add package and linux-aarch64

.github/workflows/ci.yml

@@ -3,36 +3,20 @@ name: CI
 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
+concurrency:
+  group: ci-${{ github.ref }}
+  cancel-in-progress: true
 
-      - name: Setup pixi
-        uses: prefix-dev/setup-pixi@v0.8.3
-        with:
-          run-install: false
-
-      - 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.runner }})
+    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 +30,7 @@ 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: |

envs/full_packages.txt

@@ -2,6 +2,7 @@
 # Sections: [global], [global_linux], [python], [r]
 
 # [global]
+apex
 ark
 awscli
 bamtools
@@ -12,17 +13,21 @@ deeptools
 diffutils
 ensembl-vep
 fastqc
+fastlmmc
 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 +38,14 @@ pandoc
 parallel
 perl
 picard
+polyfun
 plink
 plink2
+plinkseq
 python=3.12
 quantas
-r-base=4.4
+r-base=4.5
+regenie
 regtools
 ripgrep
 rnaseqc
@@ -48,6 +56,7 @@ sed
 snpeff
 snpsift
 star
+suppa
 tree
 trimmomatic
 unzip
@@ -57,11 +66,10 @@ wget
 
 # [global_linux]
 code-server
-fastlmmc
-gcta
-ldstore
 procps-ng
-regenie
+
+# [global_linux64]
+ldstore
 
 # [python]
 altair
@@ -107,6 +115,9 @@ pillow
 ptpython
 pyarrow
 pybigwig
+pytest
+pytest-cov
+pytest-xdist
 python-ldstore
 python-lsp-server
 qvalue
@@ -119,6 +130,7 @@ tqdm
 tensorqtl
 wand
 widgetsnbextension
+setuptools<82
 sos
 sos-bash
 sos-notebook
@@ -127,53 +139,72 @@ 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-mofa2
+bioconductor-minfi
+bioconductor-minfidata
 bioconductor-org.hs.eg.db
 bioconductor-pcatools
 bioconductor-preprocesscore
 bioconductor-psichomics
 bioconductor-qvalue
 bioconductor-sesame
 bioconductor-sesamedata
+bioconductor-singlecelltk
+bioconductor-sva
+bioconductor-txdbmaker
 r-abind
 r-argparser
 r-arrow
 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
 r-quantreg
 r-rgl
 r-rmtstat
 r-seurat
+r-testthat
 r-tidyverse
 r-watershedr
+r-xgboost

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")