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authorBen Woodcroft <donttrustben@gmail.com>2017-07-22 20:36:44 +1000
committerBen Woodcroft <donttrustben@gmail.com>2017-07-23 10:29:36 +1000
commit0620387a594be1e8069dea8cda83dfc4a0b7f2de (patch)
tree455f84f259e7c2759572ff078361c69857635256
parent63fa0ffcd43484c2d7dcf32866529c022309ff20 (diff)
downloadpatches-0620387a594be1e8069dea8cda83dfc4a0b7f2de.tar
patches-0620387a594be1e8069dea8cda83dfc4a0b7f2de.tar.gz
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.
-rw-r--r--gnu/local.mk1
-rw-r--r--gnu/packages/bioinformatics.scm10
-rw-r--r--gnu/packages/patches/bcftools-fix-makefile.patch33
3 files changed, 5 insertions, 39 deletions
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 @@ BAM files.")
(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 @@ BAM files.")
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 @@ BAM files.")
(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