From e97801a8e5a1a8c2461fc94300f9d10ca7089d2f Mon Sep 17 00:00:00 2001
From: Vipin <vipin@cbio.mskcc.org>
Date: Thu, 9 Jan 2025 09:33:16 +0100
Subject: [PATCH] recipe for scROSHI package based on CRAN repo (#52783)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* bioconda recipe conf for scROSHI package

* discarded strict package version constraints

* Update meta.yaml

---------

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 recipes/r-scroshi/build.sh  | 22 +++++++++++++++
 recipes/r-scroshi/meta.yaml | 54 +++++++++++++++++++++++++++++++++++++
 2 files changed, 76 insertions(+)
 create mode 100644 recipes/r-scroshi/build.sh
 create mode 100644 recipes/r-scroshi/meta.yaml

diff --git a/recipes/r-scroshi/build.sh b/recipes/r-scroshi/build.sh
new file mode 100644
index 0000000000000..df943f40e3e3d
--- /dev/null
+++ b/recipes/r-scroshi/build.sh
@@ -0,0 +1,22 @@
+#!/bin/bash
+
+# 'Autobrew' is being used by more and more packages these days
+# to grab static libraries from Homebrew bottles. These bottles
+# are fetched via Homebrew's --force-bottle option which grabs
+# a bottle for the build machine which may not be macOS 10.9.
+# Also, we want to use conda packages (and shared libraries) for
+# these 'system' dependencies. See:
+# https://github.com/jeroen/autobrew/issues/3
+export DISABLE_AUTOBREW=1
+
+# R refuses to build packages that mark themselves as Priority: Recommended
+mv DESCRIPTION DESCRIPTION.old
+grep -va '^Priority: ' DESCRIPTION.old > DESCRIPTION
+# shellcheck disable=SC2086
+${R} CMD INSTALL --build . ${R_ARGS}
+
+# Add more build steps here, if they are necessary.
+
+# See
+# https://docs.conda.io/projects/conda-build
+# for a list of environment variables that are set during the build process.
diff --git a/recipes/r-scroshi/meta.yaml b/recipes/r-scroshi/meta.yaml
new file mode 100644
index 0000000000000..daec214e82d2c
--- /dev/null
+++ b/recipes/r-scroshi/meta.yaml
@@ -0,0 +1,54 @@
+{% set version = '1.0.0.0' %}
+
+package:
+  name: r-scroshi
+  version: {{ version }}
+
+source:
+  url:
+    - {{ cran_mirror }}/src/contrib/scROSHI_{{ version|replace("-", "_") }}.tar.gz
+    - {{ cran_mirror }}/src/contrib/Archive/scROSHI/scROSHI_{{ version|replace("-", "_") }}.tar.gz
+  sha256: 332ed379c27d4becfae31f164e6267850cd927dbb357c3a77de1f320d65baf96
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage("r-scroshi", max_pin="x") }}
+  rpaths:
+    - lib/R/lib/
+    - lib/
+  noarch: generic
+
+requirements:
+  host:
+    - r-base >=3.6.0
+    - bioconductor-s4vectors 
+    - bioconductor-singlecellexperiment
+    - bioconductor-summarizedexperiment
+    - bioconductor-limma
+    - r-uwot
+
+  run:
+    - r-base >=3.6.0
+    - bioconductor-s4vectors 
+    - bioconductor-singlecellexperiment 
+    - bioconductor-summarizedexperiment
+    - bioconductor-limma 
+    - r-uwot 
+
+test:
+  commands:
+    - $R -e "library('scROSHI')"           # [not win]
+    - "\"%R%\" -e \"library('scROSHI')\""  # [win]
+
+about:
+  home: https://CRAN.R-project.org/package=scROSHI
+  license: MIT
+  summary: 'scROSHI: robust supervised hierarchical identification of single cells'
+  license_family: MIT
+  license_file:
+    - '{{ environ["PREFIX"] }}/lib/R/share/licenses/MIT'
+    - LICENSE
+extra:
+  identifiers:
+    - doi:10.1093/nargab/lqad058