From 788513d4e0d93deeee1d07bf361a40a0180ad1ea Mon Sep 17 00:00:00 2001
From: Andreas Enge <andreas@enge.fr>
Date: Thu, 23 Oct 2025 21:08:49 +0200
Subject: [PATCH] gnu: Remove samtools-1.2.

* gnu/packages/bioinformatics.scm (samtools-1.2): Delete variable.

Change-Id: I38effe41c32349b5b72754da07fe6696d2f21669
---
 gnu/packages/bioinformatics.scm | 57 ---------------------------------
 1 file changed, 57 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6d1e58334f5dfad9fe1144dcff4d1e92fd362e43..fe1bf8807af1c186fd567f84704e658905d650f0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11318,63 +11318,6 @@ viewer.")
     (inputs
      (list htslib-1.10 ncurses perl python zlib))))
 
-(define-public samtools-1.2
-  (package (inherit samtools)
-    (name "samtools")
-    (version "1.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri
-        (string-append "mirror://sourceforge/samtools/samtools/"
-                       version "/samtools-" version ".tar.bz2"))
-       (sha256
-        (base32
-         "1akdqb685pk9xk1nb6sa9aq8xssjjhvvc06kp4cpdqvz2157l3j2"))
-       (modules '((guix build utils)))
-       (snippet
-        ;; Delete bundled htslib and Windows binaries
-        '(for-each delete-file-recursively (list "win32" "htslib-1.2.1")))))
-    (arguments
-     `(#:make-flags
-       ,#~(list (string-append "prefix=" #$output)
-                (string-append "BGZIP="
-                               #$(this-package-input "htslib")
-                               "/bin/bgzip")
-                (string-append "HTSLIB="
-                               #$(this-package-input "htslib")
-                               "/lib/libhts.so")
-                (string-append "HTSDIR="
-                               #$(this-package-input "htslib")
-                               "/include"))
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'patch-makefile-curses
-           (lambda _
-             (substitute* "Makefile"
-               (("-lcurses") "-lncurses")
-               (("include \\$\\(HTSDIR.*") ""))))
-         (add-after 'unpack 'patch-tests
-           (lambda _
-             (substitute* "test/test.pl"
-               ;; The test script calls out to /bin/bash
-               (("/bin/bash") (which "bash"))
-               ;; There are two failing tests upstream relating to the "stats"
-               ;; subcommand in test_usage_subcommand ("did not have Usage"
-               ;; and "usage did not mention samtools stats"), so we disable
-               ;; them.
-               (("(test_usage_subcommand\\(.*\\);)" cmd)
-                (string-append "unless ($subcommand eq 'stats') {" cmd "};")))
-             ;; This test fails because the grep output doesn't look as
-             ;; expected; it is correct, though.
-             (substitute* "test/mpileup/mpileup.reg"
-               (("P 52.out.*") ""))))
-         (delete 'configure))))
-    (native-inputs
-     (list grep gawk pkg-config))
-    (inputs
-     (list htslib-for-samtools-1.2 ncurses perl python zlib))))
-
 (define-public samtools-0.1
   ;; This is the most recent version of the 0.1 line of samtools.  The input
   ;; and output formats differ greatly from that used and produced by samtools