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gnu: preseq: Update to 2.0.

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* 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.
This commit is contained in:
Ricardo Wurmus 2015-11-20 11:14:48 +01:00
parent c6a24d6e92
commit b49c5a58dc
4 changed files with 18 additions and 97 deletions
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37
gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch
View file

@ -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 *~

33
gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch
View file

@ -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)