From 5153c937e39cfeb59275594047fcccec6859f250 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 23 Apr 2015 15:23:26 +0200
Subject: [PATCH 1/3] gnu: samtools: Remove patch-makefile-curses phase.

* gnu/packages/bioinformatics.scm (samtools)[arguments]: Remove
  patch-makefile-curses phase, use make-flags instead.
---
 gnu/packages/bioinformatics.scm | 41 ++++++++++++++++++-----------------------
 1 file changed, 18 insertions(+), 23 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b654e05..65cf37f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1123,32 +1123,27 @@ distribution, coverage uniformity, strand specificity, etc.")
        ;; systems.
        #:tests? ,(string=? (or (%current-system) (%current-target-system))
                            "x86_64-linux")
-       #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")))
+       #:make-flags (list "LIBCURSES=-lncurses"
+                          (string-append "prefix=" (assoc-ref %outputs "out")))
        #:phases
        (alist-cons-after
         'unpack
-        'patch-makefile-curses
-        (lambda _
-          (substitute* "Makefile"
-            (("-lcurses") "-lncurses")))
-        (alist-cons-after
-         'unpack
-         'patch-tests
-         (lambda* (#:key inputs #:allow-other-keys)
-           (let ((bash (assoc-ref inputs "bash")))
-             (substitute* "test/test.pl"
-               ;; The test script calls out to /bin/bash
-               (("/bin/bash")
-                (string-append bash "/bin/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 ($subcommand eq 'stats') {" cmd "};")))))
-         (alist-delete
-          'configure
-          %standard-phases)))))
+        'patch-tests
+        (lambda* (#:key inputs #:allow-other-keys)
+          (let ((bash (assoc-ref inputs "bash")))
+            (substitute* "test/test.pl"
+              ;; The test script calls out to /bin/bash
+              (("/bin/bash")
+               (string-append bash "/bin/bash"))
+              ;; There are two failing tests upstream relating to the "stats"
+              ;; subcommand in test_usage_subcommand ("did not have Usage"
+              ;; and "usage did not mention samtools stats"), so we disable
+              ;; them.
+              (("(test_usage_subcommand\\(.*\\);)" cmd)
+               (string-append "unless ($subcommand eq 'stats') {" cmd "};")))))
+        (alist-delete
+         'configure
+         %standard-phases))))
     (native-inputs `(("pkg-config" ,pkg-config)))
     (inputs `(("ncurses" ,ncurses)
               ("perl" ,perl)
-- 
2.1.0