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 | |
| parent | 5bdda30b32676528bcfa0a169c30237fabaa4607 (diff) | |
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')
| -rw-r--r-- | gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch | 37 | ||||
| -rw-r--r-- | gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch | 33 |
2 files changed, 70 insertions, 0 deletions
diff --git a/gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch b/gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch new file mode 100644 index 0000000000..f8318ae0f5 --- /dev/null +++ b/gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch @@ -0,0 +1,37 @@ +This patch has been submitted upstream: https://github.com/smithlabcode/preseq/pull/15 + +From 65387b0d766e6c06a15cf8d8f9183d9a4ba644bb Mon Sep 17 00:00:00 2001 +From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> +Date: Thu, 25 Jun 2015 15:01:53 +0200 +Subject: [PATCH] Install to PREFIX + +--- + Makefile | 8 ++++++-- + 1 file changed, 6 insertions(+), 2 deletions(-) + +diff --git a/Makefile b/Makefile +index 4d0367a..e334f2f 100644 +--- a/preseq-master/Makefile ++++ b/preseq-master/Makefile +@@ -22,6 +22,10 @@ ifndef ROOT + ROOT = $(shell pwd) + endif + ++ifndef PREFIX ++PREFIX = $(ROOT) ++endif ++ + ifndef SMITHLAB_CPP + SMITHLAB_CPP=$(ROOT)/smithlab_cpp/ + endif +@@ -91,8 +95,8 @@ endif + $(CXX) $(CXXFLAGS) -o $@ $^ $(INCLUDEARGS) $(LIBS) + + install: $(PROGS) +- @mkdir -p $(ROOT)/bin +- @install -m 755 $(PROGS) $(ROOT)/bin ++ @mkdir -p $(PREFIX)/bin ++ @install -m 755 $(PROGS) $(PREFIX)/bin + + clean: + @-rm -f $(PROGS) *.o *~ 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) |