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fix(dependencies): rename PRScs csa ref dir to match rule output (#169) #170

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Merged
opain merged 5 commits into from
Jun 24, 2026
Merged

fix(dependencies): rename PRScs csa ref dir to match rule output (#169) #170

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3b1225e
fix(dependencies): rename PRScs csa ref dir to match rule output (#169)
Jun 24, 2026
72b4d1f
ci: install libuv1-dev and fail-fast on missing R deps in quick tests
Jun 24, 2026
1642371
fix backslash error in r code for action
Jun 24, 2026
aa19d4c
fix whitespace error in r code for action
Jun 24, 2026
8960f86
fix indentation error in r code for action
Jun 24, 2026
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13 changes: 9 additions & 4 deletions .github/workflows/run_quick_tests.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -34,12 +34,17 @@ jobs:
else
echo "BRANCH_NAME=${{ github.ref_name }}" >> $GITHUB_ENV
fi


- name: Install system dependencies
run: |
apt-get update
# libuv1-dev: required to compile 'fs' (>= 2.x), a transitive dep of testthat.
# zlib1g-dev: enables data.table fwrite compression (otherwise NOZLIB).
apt-get install -y libuv1-dev zlib1g-dev

- name: Install R dependencies
run: |
Rscript -e 'install.packages("testthat", repos="https://cran.rstudio.com/")'
Rscript -e 'install.packages("data.table", repos="https://cran.rstudio.com/")'
Rscript -e 'install.packages("R.utils", repos="https://cran.rstudio.com/")'
Rscript -e 'pkgs <- c("testthat", "data.table", "R.utils"); install.packages(pkgs, repos = "https://cran.rstudio.com/"); missing <- pkgs[!pkgs %in% rownames(installed.packages())]; if (length(missing)) stop("Failed to install: ", paste(missing, collapse = ", "))'

- name: Run tests
run: |
Expand Down
8 changes: 8 additions & 0 deletions pipeline/rules/dependencies.smk
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Expand Up @@ -728,6 +728,10 @@ rule download_prscs_ref_ukb:
rm -r -f {resdir}/data/prscs_ref/ukbb/ldblk_ukbb_{wildcards.population}; \
wget --no-check-certificate -O {resdir}/data/prscs_ref/ukbb/ldblk_ukbb_{wildcards.population}.tar.gz {params.url}; \
tar -zxvf {resdir}/data/prscs_ref/ukbb/ldblk_ukbb_{wildcards.population}.tar.gz -C {resdir}/data/prscs_ref/ukbb/; \
extracted_dir=$(tar -tzf {resdir}/data/prscs_ref/ukbb/ldblk_ukbb_{wildcards.population}.tar.gz | head -1 | cut -d/ -f1); \
if [ "$extracted_dir" != "ldblk_ukbb_{wildcards.population}" ]; then \
mv {resdir}/data/prscs_ref/ukbb/"$extracted_dir" {resdir}/data/prscs_ref/ukbb/ldblk_ukbb_{wildcards.population}; \
fi; \
rm {resdir}/data/prscs_ref/ukbb/ldblk_ukbb_{wildcards.population}.tar.gz
}} > {log} 2>&1
"""
Expand Down Expand Up @@ -761,6 +765,10 @@ rule download_prscs_ref_1kg:
rm -r -f {resdir}/data/prscs_ref/1kg/ldblk_1kg_{wildcards.population}; \
wget --no-check-certificate -O {resdir}/data/prscs_ref/1kg/ldblk_1kg_{wildcards.population}.tar.gz {params.url}; \
tar -zxvf {resdir}/data/prscs_ref/1kg/ldblk_1kg_{wildcards.population}.tar.gz -C {resdir}/data/prscs_ref/1kg/; \
extracted_dir=$(tar -tzf {resdir}/data/prscs_ref/1kg/ldblk_1kg_{wildcards.population}.tar.gz | head -1 | cut -d/ -f1); \
if [ "$extracted_dir" != "ldblk_1kg_{wildcards.population}" ]; then \
mv {resdir}/data/prscs_ref/1kg/"$extracted_dir" {resdir}/data/prscs_ref/1kg/ldblk_1kg_{wildcards.population}; \
fi; \
rm {resdir}/data/prscs_ref/1kg/ldblk_1kg_{wildcards.population}.tar.gz
}} > {log} 2>&1
"""
Expand Down
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