[med-svn] [Git][med-team/soapaligner][master] Preparations for initial upload.
Steffen Möller
gitlab at salsa.debian.org
Fri May 4 17:33:46 BST 2018
Steffen Möller pushed to branch master at Debian Med / soapaligner
Commits:
c7933ba9 by Steffen Moeller at 2018-05-04T18:33:03+02:00
Preparations for initial upload.
- - - - -
7 changed files:
- debian/changelog
- debian/control
- + debian/patches/UsageDoublette.patch
- debian/patches/compiler_options.patch
- + debian/patches/linkerror.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,7 +1,9 @@
-soapaligner (2.20-1) UNRELEASED; urgency=low
+soapaligner (2.20-1) unstable; urgency=low
[ Steffen Moeller ]
- * Initial release (Closes: #669917)
+ * Initial release (Closes: #669917,#897908)
+ There is a version 2.21 released as a binary for
+ which I failed to find the source code.
[ Andreas Tille ]
* Moved packaging from SVN to Git
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -4,9 +4,9 @@ Uploaders: Steffen Moeller <moeller at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 10)
-Standards-Version: 4.1.1
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/soapaligner.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/soapaligner.git
+Standards-Version: 4.1.3
+Vcs-Browser: https://salsa.debian.org/med-team/soapaligner
+Vcs-Git: https://salsa.debian.org/med-team/soapaligner.git
Homepage: http://soap.genomics.org.cn/soapaligner.html
Package: soapaligner
=====================================
debian/patches/UsageDoublette.patch
=====================================
--- /dev/null
+++ b/debian/patches/UsageDoublette.patch
@@ -0,0 +1,13 @@
+Index: soapaligner/soap.c
+===================================================================
+--- soapaligner.orig/soap.c
++++ soapaligner/soap.c
+@@ -107,7 +107,7 @@ unsigned char complementMap[256];
+
+ static SOAPOPT *opt;
+
+-void Usage(void) {
++static void Usage(void) {
+ fprintf(stdout, "\nProgram: %s\n", PROGRAM);
+ fprintf(stdout, "Compile Date: "
+ MAKE_TIME"\n");
=====================================
debian/patches/compiler_options.patch
=====================================
--- a/debian/patches/compiler_options.patch
+++ b/debian/patches/compiler_options.patch
@@ -1,22 +1,78 @@
-Index: soap2-2.20/Makefile
+Index: soapaligner/Makefile
===================================================================
---- soap2-2.20.orig/Makefile 2009-07-23 00:49:31.000000000 +0200
-+++ soap2-2.20/Makefile 2012-04-22 00:01:01.446041368 +0200
-@@ -6,7 +6,7 @@
- CC = gcc
- DEBUG_FLAGS = -g3 -Wall -O2
- PROFILE_FLAGS = -fprofile-arcs -ftest-coverage -pg
+--- soapaligner.orig/Makefile
++++ soapaligner/Makefile
+@@ -1,33 +1,40 @@
+-SHELL = /bin/sh
+-PROG = soap
+-DEBUG = NO
+-PROFILE = NO
+-PTHREADS = YES
+-CC = gcc
+-DEBUG_FLAGS = -g3 -Wall -O2
+-PROFILE_FLAGS = -fprofile-arcs -ftest-coverage -pg
-RELEASE_FLAGS = -msse3 -O3 -static -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer
-+RELEASE_FLAGS = $(DEBUG_FLAGS)
- STATIC_FLAGS = -static
- DFLAGS = -DMAKE_TIME=\""`date`"\"
- LIBS = -lm
-@@ -18,7 +18,7 @@
- DFLAGS += -DDEBUG
+-STATIC_FLAGS = -static
+-DFLAGS = -DMAKE_TIME=\""`date`"\"
+-LIBS = -lm
++SHELL ?= /bin/sh
++PROG ?= soap
++DEBUG ?= NO
++STATIC ?= NO
++PROFILE ?= NO
++PTHREADS ?= YES
++CC ?= gcc
++DEBUG_FLAGS ?= -g3 -Wall -O2
++PROFILE_FLAGS ?= -fprofile-arcs -ftest-coverage -pg
++RELEASE_FLAGS ?= -msse3 -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer
++STATIC_FLAGS ?= -static
++DFLAGS ?= -DMAKE_TIME=\""`date`"\"
++LDFLAGS ?=
++LIBS ?= -lm
+ #TARBALL_EXCLUDE = "*.(o,gz,zip)"
+ #ZIP_EXCLUDE = *.o *.gz *.zip
+
++ifeq (YES, $(STATIC))
++ CFLAGS += $(STATIC_FLAGS)
++endif
++
+ ifeq (YES, $(DEBUG))
+- CFLAGS = $(DEBUG_FLAGS) $(STATIC_FLAGS)
+- DFLAGS += -DDEBUG
++ CFLAGS += $(DEBUG_FLAGS) $(STATIC_FLAGS)
++ CFLAGS += -DDEBUG
# PTHREADS = NO
else
- CFLAGS = $(RELEASE_FLAGS) $(STATIC_FLAGS)
-+ CFLAGS = $(RELEASE_FLAGS)
++ CFLAGS += $(RELEASE_FLAGS)
endif
ifeq (YES, $(PTHREADS))
+ LIBS += -lpthread
+- DFLAGS += -DPTHREADS
++ CFLAGS += -DPTHREADS
+ endif
+
++CFLAGS += $(DFLAGS)
+ ifeq (YES, $(PROFILE))
+- DFLAGS += $(PROFILE_FLAGS)
++ CFLAGS += $(PROFILE_FLAGS)
+ endif
+
+ OBJ = SeqIO.o MiscUtilities.o MemManager.o TextConverter.o r250.o DNACount.o HSP.o Timing.o BWT.o extratools.o soapio.o BWTAln.o Match.o PairMatch.o stdaln.o kstring.o
+@@ -35,12 +42,12 @@ OBJ = SeqIO.o MiscUtilities.o MemManager
+ .SUFFIX: .c .o
+
+ .c.o:
+- $(CC) -c $(CFLAGS) $(DFLAGS) $< -o $@
++ $(CC) -c $(CFLAGS) $< -o $@
+
+ all: $(PROG)
+
+-$(PROG): $(OBJ) soap.o
+- $(CC) $(CFLAGS) $(DFLAGS) $(OBJ) soap.o -o $@ $(LIBS)
++$(PROG): $(OBJ)
++ $(CC) $(CFLAGS) $(OBJ) -o $@ $(LDFLAGS) $(LIBS)
+
+ SeqIO.o:SeqIO.h
+ r250.o: r250.h
=====================================
debian/patches/linkerror.patch
=====================================
--- /dev/null
+++ b/debian/patches/linkerror.patch
@@ -0,0 +1,35 @@
+Index: soapaligner/Makefile
+===================================================================
+--- soapaligner.orig/Makefile
++++ soapaligner/Makefile
+@@ -32,8 +32,8 @@ ifeq (YES, $(PROFILE))
+ CFLAGS += $(PROFILE_FLAGS)
+ endif
+
+-OBJ = SeqIO.o MiscUtilities.o MemManager.o TextConverter.o r250.o DNACount.o HSP.o Timing.o BWT.o extratools.o soapio.o BWTAln.o Match.o PairMatch.o stdaln.o kstring.o
+-.SUFFIX:
++OBJ = SeqIO.o MiscUtilities.o MemManager.o TextConverter.o r250.o DNACount.o HSP.o Timing.o BWT.o extratools.o soapio.o BWTAln.o Match.o PairMatch.o stdaln.o kstring.o soap.o
++
+ .SUFFIX: .c .o
+
+ .c.o:
+@@ -65,3 +65,5 @@ kstring.o:kstring.h
+
+ clean:
+ rm -f *.o $(PROG)
++
++.PHONY: clean
+Index: soapaligner/Match.c
+===================================================================
+--- soapaligner.orig/Match.c
++++ soapaligner/Match.c
+@@ -74,7 +74,8 @@
+ } \
+ }
+
+-inline void PickupHit(ALNSEQ *alnSeq, const int rr,int *site, HITTABLE *hits, const unsigned int *pacRef, const unsigned int dnaLength, unsigned short *cigar){
++/*inline */
++void PickupHit(ALNSEQ *alnSeq, const int rr,int *site, HITTABLE *hits, const unsigned int *pacRef, const unsigned int dnaLength, unsigned short *cigar){
+ #ifdef DEBUG
+ // fprintf(stderr, "Pick up for output\n");
+ #endif
=====================================
debian/patches/series
=====================================
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,3 @@
compiler_options.patch
+linkerror.patch
+UsageDoublette.patch
=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -2,7 +2,12 @@
# -*- makefile -*-
# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
+export DH_VERBOSE=1
+export DFLAGS = -DMAKE_TIME=\""be reproducible"\"
+
+export CFLAGS += -flto
+export CXXFLAGS += -flto
+export LDFLAGS += -Wl,-flto
%:
dh $@
View it on GitLab: https://salsa.debian.org/med-team/soapaligner/commit/c7933ba918b4afdb0def791a738ac1f38f4f62c8
---
View it on GitLab: https://salsa.debian.org/med-team/soapaligner/commit/c7933ba918b4afdb0def791a738ac1f38f4f62c8
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