From b49c5a58dcbc6f10ebeaef7ccb3d24ff59695db8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 Nov 2015 11:14:48 +0100 Subject: gnu: preseq: Update to 2.0. * gnu/packages/bioinformatics.scm (preseq): Update to 2.0. [source]: Add file-name field, remove patches. [arguments]: Remove unused build phases, add make flags. [inputs]: Add smithlab-cpp. * gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch: Remove file. * gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch: Remove file. * gnu-system.am (dist_patch_DATA): Remove them. --- .../patches/preseq-1.0.2-link-with-libbam.patch | 33 ---------------------- 1 file changed, 33 deletions(-) delete mode 100644 gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch (limited to 'gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch') diff --git a/gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch b/gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch deleted file mode 100644 index 035a3b1fe4..0000000000 --- a/gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch +++ /dev/null @@ -1,33 +0,0 @@ -This patch has been submitted upstream: https://github.com/smithlabcode/preseq/pull/15 - -From a937a54d56e8a6ff06237471e568154d1fa5f267 Mon Sep 17 00:00:00 2001 -From: Ricardo Wurmus -Date: Thu, 25 Jun 2015 15:02:35 +0200 -Subject: [PATCH] Link with libbam.a if provided via LIBBAM - ---- - Makefile | 7 +++++++ - 1 file changed, 7 insertions(+) - -diff --git a/Makefile b/Makefile -index e334f2f..de310e4 100644 ---- a/preseq-master/Makefile -+++ b/preseq-master/Makefile -@@ -83,10 +83,17 @@ $(PROGS): $(addprefix $(SMITHLAB_CPP)/, \ - preseq: continued_fraction.o load_data_for_complexity.o moment_sequence.o - - ifdef SAMTOOLS_DIR -+ifdef LIBBAM -+LIBS += -pthread -+bam2mr preseq: $(addprefix $(SMITHLAB_CPP)/, SAM.o) \ -+ $(LIBBAM) -+else - bam2mr preseq: $(addprefix $(SMITHLAB_CPP)/, SAM.o) \ - $(addprefix $(SAMTOOLS_DIR)/, sam.o bam.o bam_import.o bam_pileup.o \ - faidx.o bam_aux.o kstring.o knetfile.o sam_header.o razf.o bgzf.o) - endif -+endif # SAMTOOLS_DIR -+ - - %.o: %.cpp %.hpp - $(CXX) $(CXXFLAGS) -c -o $@ $< $(INCLUDEARGS) -- cgit v1.2.3