From b49c5a58dcbc6f10ebeaef7ccb3d24ff59695db8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
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-install-to-PREFIX.patch   | 37 ----------------------
 .../patches/preseq-1.0.2-link-with-libbam.patch    | 33 -------------------
 2 files changed, 70 deletions(-)
 delete mode 100644 gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch
 delete 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
deleted file mode 100644
index f8318ae0f5..0000000000
--- a/gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch
+++ /dev/null
@@ -1,37 +0,0 @@
-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
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 <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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