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09/11: gnu: bcftools: Update to 1.5.
From: |
Ben Woodcroft |
Subject: |
09/11: gnu: bcftools: Update to 1.5. |
Date: |
Sat, 22 Jul 2017 20:32:01 -0400 (EDT) |
benwoodcroft pushed a commit to branch master
in repository guix.
commit 0620387a594be1e8069dea8cda83dfc4a0b7f2de
Author: Ben Woodcroft <address@hidden>
Date: Sat Jul 22 20:36:44 2017 +1000
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(-)
diff --git a/gnu/local.mk b/gnu/local.mk
index 3397216..8d3916e 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 3e3aaeb..d9f7e2a 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 614f5fd..0000000
--- 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
- branch master updated (c62d1a6 -> f3f68a4), Ben Woodcroft, 2017/07/22
- 03/11: gnu: samtools: Update to 1.4.1., Ben Woodcroft, 2017/07/22
- 06/11: gnu: python-pysam: Update to 0.11.2.2., Ben Woodcroft, 2017/07/22
- 01/11: gnu: samtools: Use "modify-phases" syntax., Ben Woodcroft, 2017/07/22
- 02/11: gnu: htslib: Update to 1.4.1., Ben Woodcroft, 2017/07/22
- 05/11: gnu: bamm: Use htslib-1.3., Ben Woodcroft, 2017/07/22
- 07/11: gnu: htslib: Update to 1.5., Ben Woodcroft, 2017/07/22
- 09/11: gnu: bcftools: Update to 1.5.,
Ben Woodcroft <=
- 04/11: gnu: bcftools: Update to 1.4.1., Ben Woodcroft, 2017/07/22
- 08/11: gnu: samtools: Update to 1.5., Ben Woodcroft, 2017/07/22
- 11/11: gnu: metabat: Update to 2.11.1., Ben Woodcroft, 2017/07/22
- 10/11: gnu: python-plastid: Update to 0.4.8., Ben Woodcroft, 2017/07/22