diff options
| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-06-23 10:54:00 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-07-08 17:05:00 +0200 |
| commit | 56e373ef75d161325d4878f8cfaafffa7dba24a5 (patch) | |
| tree | 61eab520e4526306959992ba84b174af3e198620 /gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch | |
| parent | 5bdda30b32676528bcfa0a169c30237fabaa4607 (diff) | |
| download | guix-56e373ef75d161325d4878f8cfaafffa7dba24a5.tar.gz | |
gnu: Add preseq.
* gnu/packages/bioinformatics.scm (preseq): New variable. * gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch: New file. * gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch: New file. * gnu-system.am (dist_patch_DATA): Add them.
Diffstat (limited to 'gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch')
| -rw-r--r-- | gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch | 33 |
1 files changed, 33 insertions, 0 deletions
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 new file mode 100644 index 0000000000..035a3b1fe4 --- /dev/null +++ b/gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch @@ -0,0 +1,33 @@ +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 <ricardo.wurmus@mdc-berlin.de> +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) |