From 02df0a8a7d4712398d90f8635d4004e76bbc9f51 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 22 Apr 2024 16:34:17 +0200
Subject: gnu: Add r-saige.

* gnu/packages/bioinformatics.scm (r-saige): New variable.

Change-Id: Id5bda4d25ca61fe26d11bae0af19900fd0f0080e
---
 gnu/packages/bioinformatics.scm | 56 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 56 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d313835249..aa6bce5591 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1141,6 +1141,62 @@ (define-public r-scenic
       ;; GPLv3.
       (license license:gpl3))))
 
+(define-public r-saige
+  (let ((commit "c6717ba9c5a967bcf612e97566d845397b1b7167")
+        (revision "1"))
+    (package
+      (name "r-saige")
+      (version (git-version "1.3.4" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/saigegit/SAIGE")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0c3211whqazycs9ivwdz23imj45j4na2xzcfq5l989ykkgmqnjzs"))))
+      (properties `((upstream-name . "SAIGE")))
+      (build-system r-build-system)
+      (arguments
+       (list
+        #:phases
+        '(modify-phases %standard-phases
+           (add-after 'unpack 'do-not-download-packages
+             (lambda _
+               ;; Pretend to be a Conda build to avoid having to install
+               ;; things with pip and cget.
+               (setenv "CONDA_BUILD" "1")))
+           (add-after 'unpack 'link-with-openblas
+             (lambda* (#:key inputs #:allow-other-keys)
+               (substitute* "src/Makevars"
+                 (("-llapack")
+                  (search-input-file inputs
+                                     "/lib/libopenblas.so"))))))))
+      (inputs (list openblas savvy superlu zlib zstd))
+      (propagated-inputs (list r-bh
+                               r-data-table
+                               r-dplyr
+                               r-matrix
+                               r-metaskat
+                               r-optparse
+                               r-qlcmatrix
+                               r-rcpp
+                               r-rcpparmadillo
+                               r-rcppeigen
+                               r-rcppparallel
+                               r-rhpcblasctl
+                               r-rsqlite
+                               r-skat
+                               r-spatest))
+      (home-page "https://github.com/saigegit/SAIGE")
+      (synopsis "Genome-wide association tests in large-scale data sets")
+      (description "SAIGE is a package for efficiently controlling for
+case-control imbalance and sample relatedness in single-variant assoc
+tests (SAIGE) and controlling for sample relatedness in region-based assoc
+tests in large cohorts and biobanks (SAIGE-GENE+).")
+      (license license:gpl2+))))
+
 (define-public r-singlet
   (let ((commit "765a6c45081807a1522f0e8983e2417822a36f36")
         (revision "1"))
-- 
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