From 8bfb5c0bd2cb6959b1cedf64eb7cc033b72724f4 Mon Sep 17 00:00:00 2001 From: Daniel Nachun Date: Fri, 31 Jul 2026 11:32:48 -0700 Subject: [PATCH 1/5] add package and linux-aarch64 --- .github/workflows/ci.yml | 39 ++++++++++++--------------------------- envs/full_packages.txt | 34 ++++++++++++++++++++++++++++++++-- 2 files changed, 44 insertions(+), 29 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index bfbd1bc..554b98c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -4,35 +4,20 @@ on: pull_request: jobs: - linux-64: - runs-on: ubuntu-latest - strategy: - fail-fast: false - - steps: - - name: Checkout pull request branch - uses: actions/checkout@v4 - with: - fetch-depth: 0 - - - name: Setup pixi - uses: prefix-dev/setup-pixi@v0.8.3 - with: - run-install: false + concurrency: + group: ci-${{ github.ref }} + cancel-in-progress: true - - name: Run setup script - shell: pixi exec --spec sed -- bash -e {0} - env: - INSTALL_TYPE: full - run: | - sed -i "s?main?${{ github.event.pull_request.head.ref }}?g" pixi-setup.sh - sed -i "s?init.sh | bash?init.sh | sed 's,main,${{ github.event.pull_request.head.ref }},g' | bash?" pixi-setup.sh - printf "\n1\n" | ./pixi-setup.sh - - osx-arm64: - runs-on: macos-14 +jobs: + ci: + name: CI (${{ matrix.platform }} / ${{ matrix.environment }}) + runs-on: ${{ matrix.runner }} + env: + CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} strategy: fail-fast: false + matrix: + runner: [ubuntu-latest, macos-latest, ubuntu-24.04-arm] steps: - name: Checkout pull request branch @@ -46,7 +31,7 @@ jobs: run-install: false - name: Run setup script - shell: pixi exec --spec sed -- zsh -e {0} + shell: pixi exec --spec sed --spec bash -- bash -e {0} env: INSTALL_TYPE: full run: | diff --git a/envs/full_packages.txt b/envs/full_packages.txt index d9f39ad..f3adc9f 100644 --- a/envs/full_packages.txt +++ b/envs/full_packages.txt @@ -2,11 +2,13 @@ # Sections: [global], [global_linux], [python], [r] # [global] +apex ark awscli bamtools bcftools bedtools +coreutils curl deeptools diffutils @@ -16,13 +18,16 @@ fastp findutils gatk4 gawk +gcta gffread git go-ghq +gregor grep gtex-pipeline-gene_model gtex-pipeline-qtl gtex-pipeline-rnaseq +gzip htslib king kent-tools @@ -33,11 +38,12 @@ pandoc parallel perl picard +polyfun plink plink2 python=3.12 quantas -r-base=4.4 +r-base=4.5 regtools ripgrep rnaseqc @@ -48,6 +54,7 @@ sed snpeff snpsift star +suppa tree trimmomatic unzip @@ -58,7 +65,6 @@ wget # [global_linux] code-server fastlmmc -gcta ldstore procps-ng regenie @@ -107,6 +113,9 @@ pillow ptpython pyarrow pybigwig +pytest +pytest-cov +pytest-xdist python-ldstore python-lsp-server qvalue @@ -119,6 +128,7 @@ tqdm tensorqtl wand widgetsnbextension +setuptools<82 sos sos-bash sos-notebook @@ -127,13 +137,20 @@ sos-r # [r] bioconductor-annotationdbi +bioconductor-annotationhub +bioconductor-biomart bioconductor-clusterprofiler bioconductor-edger bioconductor-genomeinfodb bioconductor-genomeinfodbdata bioconductor-illuminahumanmethylation450kmanifest bioconductor-illuminahumanmethylationepicmanifest +bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 +bioconductor-impute +bioconductor-intact bioconductor-limma +bioconductor-minfi +bioconductor-minfidata bioconductor-mofa2 bioconductor-org.hs.eg.db bioconductor-pcatools @@ -142,6 +159,9 @@ bioconductor-psichomics bioconductor-qvalue bioconductor-sesame bioconductor-sesamedata +bioconductor-singlecelltk +bioconductor-sva +bioconductor-txdbmaker r-abind r-argparser r-arrow @@ -149,25 +169,33 @@ r-ape r-bedtoolsr r-biocmanager r-bitops +r-catboost r-catools r-complexupset r-corrplot +r-covr r-devtools r-flashpcar r-genio +r-ggnewscale r-gplots r-gtools r-gwasrapidd r-httpgd r-hudson r-igraph +r-itertools r-irkernel +r-jackstraw +r-jsonlite r-languageserver r-mediation r-missforest r-optparse r-pacman r-pecotmr +r-peer +r-pkgdown r-profvis r-qqman r-qrank @@ -175,5 +203,7 @@ r-quantreg r-rgl r-rmtstat r-seurat +r-testthat r-tidyverse r-watershedr +r-xgboost From 49b5c6e002ac5f1f1081374219006f04a1c19293 Mon Sep 17 00:00:00 2001 From: Daniel Nachun Date: Fri, 31 Jul 2026 11:34:05 -0700 Subject: [PATCH 2/5] fix typo --- .github/workflows/ci.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 554b98c..ad8eb6f 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -3,8 +3,7 @@ name: CI on: pull_request: -jobs: - concurrency: +concurrency: group: ci-${{ github.ref }} cancel-in-progress: true From 1e051090609ecf1f7308a443c6134854d6f1a919 Mon Sep 17 00:00:00 2001 From: Daniel Nachun Date: Sat, 1 Aug 2026 10:06:59 -0700 Subject: [PATCH 3/5] update some packages --- .github/workflows/ci.yml | 2 +- envs/full_packages.txt | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ad8eb6f..a7f3c2f 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -9,7 +9,7 @@ concurrency: jobs: ci: - name: CI (${{ matrix.platform }} / ${{ matrix.environment }}) + name: CI (${{ matrix.runner }}) runs-on: ${{ matrix.runner }} env: CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} diff --git a/envs/full_packages.txt b/envs/full_packages.txt index f3adc9f..fb54177 100644 --- a/envs/full_packages.txt +++ b/envs/full_packages.txt @@ -8,12 +8,12 @@ awscli bamtools bcftools bedtools -coreutils curl deeptools diffutils ensembl-vep fastqc +fastlmmc fastp findutils gatk4 @@ -41,9 +41,11 @@ picard polyfun plink plink2 +plinkseq python=3.12 quantas r-base=4.5 +regenie regtools ripgrep rnaseqc @@ -64,10 +66,8 @@ wget # [global_linux] code-server -fastlmmc ldstore procps-ng -regenie # [python] altair From 0f111d9152fa3c6e7b1f99014727e060ddacb980 Mon Sep 17 00:00:00 2001 From: Daniel Nachun Date: Sat, 1 Aug 2026 16:42:45 -0700 Subject: [PATCH 4/5] remove package --- envs/full_packages.txt | 1 - 1 file changed, 1 deletion(-) diff --git a/envs/full_packages.txt b/envs/full_packages.txt index fb54177..368a780 100644 --- a/envs/full_packages.txt +++ b/envs/full_packages.txt @@ -151,7 +151,6 @@ bioconductor-intact bioconductor-limma bioconductor-minfi bioconductor-minfidata -bioconductor-mofa2 bioconductor-org.hs.eg.db bioconductor-pcatools bioconductor-preprocesscore From fbdc70a29532d3008f5f442da10932dd2ae6cb68 Mon Sep 17 00:00:00 2001 From: Daniel Nachun Date: Sun, 2 Aug 2026 23:23:52 -0700 Subject: [PATCH 5/5] restrict ldstore to linux-64 --- envs/full_packages.txt | 4 +++- pixi-setup.sh | 4 ++++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/envs/full_packages.txt b/envs/full_packages.txt index 368a780..0d9bf63 100644 --- a/envs/full_packages.txt +++ b/envs/full_packages.txt @@ -66,9 +66,11 @@ wget # [global_linux] code-server -ldstore procps-ng +# [global_linux64] +ldstore + # [python] altair bash_kernel diff --git a/pixi-setup.sh b/pixi-setup.sh index 6d266de..7206caa 100755 --- a/pixi-setup.sh +++ b/pixi-setup.sh @@ -151,8 +151,12 @@ else safe_expose_remove coreutils kill safe_expose_remove coreutils uptime install_global_packages <(extract_section "${_full_file}" "global_linux") + if [[ $(uname -a) =~ .*x86_64.* ]]; then + install_global_packages <(extract_section "${_full_file}" "global_linux64") + fi fi + echo "Installing recommended R libraries ..." inject_packages r-base <(extract_section "${_full_file}" "r")