From d009b763dd5c1abbb6af7b97e87b0f47feb43d6a Mon Sep 17 00:00:00 2001
From: Edmund Miller <emiller@jodie.attlocal.net>
Date: Wed, 18 Sep 2024 11:12:07 -0500
Subject: [PATCH] chore: Copy bioconda build recipe

https://github.com/bioconda/bioconda-recipes/blob/c3dbcc1ccf2ec4fac48e6131dae3b5fdac3a4737/recipes/bioconductor-grohmm/meta.yaml
---
 recipe/build.sh  | 11 +++++++++
 recipe/meta.yaml | 60 ++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 71 insertions(+)
 create mode 100644 recipe/build.sh
 create mode 100644 recipe/meta.yaml

diff --git a/recipe/build.sh b/recipe/build.sh
new file mode 100644
index 0000000..5ea71a1
--- /dev/null
+++ b/recipe/build.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+mv DESCRIPTION DESCRIPTION.old
+grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION
+mkdir -p ~/.R
+echo -e "CC=$CC
+FC=$FC
+CXX=$CXX
+CXX98=$CXX
+CXX11=$CXX
+CXX14=$CXX" > ~/.R/Makevars
+$R CMD INSTALL --build .
diff --git a/recipe/meta.yaml b/recipe/meta.yaml
new file mode 100644
index 0000000..87b8145
--- /dev/null
+++ b/recipe/meta.yaml
@@ -0,0 +1,60 @@
+{% set version = "1.36.0" %}
+{% set name = "groHMM" %}
+{% set bioc = "3.18" %}
+
+package:
+  name: 'bioconductor-{{ name|lower }}'
+  version: '{{ version }}'
+source:
+  url:
+    - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz'
+    - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz'
+    - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz'
+    - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
+  md5: 0b1077948ddc9895c57188ca2560bc10
+build:
+  number: 1
+  rpaths:
+    - lib/R/lib/
+    - lib/
+  run_exports: '{{ pin_subpackage("bioconductor-grohmm", max_pin="x.x") }}'
+# Suggests: BiocStyle, GenomicFeatures, edgeR, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene
+requirements:
+  host:
+    - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0'
+    - 'bioconductor-genomicalignments >=1.38.0,<1.39.0'
+    - 'bioconductor-genomicranges >=1.54.0,<1.55.0'
+    - 'bioconductor-iranges >=2.36.0,<2.37.0'
+    - 'bioconductor-rtracklayer >=1.62.0,<1.63.0'
+    - 'bioconductor-s4vectors >=0.40.0,<0.41.0'
+    - r-base
+    - r-mass
+    - libblas
+    - liblapack
+  run:
+    - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0'
+    - 'bioconductor-genomicalignments >=1.38.0,<1.39.0'
+    - 'bioconductor-genomicranges >=1.54.0,<1.55.0'
+    - 'bioconductor-iranges >=2.36.0,<2.37.0'
+    - 'bioconductor-rtracklayer >=1.62.0,<1.63.0'
+    - 'bioconductor-s4vectors >=0.40.0,<0.41.0'
+    - r-base
+    - r-mass
+  build:
+    - {{ compiler('c') }}
+    - make
+test:
+  commands:
+    - '$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 }}