From 6a0ffd4dbdf10975bd17e629be971af75989f0d5 Mon Sep 17 00:00:00 2001
From: Edmund Miller <emiller@jodie.attlocal.net>
Date: Wed, 18 Sep 2024 11:29:54 -0500
Subject: [PATCH] build: Try rattler-build

---
 recipe/meta.yaml   | 60 ---------------------------------------
 recipe/recipe.yaml | 71 ++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 71 insertions(+), 60 deletions(-)
 delete mode 100644 recipe/meta.yaml
 create mode 100644 recipe/recipe.yaml

diff --git a/recipe/meta.yaml b/recipe/meta.yaml
deleted file mode 100644
index 87b8145..0000000
--- a/recipe/meta.yaml
+++ /dev/null
@@ -1,60 +0,0 @@
-{% set version = "1.36.0" %}
-{% set name = "groHMM" %}
-{% set bioc = "3.18" %}
-
-package:
-  name: 'bioconductor-{{ name|lower }}'
-  version: '{{ version }}'
-source:
-  url:
-    - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz'
-    - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz'
-    - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz'
-    - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
-  md5: 0b1077948ddc9895c57188ca2560bc10
-build:
-  number: 1
-  rpaths:
-    - lib/R/lib/
-    - lib/
-  run_exports: '{{ pin_subpackage("bioconductor-grohmm", max_pin="x.x") }}'
-# Suggests: BiocStyle, GenomicFeatures, edgeR, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene
-requirements:
-  host:
-    - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0'
-    - 'bioconductor-genomicalignments >=1.38.0,<1.39.0'
-    - 'bioconductor-genomicranges >=1.54.0,<1.55.0'
-    - 'bioconductor-iranges >=2.36.0,<2.37.0'
-    - 'bioconductor-rtracklayer >=1.62.0,<1.63.0'
-    - 'bioconductor-s4vectors >=0.40.0,<0.41.0'
-    - r-base
-    - r-mass
-    - libblas
-    - liblapack
-  run:
-    - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0'
-    - 'bioconductor-genomicalignments >=1.38.0,<1.39.0'
-    - 'bioconductor-genomicranges >=1.54.0,<1.55.0'
-    - 'bioconductor-iranges >=2.36.0,<2.37.0'
-    - 'bioconductor-rtracklayer >=1.62.0,<1.63.0'
-    - 'bioconductor-s4vectors >=0.40.0,<0.41.0'
-    - r-base
-    - r-mass
-  build:
-    - {{ compiler('c') }}
-    - make
-test:
-  commands:
-    - '$R -e "library(''{{ name }}'')"'
-about:
-  home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
-  license: GPL-3.0-only
-  summary: 'GRO-seq Analysis Pipeline'
-  description: 'A pipeline for the analysis of GRO-seq data.'
-  license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
-
-extra:
-  additional-platforms:
-    - linux-aarch64
-  identifiers:
-    - biotools:{{ name|lower }}
diff --git a/recipe/recipe.yaml b/recipe/recipe.yaml
new file mode 100644
index 0000000..87ed1d4
--- /dev/null
+++ b/recipe/recipe.yaml
@@ -0,0 +1,71 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/prefix-dev/recipe-format/main/schema.json
+# Suggests: BiocStyle, GenomicFeatures, edgeR, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene
+schema_version: 1
+
+context:
+  version: 1.36.0
+  name: groHMM
+  bioc: 3.18
+
+package:
+  name: bioconductor-${{ name|lower }}
+  version: ${{ version }}
+
+source:
+  url:
+    - https://bioconductor.org/packages/${{ bioc }}/bioc/src/contrib/${{ name }}_${{ version }}.tar.gz
+    - https://bioconductor.org/packages/${{ bioc }}/bioc/src/contrib/Archive/${{ name }}/${{ name }}_${{ version }}.tar.gz
+    - https://bioarchive.galaxyproject.org/${{ name }}_${{ version }}.tar.gz
+    - https://depot.galaxyproject.org/software/bioconductor-${{ name|lower }}/bioconductor-${{ name|lower }}_${{ version }}_src_all.tar.gz
+  md5: 0b1077948ddc9895c57188ca2560bc10
+
+build:
+  number: 1
+  dynamic_linking:
+    rpaths:
+      - lib/R/lib/
+      - lib/
+
+requirements:
+  host:
+    - bioconductor-genomeinfodb >=1.38.0,<1.39.0
+    - bioconductor-genomicalignments >=1.38.0,<1.39.0
+    - bioconductor-genomicranges >=1.54.0,<1.55.0
+    - bioconductor-iranges >=2.36.0,<2.37.0
+    - bioconductor-rtracklayer >=1.62.0,<1.63.0
+    - bioconductor-s4vectors >=0.40.0,<0.41.0
+    - r-base
+    - r-mass
+    - libblas
+    - liblapack
+  run:
+    - bioconductor-genomeinfodb >=1.38.0,<1.39.0
+    - bioconductor-genomicalignments >=1.38.0,<1.39.0
+    - bioconductor-genomicranges >=1.54.0,<1.55.0
+    - bioconductor-iranges >=2.36.0,<2.37.0
+    - bioconductor-rtracklayer >=1.62.0,<1.63.0
+    - bioconductor-s4vectors >=0.40.0,<0.41.0
+    - r-base
+    - r-mass
+  build:
+    - ${{ compiler('c') }}
+    - make
+  run_exports: ${{ pin_subpackage("bioconductor-grohmm", upper_bound="x.x") }}
+
+tests:
+  - script:
+      - $R -e "library('${{ name }}')"
+
+about:
+  license: GPL-3.0-only
+  summary: GRO-seq Analysis Pipeline
+  description: A pipeline for the analysis of GRO-seq data.
+  # FIXME license_file: ${{ env.get("PREFIX") }}/lib/R/share/licenses/GPL-3
+  homepage: https://bioconductor.org/packages/${{ bioc }}/bioc/html/${{ name }}.html
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+  identifiers:
+    - biotools:${{ name|lower }}
+