Merge pull request #20 from cumc/update_recipe

overhaul conda workflow

.github/workflows/conda_build.yml

@@ -0,0 +1,107 @@
+name: Build conda package
+
+on:
+ workflow_dispatch:
+ inputs:
+ version:
+ description: Version to build package for
+ required: true
+
+jobs:
+ build_package_linux:
+ name: Build conda package for linux-64
+ runs-on: ubuntu-latest
+ strategy:
+ fail-fast: false
+ env:
+ ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_API_TOKEN }}
+
+ steps:
+ - name: Checkout pull request branch
+ uses: actions/checkout@v3
+ with:
+ fetch-depth: 0
+
+ - name: Create recipe from template
+ run: |
+ mkdir /tmp/recipe
+ cp recipe/meta.yaml /tmp/recipe/meta.yaml
+ cp recipe/build.sh /tmp/recipe/build.sh
+ version=${{ github.event.inputs.version }}
+ wget https://github.com/cumc/pecotmr/archive/${version}.tar.gz
+ sha256sum=$(sha256sum ${version}.tar.gz | cut -d ' ' -f 1)
+ sed -i "s/VERSION_PLACEHOLDER/${version}/g" /tmp/recipe/meta.yaml
+ sed -i "s/SHA256SUM_PLACEHOLDER/${sha256sum}/g" /tmp/recipe/meta.yaml
+
+ - name: Setup up docker buildx
+ uses: docker/setup-buildx-action@v2
+
+ - name: Build and export docker containers
+ uses: docker/build-push-action@v4
+ with:
+ load: true
+ file: .github/mambaforge_container.df
+ tags: conda_mambabuild:latest
+
+ - name: Build conda packages
+ run: docker run --rm --volume /tmp:/tmp --volume $(pwd) --workdir $(pwd) conda_mambabuild conda mambabuild --output-folder /tmp/conda-bld /tmp/recipe
+
+ - name: Setup micromamba
+ uses: mamba-org/setup-micromamba@v1
+ with:
+ environment-name: anaconda-client
+ create-args: anaconda-client
+ generate-run-shell: true
+
+ - name: Upload packages
+ shell: micromamba-shell {0}
+ run: anaconda upload --force /tmp/conda-bld/linux-64/*.tar.bz2
+
+ build_package_macos:
+ name: Build conda package for osx-64
+ runs-on: macos-latest
+ strategy:
+ fail-fast: false
+ env:
+ ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_API_TOKEN }}
+
+ steps:
+ - name: Checkout pull request branch
+ uses: actions/checkout@v3
+ with:
+ fetch-depth: 0
+
+ - name: Setup micromamba
+ uses: mamba-org/setup-micromamba@v1
+ with:
+ environment-name: boa
+ create-args: boa conda-verify anaconda-client sed
+ generate-run-shell: true
+
+ - name: Create recipe from template
+ shell: micromamba-shell {0}
+ run: |
+ mkdir /tmp/recipe
+ cp recipe/meta.yaml /tmp/recipe/meta.yaml
+ cp recipe/build.sh /tmp/recipe/build.sh
+ version=${{ github.event.inputs.version }}
+ wget https://github.com/cumc/pecotmr/archive/${version}.tar.gz
+ sha256sum=$(sha256sum ${version}.tar.gz | cut -d ' ' -f 1)
+ sed -i "s/VERSION_PLACEHOLDER/${version}/g" /tmp/recipe/meta.yaml
+ sed -i "s/SHA256SUM_PLACEHOLDER/${sha256sum}/g" /tmp/recipe/meta.yaml
+
+ - name: Set up channels
+ shell: micromamba-shell {0}
+ run: |
+ conda config --file /Users/runner/micromamba-bin/.condarc --append channels bioconda
+ conda config --file /Users/runner/micromamba-bin/.condarc --append channels nodefaults
+ xargs -I % conda config --file /Users/runner/micromamba-bin/.condarc --prepend channels % < .custom_channels
+ conda config --show-sources
+
+ - name: Build conda package
+ shell: micromamba-shell {0}
+ run: conda mambabuild --output-folder /tmp/conda-bld /tmp/recipe
+
+ - name: Upload package
+ shell: micromamba-shell {0}
+ run: anaconda upload --force /tmp/conda-bld/osx-64/*.tar.bz2

.github/workflows/release.yml

@@ -27,6 +27,7 @@ jobs:
  github_token: ${{ secrets.GITHUB_TOKEN }}
  custom_tag: ${{ github.events.input.tag }}
  commit_sha: ${{ github.events.input.commit }}
+ tag_prefix: ""
 
  - name: Create a GitHub release
  uses: ncipollo/release-action@v1

recipe/build.sh

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+
+export DISABLE_AUTOBREW=1
+
+# shellcheck disable=SC2086
+${R} CMD INSTALL --build . ${R_ARGS}

recipe/meta.yaml

@@ -0,0 +1,93 @@
+{% set version = "VERSION_PLACEHOLDER" %}
+{% set name = "pecotmr" %}
+
+package:
+ name: r-{{ name }}
+ version: {{ version }}
+
+source:
+ url: https://github.com/cumc/{{ name }}/archive/{{ version }}.tar.gz
+ sha256: SHA256SUM_PLACEHOLDER
+
+build:
+ merge_build_host: true # [win]
+ number: 0
+ rpaths:
+ - lib/R/lib/
+ - lib/
+
+requirements:
+ build:
+ - cross-r-base {{ r_base }} # [build_platform != target_platform]
+ host:
+ - bioconductor-qvalue
+ - r-bedtoolsr
+ - r-base=4.2
+ - r-coloc
+ - r-data.table
+ - r-domc
+ - r-dplyr
+ - r-gbj
+ - r-ggplot2
+ - r-ggnewscale
+ - r-ggrepel
+ - r-ggvenn
+ - r-glmnet
+ - r-harmonicmeanp
+ - r-magrittr
+ - r-matrix
+ - r-mr.ash.alpha
+ - r-mr.mash.alpha
+ - r-pgenlibr
+ - r-plink2r
+ - r-purrr
+ - r-rcpp
+ - r-readr
+ - r-rfast
+ - r-rlab
+ - r-stringr
+ - r-susier
+ - r-vctrs
+ run:
+ - bioconductor-qvalue
+ - r-bedtoolsr
+ - r-base=4.2
+ - r-coloc
+ - r-data.table
+ - r-domc
+ - r-dplyr
+ - r-gbj
+ - r-ggplot2
+ - r-ggnewscale
+ - r-ggrepel
+ - r-ggvenn
+ - r-glmnet
+ - r-harmonicmeanp
+ - r-magrittr
+ - r-matrix
+ - r-mr.ash.alpha
+ - r-mr.mash.alpha
+ - r-pgenlibr
+ - r-plink2r
+ - r-purrr
+ - r-rcpp
+ - r-readr
+ - r-rfast
+ - r-rlab
+ - r-stringr
+ - r-susier
+ - r-vctrs
+
+test:
+ commands:
+ - $R -e "library('{{ name }}')"
+
+about:
+ home: https://github.com/stephenslab/mvsusier
+ license: GPL-3.0-or-later
+ license_file: LICENSE.md
+ summary: pecotmr implements pair-wise enrichment, colocalization, TWAS and Mendelian Randomization to integrate QTL and GWAS analysis based on a fine-mapped single effects model.
+
+extra:
+ recipe-maintainers:
+ - danielnachun