add missing packages

.github/workflows/ci.yml

@@ -22,29 +22,8 @@ jobs:
 
       - name: Run setup script
         shell: pixi exec --spec sed -- bash -e {0}
-        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-64:
-    runs-on: macos-13
-    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
-
-      - name: Run setup script
-        shell: pixi exec --spec sed -- zsh -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
@@ -68,7 +47,9 @@ jobs:
 
       - name: Run setup script
         shell: pixi exec --spec sed -- zsh -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
+          printf "\n1\n" | ./pixi-setup.sh

.github/workflows/dispatch_ci.yml

@@ -27,29 +27,6 @@ jobs:
           sed -i "s?init.sh | bash?init.sh | sed 's,StatFunGen/pixi-setup/main,${{ github.repository }}/${{ github.ref_name }},g' | bash?" pixi-setup.sh
           printf "\n1\n" | ./pixi-setup.sh
 
-  osx-64_pixi:
-    runs-on: macos-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
-
-      - name: Run setup script
-        shell: pixi exec --spec sed -- bash -e {0}
-        run: |
-          sed -i "s?StatFunGen/pixi-setup/main?${{ github.repository }}/${{ github.ref_name }}?g" pixi-setup.sh
-          sed -i "s?init.sh | bash?init.sh | sed 's,StatFunGen/pixi-setup/main,${{ github.repository }}/${{ github.ref_name }},g' | bash?" pixi-setup.sh
-          printf "\n1\n" | ./pixi-setup.sh
-
   osx-arm64_pixi:
     runs-on: macos-14
     strategy:
@@ -71,4 +48,4 @@ jobs:
         run: |
           sed -i "s?StatFunGen/pixi-setup/main?${{ github.repository }}/${{ github.ref_name }}?g" pixi-setup.sh
           sed -i "s?init.sh | bash?init.sh | sed 's,StatFunGen/pixi-setup/main,${{ github.repository }}/${{ github.ref_name }},g' | bash?" pixi-setup.sh
-          printf "\n1\n" | ./pixi-setup.sh
+          printf "\n1\n" | ./pixi-setup.sh

envs/full_packages.txt

@@ -128,11 +128,11 @@ sos-r
 bioconductor-annotationdbi
 bioconductor-clusterprofiler
 bioconductor-edger
+bioconductor-genomeinfodb
+bioconductor-genomeinfodbdata
 bioconductor-illuminahumanmethylation450kmanifest
 bioconductor-illuminahumanmethylationepicmanifest
-bioconductor-impute
 bioconductor-limma
-bioconductor-minfi
 bioconductor-mofa2
 bioconductor-org.hs.eg.db
 bioconductor-pcatools
@@ -142,6 +142,7 @@ bioconductor-qvalue
 bioconductor-sesame
 bioconductor-sesamedata
 r-abind
+r-argparser
 r-arrow
 r-ape
 r-bedtoolsr

init.sh

@@ -51,10 +51,3 @@ else
    code-server --install-extension ionutvmi.path-autocomplete
    code-server --install-extension usernamehw.errorlens
 fi
-
-# Temporary fix to run post-link scripts (only present in full install with bioconductor packages)
-if [ -f "${PIXI_HOME}/envs/r-base/bin/.bioconductor-genomeinfodbdata-post-link.sh" ]; then
-    bash -c "PREFIX=${PIXI_HOME}/envs/r-base PATH=${PIXI_HOME}/envs/r-base/bin:${PATH} .bioconductor-genomeinfodbdata-post-link.sh"
-fi
-find ${PIXI_HOME}/envs/r-base/bin -name '*bioconductor-*-post-link.sh' | \
-xargs -I % bash -c "PREFIX=${PIXI_HOME}/envs/r-base PATH=${PIXI_HOME}/envs/r-base/bin:${PATH} %"

pixi-setup.sh

@@ -30,7 +30,7 @@ install_global_packages() {
     missing_pkgs=$(comm -13 <(echo "$existing_pkgs" | sort -u) <(sort -u ${package_list}))
 
     if (($(echo ${missing_pkgs} | wc -w) > 0 )); then
-        pixi global install $(echo ${missing_pkgs} | tr '\n' ' ')
+        pixi global install --run-post-link-scripts $(echo ${missing_pkgs} | tr '\n' ' ')
     fi
 }
 
@@ -48,7 +48,7 @@ inject_packages() {
     fi
 
     if (( $(echo ${missing_pkgs} | wc -w) > 0 )); then
-        pixi global install --environment ${environment} $(echo ${missing_pkgs} | tr '\n' ' ')
+        pixi global install --run-post-link-scripts --environment ${environment} $(echo ${missing_pkgs} | tr '\n' ' ')
     fi
 }
 
@@ -74,21 +74,36 @@ export PIXI_HOME="${_user_pixi_home:-${_default_pixi_home}}"
 export RATTLER_CACHE_DIR="${PIXI_HOME}/cache"
 echo "Using PIXI_HOME=${PIXI_HOME}"
 
-# --- Prompt: install type ---
-echo ""
-echo "Choose installation type:"
-echo "  1) minimal - Essential CLI tools + Python data science + base R"
-echo "               ~5 GB, ~100k files"
-echo "  2) full    - Complete bioinformatics environment (samtools, GATK, plink,"
-echo "               STAR, Seurat, bioconductor packages, etc.)"
-echo "               ~35 GB, ~350k files"
-echo ""
-read -r -p "Install type [1=minimal, 2=full, default=1]: " _install_type_input
-case "${_install_type_input:-1}" in
-    2|full)    INSTALL_TYPE="full" ;;
-    *)         INSTALL_TYPE="minimal" ;;
-esac
-echo "Installation type: ${INSTALL_TYPE}"
+# --- Install type ---
+# Allow a preset INSTALL_TYPE env var to override the prompt (e.g. for
+# non-interactive runs). A set-but-invalid value is a hard error.
+if [[ -n "${INSTALL_TYPE:-}" ]]; then
+    case "$(echo "${INSTALL_TYPE}" | tr '[:upper:]' '[:lower:]')" in
+        2|full)    INSTALL_TYPE="full" ;;
+        1|minimal) INSTALL_TYPE="minimal" ;;
+        *)
+            echo "ERROR: invalid INSTALL_TYPE='${INSTALL_TYPE}' (expected 'minimal'/'1' or 'full'/'2')" >&2
+            exit 1
+            ;;
+    esac
+    echo "Installation type: ${INSTALL_TYPE} (from INSTALL_TYPE environment variable)"
+else
+    # --- Prompt: install type ---
+    echo ""
+    echo "Choose installation type:"
+    echo "  1) minimal - Essential CLI tools + Python data science + base R"
+    echo "               ~5 GB, ~100k files"
+    echo "  2) full    - Complete bioinformatics environment (samtools, GATK, plink,"
+    echo "               STAR, Seurat, bioconductor packages, etc.)"
+    echo "               ~35 GB, ~350k files"
+    echo ""
+    read -r -p "Install type [1=minimal, 2=full, default=1]: " _install_type_input
+    case "${_install_type_input:-1}" in
+        2|full)    INSTALL_TYPE="full" ;;
+        *)         INSTALL_TYPE="minimal" ;;
+    esac
+    echo "Installation type: ${INSTALL_TYPE}"
+fi
 
 # Ensure PIXI_HOME exists
 mkdir -p "${PIXI_HOME}"