Merge pull request #7 from RuiDongDR/main

gaow · web-flow · commit 8d0265978161 · 2026-02-26T17:09:17.000-05:00
add minimal installation and allow user to set installation path
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -25,7 +25,7 @@ jobs:
         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
-          ./pixi-setup.sh
+          printf "\n1\n" | ./pixi-setup.sh
 
   osx-64:
     runs-on: macos-13
@@ -48,7 +48,7 @@ jobs:
         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
-          ./pixi-setup.sh
+          printf "\n1\n" | ./pixi-setup.sh
 
   osx-arm64:
     runs-on: macos-14
@@ -71,4 +71,4 @@ jobs:
         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
-          ./pixi-setup.sh
+          printf "\n1\n" | ./pixi-setup.sh
diff --git a/.github/workflows/dispatch_ci.yml b/.github/workflows/dispatch_ci.yml
@@ -23,9 +23,9 @@ 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
-          ./pixi-setup.sh
+          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-64_pixi:
     runs-on: macos-latest
@@ -46,9 +46,9 @@ 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
-          ./pixi-setup.sh
+          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
@@ -69,6 +69,6 @@ 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
-          ./pixi-setup.sh
+          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
diff --git a/envs/full_packages.txt b/envs/full_packages.txt
@@ -0,0 +1,191 @@
+# Full package list - complete bioinformatics environment
+# Sections: [global], [global_linux], [python], [r]
+
+# [global]
+ark
+awscli
+bamtools
+bcftools
+bedtools
+curl
+deeptools
+diffutils
+ensembl-vep
+fastqc
+fastp
+findutils
+gatk4
+gawk
+gffread
+git
+go-ghq
+grep
+gtex-pipeline-gene_model
+gtex-pipeline-qtl
+gtex-pipeline-rnaseq
+htslib
+king
+kent-tools
+less
+metal
+multiqc
+pandoc
+parallel
+perl
+picard
+plink
+plink2
+python=3.12
+quantas
+r-base=4.4
+regtools
+ripgrep
+rnaseqc
+rsem
+ruby
+samtools
+sed
+snpeff
+snpsift
+star
+tree
+trimmomatic
+unzip
+util-linux
+vim
+wget
+
+# [global_linux]
+code-server
+fastlmmc
+gcta
+ldstore
+procps-ng
+regenie
+
+# [python]
+altair
+bash_kernel
+bitarray
+cython
+dill
+feather-format
+imageio
+ipykernel
+ipywidgets
+ipympl
+ipyparallel
+ipython
+jedi-language-server
+jupyterlab
+jupyter_client
+jupyter_console
+jupyter_core
+jupyter_server
+jupyter-lsp
+jupyterlab-lsp
+jupyterlab-sos
+jupyterhub
+markdown
+markdown-kernel
+matplotlib-base
+mofapy2
+multipy
+nb_conda_kernels
+nbconvert-core
+nbdime
+nbformat
+notebook
+numba
+numexpr
+numpy
+openpyxl
+pandas
+pgenlib
+pillow
+ptpython
+pyarrow
+pybigwig
+python-ldstore
+python-lsp-server
+qvalue
+scikit-learn
+scipy
+seaborn
+statsmodels
+sympy
+tqdm
+tensorqtl
+wand
+widgetsnbextension
+sos
+sos-bash
+sos-notebook
+sos-python
+sos-r
+
+# [r]
+bioconductor-annotationdbi
+bioconductor-clusterprofiler
+bioconductor-edger
+bioconductor-illuminahumanmethylation450kmanifest
+bioconductor-illuminahumanmethylationepicmanifest
+bioconductor-impute
+bioconductor-limma
+bioconductor-minfi
+bioconductor-mofa2
+bioconductor-org.hs.eg.db
+bioconductor-pcatools
+bioconductor-preprocesscore
+bioconductor-psichomics
+bioconductor-qvalue
+bioconductor-sesame
+bioconductor-sesamedata
+bioconductor-variantannotation
+r-abind
+r-arrow
+r-ape
+r-bedtoolsr
+r-bigsnpr
+r-biocmanager
+r-bitops
+r-catools
+r-colocboost
+r-complexupset
+r-corrplot
+r-devtools
+r-flashpcar
+r-fsusier
+r-gbj
+r-genio
+r-glmnet
+r-gplots
+r-gtools
+r-gwasrapidd
+r-harmonicmeanp
+r-httpgd
+r-hudson
+r-igraph
+r-irkernel
+r-languageserver
+r-mediation
+r-missforest
+r-mr.ash.alpha
+r-mr.mash.alpha
+r-mvsusier
+r-pacman
+r-pecotmr
+r-pgenlibr
+r-plinkqc
+r-profvis
+r-qgg
+r-qqman
+r-qrank
+r-quadprog
+r-quantreg
+r-rfast
+r-rgl
+r-rmtstat
+r-seurat
+r-tidyverse
+r-watershedr
diff --git a/envs/minimal_packages.txt b/envs/minimal_packages.txt
@@ -0,0 +1,74 @@
+# Minimal package list - general purpose only, no bioinformatics tools
+# Sections: [global], [python], [r]
+
+# [global]
+curl
+diffutils
+findutils
+gawk
+git
+grep
+less
+parallel
+pandoc
+perl
+python=3.12
+r-base=4.4
+ripgrep
+ruby
+sed
+tree
+unzip
+vim
+wget
+
+# [python]
+cython
+dill
+ipykernel
+ipywidgets
+ipympl
+ipyparallel
+ipython
+jedi-language-server
+jupyterlab
+jupyter_client
+jupyter_console
+jupyter_core
+jupyter_server
+jupyter-lsp
+jupyterlab-lsp
+matplotlib-base
+nb_conda_kernels
+nbconvert-core
+nbdime
+nbformat
+notebook
+numba
+numexpr
+numpy
+openpyxl
+pandas
+pillow
+ptpython
+pyarrow
+python-lsp-server
+scikit-learn
+scipy
+seaborn
+statsmodels
+sympy
+tqdm
+widgetsnbextension
+
+# [r]
+r-biocmanager
+r-corrplot
+r-devtools
+r-glmnet
+r-httpgd
+r-igraph
+r-irkernel
+r-languageserver
+r-pacman
+r-tidyverse
diff --git a/init.sh b/init.sh
@@ -1,10 +1,13 @@
 #!/usr/bin/env bash
 
-set -o errexit -o nounset -o xtrace -o pipefail
+set -o errexit -o nounset -o pipefail
+
+# Use PIXI_HOME if set (e.g. custom HPC path), otherwise fall back to default
+PIXI_HOME="${PIXI_HOME:-${HOME}/.pixi}"
 
 # Use Rprofile.site so that only pixi-installed R can see r-base packages
-mkdir -p ${HOME}/.pixi/envs/python/lib/R/etc
-echo ".libPaths('${HOME}/.pixi/envs/r-base/lib/R/library')" > ${HOME}/.pixi/envs/python/lib/R/etc/Rprofile.site
+mkdir -p ${PIXI_HOME}/envs/python/lib/R/etc
+echo ".libPaths('${PIXI_HOME}/envs/r-base/lib/R/library')" > ${PIXI_HOME}/envs/python/lib/R/etc/Rprofile.site
 
 # Create config files for rstudio
 mkdir -p ${HOME}/.config/rstudio
@@ -13,18 +16,18 @@ directory=${HOME}/.local/var/lib/rstudio-server
 EOF
 
 tee ${HOME}/.config/rstudio/rserver.conf << EOF
-rsession-which-r=${HOME}/.pixi/envs/r-base/bin/R
+rsession-which-r=${PIXI_HOME}/envs/r-base/bin/R
 auth-none=1
 database-config-file=${HOME}/.config/rstudio/database.conf
 server-daemonize=0
 server-data-dir=${HOME}/.local/var/run/rstudio-server
 server-user=${USER}
 EOF
 
-# Register Juypter kernels
-find ${HOME}/.pixi/envs/python/share/jupyter/kernels/ -maxdepth 1 -mindepth 1 -type d | \
+# Register Jupyter kernels
+find ${PIXI_HOME}/envs/python/share/jupyter/kernels/ -maxdepth 1 -mindepth 1 -type d | \
     xargs -I % jupyter-kernelspec install --log-level=50 --user %
-find ${HOME}/.pixi/envs/r-base/share/jupyter/kernels/ -maxdepth 1 -mindepth 1 -type d | \
+find ${PIXI_HOME}/envs/r-base/share/jupyter/kernels/ -maxdepth 1 -mindepth 1 -type d | \
     xargs -I % jupyter-kernelspec install --log-level=50 --user %
 # ark --install
 
@@ -49,7 +52,9 @@ else
    code-server --install-extension usernamehw.errorlens
 fi
 
-# Temporary fix to run post-link scripts
-bash -c "PREFIX=${HOME}/.pixi/envs/r-base PATH=${HOME}/.pixi/envs/r-base/bin:${PATH} .bioconductor-genomeinfodbdata-post-link.sh"
-find ${HOME}/.pixi/envs/r-base/bin -name '*bioconductor-*-post-link.sh' | \
-xargs -I % bash -c "PREFIX=${HOME}/.pixi/envs/r-base PATH=${HOME}/.pixi/envs/r-base/bin:${PATH} %"
+# 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} %"
diff --git a/pixi-install.sh b/pixi-install.sh
diff --git a/pixi-setup.sh b/pixi-setup.sh
