From 0620387a594be1e8069dea8cda83dfc4a0b7f2de Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Sat, 22 Jul 2017 20:36:44 +1000
Subject: gnu: bcftools: Update to 1.5.

* gnu/packages/bioinformatics.scm (bcftools): Update to 1.5.
[origin]: Remove fix-makefile patch.
[arguments]: Add configure flags, add LIBS make flag.  Do not delete
configure phase.
* gnu/packages/patches/bcftools-fix-makefile.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
---
 gnu/local.mk                                     |  1 -
 gnu/packages/bioinformatics.scm                  | 10 +++----
 gnu/packages/patches/bcftools-fix-makefile.patch | 33 ------------------------
 3 files changed, 5 insertions(+), 39 deletions(-)
 delete mode 100644 gnu/packages/patches/bcftools-fix-makefile.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 3397216e15..8d3916e26d 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -522,7 +522,6 @@ 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 3e3aaeb657..d9f7e2a5e1 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 "1.4.1")
+    (version "1.5")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -308,18 +308,19 @@ (define-public bcftools
                     version "/bcftools-" version ".tar.bz2"))
               (sha256
                (base32
-                "024xv59bzv148b6w3das4jmldf7rywsf8y1fbqznap008qc8gl6p"))
-              (patches (search-patches "bcftools-fix-makefile.patch"))
+                "0093hkkvxmbwfaa7905s6185jymynvg42kq6sxv7fili11l5mxwz"))
               (modules '((guix build utils)))
               (snippet
                ;; Delete bundled htslib.
-               '(delete-file-recursively "htslib-1.4.1"))))
+               '(delete-file-recursively "htslib-1.5"))))
     (build-system gnu-build-system)
     (arguments
      `(#:test-target "test"
+       #:configure-flags (list "--with-htslib=system")
        #:make-flags
        (list
         "USE_GPL=1"
+        "LIBS=-lgsl -lgslcblas"
         (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.so")
@@ -328,7 +329,6 @@ (define-public bcftools
         (string-append "PACKAGE_VERSION=" ,version))
        #:phases
        (modify-phases %standard-phases
-         (delete 'configure)
          (add-before 'check 'patch-tests
            (lambda _
              (substitute* "test/test.pl"
diff --git a/gnu/packages/patches/bcftools-fix-makefile.patch b/gnu/packages/patches/bcftools-fix-makefile.patch
deleted file mode 100644
index 614f5fd6bd..0000000000
--- a/gnu/packages/patches/bcftools-fix-makefile.patch
+++ /dev/null
@@ -1,33 +0,0 @@
-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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