yaml --show-failed-logs -s spras/Snakefile - name: Setup PNPM uses: pnpm/action-setup@v4 with: diff --git a/datasets/rn-muscle-skeletal/Snakefile b/datasets/rn-muscle-skeletal/Snakefile index 3f59640..c8ab720 100644 --- a/datasets/rn-muscle-skeletal/Snakefile +++ b/datasets/rn-muscle-skeletal/Snakefile @@ -8,7 +8,7 @@ rule get_interactome: output: "raw/Muscle_Skeletal-Dec2018.tsv" shell: - "uv run gdown https://drive.google.com/file/d/1mkvWrCkeDz1DU-PSEsRaGNM20EcpVLwE/view?usp=sharing -O raw/Muscle_Skeletal-Dec2018.tsv" + "uv run gdown https://drive.google.com/uc?id=1mkvWrCkeDz1DU-PSEsRaGNM20EcpVLwE -O raw/Muscle_Skeletal-Dec2018.tsv" rule process_interactome: input: diff --git a/run_snakemake.sh b/run_snakemake.sh index 16ce288..4ca771f 100755 --- a/run_snakemake.sh +++ b/run_snakemake.sh @@ -15,6 +15,7 @@ cd "$(dirname "$0")" main() { uv run snakemake --cores 1 -d datasets/yeast-osmotic-stress -s datasets/yeast-osmotic-stress/Snakefile uv run snakemake --cores 1 -d datasets/hiv -s datasets/hiv/Snakefile + uv run snakemake --cores 1 -d datasets/rn-muscle-skeletal -s datasets/rn-muscle-skeletal/Snakefile } main "$@"