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| author | Ben Woodcroft <donttrustben@gmail.com> | 2017-07-22 20:36:44 +1000 |
|---|---|---|
| committer | Ben Woodcroft <donttrustben@gmail.com> | 2017-07-23 10:29:36 +1000 |
| commit | 0620387a594be1e8069dea8cda83dfc4a0b7f2de (patch) | |
| tree | 455f84f259e7c2759572ff078361c69857635256 /gnu/packages | |
| parent | 63fa0ffcd43484c2d7dcf32866529c022309ff20 (diff) | |
| download | guix-patches-0620387a594be1e8069dea8cda83dfc4a0b7f2de.tar guix-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.
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 10 | ||||
| -rw-r--r-- | gnu/packages/patches/bcftools-fix-makefile.patch | 33 |
2 files changed, 5 insertions, 38 deletions
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 |