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gnu: bcftools: Update to 1.4.1.

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* 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.
This commit is contained in:
Ben Woodcroft 2017-04-07 19:21:28 +10:00
parent 4ab1644049
commit 98593f9f51
No known key found for this signature in database
GPG key ID: 2A6AD9F4AAC20DF6
3 changed files with 41 additions and 13 deletions
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1
gnu/local.mk
View file

@ -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 \

20
gnu/packages/bioinformatics.scm
View file

@ -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 _

33
gnu/packages/patches/bcftools-fix-makefile.patch Normal file
View file

@ -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