From 23fdb5a69c0aede825628221c81a1cb2f8fd02cb Mon Sep 17 00:00:00 2001
From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Date: Wed, 22 Dec 2021 21:37:35 -0500
Subject: gnu: samtools: Update to 1.14.

* gnu/packages/bioinformatics.scm (samtools): Update to 1.14.
[modules]: Delete argument.
[phases]{install-library, install-headers}: Delete phases.  This version no
longer includes the legacy library (it links to htslib directly).
(samtools-1.12): New variable.
---
 gnu/packages/bioinformatics.scm | 70 +++++++++++++++++++++++++++--------------
 1 file changed, 46 insertions(+), 24 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 36167d0ba0..32f123a723 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6144,7 +6144,7 @@ to the user's query of interest.")
 (define-public samtools
   (package
     (name "samtools")
-    (version "1.12")
+    (version "1.14")
     (source
      (origin
        (method url-fetch)
@@ -6153,40 +6153,21 @@ to the user's query of interest.")
                        version "/samtools-" version ".tar.bz2"))
        (sha256
         (base32
-         "1jrdj2idpma5ja9cg0rr73b565vdbr9wyy6zig54bidicc2pg8vd"))
+         "0x3xdda78ac5vx66b3jdsv9sfhyz4npl4znl1zbaf3lbm6xdlhck"))
        (modules '((guix build utils)))
        (snippet '(begin
                    ;; Delete bundled htslib.
-                   (delete-file-recursively "htslib-1.12")
-                   #t))))
+                   (delete-file-recursively "htslib-1.14")))))
     (build-system gnu-build-system)
     (arguments
-     `(#:modules ((ice-9 ftw)
-                  (ice-9 regex)
-                  (guix build gnu-build-system)
-                  (guix build utils))
-       #:configure-flags (list "--with-ncurses")
+     `(#:configure-flags (list "--with-ncurses")
        #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'patch-tests
            (lambda _
              (substitute* "test/test.pl"
                ;; The test script calls out to /bin/bash
-               (("/bin/bash") (which "bash")))
-             #t))
-         (add-after 'install 'install-library
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let ((lib (string-append (assoc-ref outputs "out") "/lib")))
-               (install-file "libbam.a" lib)
-               #t)))
-         (add-after 'install 'install-headers
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let ((include (string-append (assoc-ref outputs "out")
-                                           "/include/samtools/")))
-               (for-each (lambda (file)
-                           (install-file file include))
-                         (scandir "." (lambda (name) (string-match "\\.h$" name))))
-               #t))))))
+               (("/bin/bash") (which "bash"))))))))
     (native-inputs (list pkg-config))
     (inputs
      (list htslib ncurses perl python zlib))
@@ -6199,6 +6180,47 @@ variant calling (in conjunction with bcftools), and a simple alignment
 viewer.")
     (license license:expat)))
 
+(define-public samtools-1.12
+  (package/inherit samtools
+    (version "1.12")
+    (source
+     (origin
+       (method url-fetch)
+       (uri
+        (string-append "mirror://sourceforge/samtools/samtools/"
+                       version "/samtools-" version ".tar.bz2"))
+       (sha256
+        (base32
+         "1jrdj2idpma5ja9cg0rr73b565vdbr9wyy6zig54bidicc2pg8vd"))
+       (modules '((guix build utils)))
+       (snippet '(begin
+                   ;; Delete bundled htslib.
+                   (delete-file-recursively "htslib-1.12")))))
+    (arguments
+     (substitute-keyword-arguments (package-arguments samtools)
+       ((#:modules _ #f)
+        '((ice-9 ftw)
+          (ice-9 regex)
+          (guix build gnu-build-system)
+          (guix build utils)))
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (add-after 'install 'install-library
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let ((lib (string-append (assoc-ref outputs "out") "/lib")))
+                 (install-file "libbam.a" lib))))
+           (add-after 'install 'install-headers
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let ((include (string-append (assoc-ref outputs "out")
+                                             "/include/samtools/")))
+                 (for-each (lambda (file)
+                             (install-file file include))
+                           (scandir "." (lambda (name)
+                                          (string-match "\\.h$" name)))))))))))
+    (native-inputs (list pkg-config))
+    (inputs
+     (list htslib-1.12 ncurses perl python zlib))))
+
 (define-public samtools-1.10
   (package (inherit samtools)
     (name "samtools")
-- 
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