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| author | Ben Woodcroft <donttrustben@gmail.com> | 2017-04-07 19:21:28 +1000 |
|---|---|---|
| committer | Ben Woodcroft <donttrustben@gmail.com> | 2017-07-23 10:29:35 +1000 |
| commit | 98593f9f51c8f6e3c2208d8443fdf08cf4d633bb (patch) | |
| tree | e772fee04adedb87fa1ff5ff42fbf91c38f99710 | |
| parent | 4ab1644049ad2d1cf7a997dfa910a4d7d646e49f (diff) | |
| download | patches-98593f9f51c8f6e3c2208d8443fdf08cf4d633bb.tar patches-98593f9f51c8f6e3c2208d8443fdf08cf4d633bb.tar.gz | |
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.
| -rw-r--r-- | gnu/local.mk | 1 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 20 | ||||
| -rw-r--r-- | gnu/packages/patches/bcftools-fix-makefile.patch | 33 |
3 files changed, 41 insertions, 13 deletions
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 @@ BAM files.") (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 @@ BAM files.") 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 @@ BAM files.") "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 |