From 98593f9f51c8f6e3c2208d8443fdf08cf4d633bb Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Fri, 7 Apr 2017 19:21:28 +1000
Subject: gnu: bcftools: Update to 1.4.1.

* gnu/packages/bioinformatics.scm (bcftools): Update to 1.4.1.
[arguments]: Move Makefile modifications from here ...
[source]: ... to added patch.  Adjust patch for update to 1.4.
* gnu/packages/patches/bcftools-fix-makefile.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
---
 gnu/local.mk                                     |  1 +
 gnu/packages/bioinformatics.scm                  | 20 +++++---------
 gnu/packages/patches/bcftools-fix-makefile.patch | 33 ++++++++++++++++++++++++
 3 files changed, 41 insertions(+), 13 deletions(-)
 create mode 100644 gnu/packages/patches/bcftools-fix-makefile.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 8d3916e26d..3397216e15 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -522,6 +522,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/awesome-reproducible-png.patch		\
   %D%/packages/patches/azr3.patch				\
   %D%/packages/patches/bash-completion-directories.patch	\
+  %D%/packages/patches/bcftools-fix-makefile.patch              \
   %D%/packages/patches/binutils-ld-new-dtags.patch		\
   %D%/packages/patches/binutils-loongson-workaround.patch	\
   %D%/packages/patches/binutils-mips-bash-bug.patch		\
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f5122a1802..87da4aed15 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -300,7 +300,7 @@ (define-public bamtools
 (define-public bcftools
   (package
     (name "bcftools")
-    (version "1.3.1")
+    (version "1.4.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -308,11 +308,12 @@ (define-public bcftools
                     version "/bcftools-" version ".tar.bz2"))
               (sha256
                (base32
-                "095ry68vmz9q5s1scjsa698dhgyvgw5aicz24c19iwfbai07mhqj"))
+                "024xv59bzv148b6w3das4jmldf7rywsf8y1fbqznap008qc8gl6p"))
+              (patches (search-patches "bcftools-fix-makefile.patch"))
               (modules '((guix build utils)))
               (snippet
                ;; Delete bundled htslib.
-               '(delete-file-recursively "htslib-1.3.1"))))
+               '(delete-file-recursively "htslib-1.4.1"))))
     (build-system gnu-build-system)
     (arguments
      `(#:test-target "test"
@@ -321,19 +322,12 @@ (define-public bcftools
         "USE_GPL=1"
         (string-append "prefix=" (assoc-ref %outputs "out"))
         (string-append "HTSDIR=" (assoc-ref %build-inputs "htslib") "/include")
-        (string-append "HTSLIB=" (assoc-ref %build-inputs "htslib") "/lib/libhts.a")
+        (string-append "HTSLIB=" (assoc-ref %build-inputs "htslib") "/lib/libhts.so")
         (string-append "BGZIP=" (assoc-ref %build-inputs "htslib") "/bin/bgzip")
-        (string-append "TABIX=" (assoc-ref %build-inputs "htslib") "/bin/tabix"))
+        (string-append "TABIX=" (assoc-ref %build-inputs "htslib") "/bin/tabix")
+        (string-append "PACKAGE_VERSION=" ,version))
        #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'patch-Makefile
-           (lambda _
-             (substitute* "Makefile"
-               ;; Do not attempt to build htslib.
-               (("^include \\$\\(HTSDIR\\)/htslib\\.mk") "")
-               ;; Link against GSL cblas.
-               (("-lcblas") "-lgslcblas"))
-             #t))
          (delete 'configure)
          (add-before 'check 'patch-tests
            (lambda _
diff --git a/gnu/packages/patches/bcftools-fix-makefile.patch b/gnu/packages/patches/bcftools-fix-makefile.patch
new file mode 100644
index 0000000000..614f5fd6bd
--- /dev/null
+++ b/gnu/packages/patches/bcftools-fix-makefile.patch
@@ -0,0 +1,33 @@
+diff --git a/Makefile b/Makefile
+index edd2c4a..73b25ea 100644
+--- a/Makefile
++++ b/Makefile
+@@ -30,8 +30,8 @@ all: $(PROG) $(TEST_PROG)
+ 
+ # Adjust $(HTSDIR) to point to your top-level htslib directory
+ HTSDIR = htslib-1.4.1
+-include $(HTSDIR)/htslib.mk
+-include $(HTSDIR)/htslib_static.mk
++#include $(HTSDIR)/htslib.mk
++#include $(HTSDIR)/htslib_static.mk
+ HTSLIB = $(HTSDIR)/libhts.a
+ BGZIP  = $(HTSDIR)/bgzip
+ TABIX  = $(HTSDIR)/tabix
+@@ -73,7 +73,7 @@ GSL_LIBS       =
+ ifdef USE_GPL
+     EXTRA_CPPFLAGS += -DUSE_GPL
+     OBJS += polysomy.o peakfit.o
+-    GSL_LIBS = -lgsl -lcblas
++    GSL_LIBS = -lgsl -lgslcblas
+ endif
+ 
+ prefix      = /usr/local
+@@ -217,7 +217,7 @@ test/test-regidx.o: test/test-regidx.c regidx.h
+ test/test-regidx: test/test-regidx.o regidx.o $(HTSLIB)
+ 	$(CC) $(ALL_LDFLAGS) -o $@ $^ $(HTSLIB) -lpthread $(HTSLIB_LIBS) $(ALL_LIBS)
+ 
+-bcftools: $(HTSLIB) $(OBJS)
++bcftools: $(OBJS)
+ 	$(CC) $(ALL_LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread $(HTSLIB_LIBS) $(GSL_LIBS) $(ALL_LIBS)
+ 
+ doc/bcftools.1: doc/bcftools.txt
-- 
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