From 56e373ef75d161325d4878f8cfaafffa7dba24a5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 23 Jun 2015 10:54:00 +0200
Subject: 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.
---
 .../patches/preseq-1.0.2-install-to-PREFIX.patch   | 37 ++++++++++++++++++++++
 .../patches/preseq-1.0.2-link-with-libbam.patch    | 33 +++++++++++++++++++
 2 files changed, 70 insertions(+)
 create mode 100644 gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch
 create mode 100644 gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch

(limited to 'gnu/packages/patches')

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)
-- 
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