fixed various issues about the GNU building scripts

diff --git a/Makefile.am b/Makefile.am
index e2304f7a849193fa1a5942903737295af4fc8d62..2f22f3b8446127bbaad95d8482b544210639c86f 100644 (file)
--- a/Makefile.am
+++ b/Makefile.am
@@ -15,42 +15,4 @@ samtools_LDADD = -lm -lz -lcurses
 
 razip_SOURCES = razip.c razf.c
 razip_LDADD = -lm -lz
-dist_bin_SCRIPTS = bowtie2sam.pl export2sam.pl novo2sam.pl samtools.pl soap2sam.pl wgsim_eval.pl zoom2sam.pl
-bin_PROGRAMS = faidx maq2sam-short maq2sam-long md5fa md5sum-lite wgsim
 
-faidx_SOURCES = ../faidx.c ../faidx.c
-#faidx_LDFLAGS = -D_NO_RAZF -DFAIDX_MAIN 
-
-md5fa_SOURCES = md5.c md5.h md5fa.c ../kseq.h
-#md5fa_LDADD = -lz
-
-md5sum_lite_SOURCES = md5.c md5.h
-#md5sum_lite_LDFLAGS = -DMD5SUM_MAIN
-
-maq2sam_short_SOURCES = maq2sam.c
-#maq2sam_short_LDADD = -lz
-
-maq2sam_long_SOURCES = maq2sam.c
-#maq2sam_long_LDADD = -lz
-
-wgsim_SOURCES = wgsim.c 
-wgsim_LDADD = -lm 
-
-faidx:../faidx.c ../faidx.h
-       $(CC) $(CFLAGS) -D_NO_RAZF -DFAIDX_MAIN -o $@ ../faidx.c
-md5fa:md5.o md5fa.o md5.h ../kseq.h
-       $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz
-md5fa.o:md5.h md5fa.c
-       $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c
-md5sum-lite:md5sum-lite.o
-       $(CC) $(CFLAGS) -o $@ md5sum-lite.o
-md5sum-lite.o:md5.c md5.h
-       $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c
-maq2sam-short:maq2sam-short.o
-       $(CC) $(CFLAGS) -o $@ maq2sam-short.o -lz 
-maq2sam-short.o:maq2sam.c
-       $(CC) -c $(CFLAGS) -o $@ maq2sam.c 
-maq2sam-long:maq2sam-long.o
-       $(CC) $(CFLAGS) -o $@ maq2sam-long.o -lz 
-maq2sam-long.o:maq2sam.c
-       $(CC) -c $(CFLAGS) -DMAQ_LONGREADS -D_MAQ_LONGREADS -o $@ maq2sam.c 

diff --git a/autogen.sh b/autogen.sh
index 99f0a5f9494b00d9b47fa7b43b6e8b5383b93142..117462c7ffdc340972417c6793a9c1a17d65edee 100644 (file)
--- a/autogen.sh
+++ b/autogen.sh
@@ -15,37 +15,3 @@ run aclocal
 run autoheader
 run automake -a
 run autoconf
-#!/bin/sh
-
-run ()
-{
-    echo "running: $*"
-    eval $*
-
-    if test $? != 0 ; then
-       echo "error: while running '$*'"
-       exit 1
-    fi
-}
-
-run aclocal
-run autoheader
-run automake -a
-run autoconf
-#!/bin/sh
-
-run ()
-{
-    echo "running: $*"
-    eval $*
-
-    if test $? != 0 ; then
-       echo "error: while running '$*'"
-       exit 1
-    fi
-}
-
-run aclocal
-run autoheader
-run automake -a
-run autoconf

diff --git a/cleanup.sh b/cleanup.sh
index 96381e6d3319de37db4dfa854b497b855139f160..899479e7df35595bc9e1bf8b31d0aa609c4a1fb2 100644 (file)
--- a/cleanup.sh
+++ b/cleanup.sh
@@ -2,11 +2,3 @@ if [ -f "Makefile" ]; then
        make distclean
 fi
 rm -fr *~ .in .gdb_history Makefile.in aclocal.m4 configure autom4*.cache config.guess config.h.in config.sub depcomp install-sh missing mkinstalldirs
-if [ -f "Makefile" ]; then
-       make distclean
-fi
-rm -fr *~ .in .gdb_history Makefile.in aclocal.m4 configure autom4*.cache config.guess config.h.in config.sub depcomp install-sh missing mkinstalldirs
-if [ -f "Makefile" ]; then
-       make distclean
-fi
-rm -fr *~ .in .gdb_history Makefile.in aclocal.m4 configure autom4*.cache config.guess config.h.in config.sub depcomp install-sh missing mkinstalldirs

diff --git a/configure.ac b/configure.ac
index 7bd869662743dc66c146a4c4b80cc6859a55e3f0..d8d25e1d7e261592a75c9ced045703038db78efd 100644 (file)
--- a/configure.ac
+++ b/configure.ac
@@ -6,7 +6,6 @@ AC_CANONICAL_HOST
 AC_PROG_INSTALL
 
 AC_PROG_CC
-AC_PROG_CXX
 
 # set CFLAGS and CXXFLAGS
 user_CFLAGS="${CFLAGS} -D_IOLIB=2 -D_FILE_OFFSET_BITS=64"
@@ -33,76 +32,4 @@ AC_HEADER_STDBOOL
 AC_TYPE_OFF_T
 AC_TYPE_SIZE_T
 
-AC_OUTPUT([Makefile misc/Makefile])
-AC_INIT(SAMTOOLS, 0.1.3)
-AM_CONFIG_HEADER(config.h)
-AM_INIT_AUTOMAKE([no-dependencies])
-AC_CANONICAL_HOST
-
-AC_PROG_INSTALL
-
-AC_PROG_CC
-AC_PROG_CXX
-
-# set CFLAGS and CXXFLAGS
-user_CFLAGS="${CFLAGS} -D_IOLIB=2 -D_FILE_OFFSET_BITS=64"
-generic_CFLAGS="-Wall -L."
-
-AC_ARG_ENABLE(norazf, [  --disable-razf          disable razf support],
-                         [user_DFLAGS="${user_DFLAGS} -D_NO_RAZF"], [])
-AC_ARG_ENABLE(nocurses, [  --disable-curses      disable curses support],
-                         [user_DFLAGS="${user_DFLAGS} -D_NO_CURSES"], [])
-CFLAGS="${generic_CFLAGS} ${user_CFLAGS}"
-CXXFLAGS=$CFLAGS
-
-AC_STDC_HEADERS
-AC_CHECK_FUNCS([bzero memset pow sqrt strcasecmp strdup strstr strtol])
-AC_CHECK_HEADERS([zlib.h fcntl.h malloc.h stddef.h])
-AC_CHECK_TYPES([ptrdiff_t])
-AC_C_CONST
-AC_C_INLINE
-AC_FUNC_FSEEKO
-AC_FUNC_MALLOC
-AC_FUNC_MEMCMP
-AC_FUNC_REALLOC
-AC_HEADER_STDBOOL
-AC_TYPE_OFF_T
-AC_TYPE_SIZE_T
-
-AC_OUTPUT([Makefile misc/Makefile])
-AC_INIT(SAMTOOLS, 0.1.3)
-AM_CONFIG_HEADER(config.h)
-AM_INIT_AUTOMAKE([no-dependencies])
-AC_CANONICAL_HOST
-
-AC_PROG_INSTALL
-
-AC_PROG_CC
-AC_PROG_CXX
-
-# set CFLAGS and CXXFLAGS
-user_CFLAGS="${CFLAGS} -D_IOLIB=2 -D_FILE_OFFSET_BITS=64"
-generic_CFLAGS="-Wall -L."
-
-AC_ARG_ENABLE(norazf, [  --disable-razf          disable razf support],
-                         [user_DFLAGS="${user_DFLAGS} -D_NO_RAZF"], [])
-AC_ARG_ENABLE(nocurses, [  --disable-curses      disable curses support],
-                         [user_DFLAGS="${user_DFLAGS} -D_NO_CURSES"], [])
-CFLAGS="${generic_CFLAGS} ${user_CFLAGS}"
-CXXFLAGS=$CFLAGS
-
-AC_STDC_HEADERS
-AC_CHECK_FUNCS([bzero memset pow sqrt strcasecmp strdup strstr strtol])
-AC_CHECK_HEADERS([zlib.h fcntl.h malloc.h stddef.h])
-AC_CHECK_TYPES([ptrdiff_t])
-AC_C_CONST
-AC_C_INLINE
-AC_FUNC_FSEEKO
-AC_FUNC_MALLOC
-AC_FUNC_MEMCMP
-AC_FUNC_REALLOC
-AC_HEADER_STDBOOL
-AC_TYPE_OFF_T
-AC_TYPE_SIZE_T
-
-AC_OUTPUT([Makefile misc/Makefile])
+AC_OUTPUT([Makefile misc/Makefile])
\ No newline at end of file

diff --git a/misc/Makefile.am b/misc/Makefile.am
new file mode 100644 (file)
index 0000000..6caaf63
--- /dev/null
+++ b/misc/Makefile.am
@@ -0,0 +1,39 @@
+dist_bin_SCRIPTS = bowtie2sam.pl export2sam.pl novo2sam.pl samtools.pl soap2sam.pl wgsim_eval.pl zoom2sam.pl
+bin_PROGRAMS = faidx maq2sam-short maq2sam-long md5fa md5sum-lite wgsim
+
+faidx_SOURCES = ../faidx.c ../faidx.c
+#faidx_LDFLAGS = -D_NO_RAZF -DFAIDX_MAIN 
+
+md5fa_SOURCES = md5.c md5.h md5fa.c ../kseq.h
+#md5fa_LDADD = -lz
+
+md5sum_lite_SOURCES = md5.c md5.h
+#md5sum_lite_LDFLAGS = -DMD5SUM_MAIN
+
+maq2sam_short_SOURCES = maq2sam.c
+#maq2sam_short_LDADD = -lz
+
+maq2sam_long_SOURCES = maq2sam.c
+#maq2sam_long_LDADD = -lz
+
+wgsim_SOURCES = wgsim.c 
+wgsim_LDADD = -lm 
+
+faidx:../faidx.c ../faidx.h
+       $(CC) $(CFLAGS) -D_NO_RAZF -DFAIDX_MAIN -o $@ ../faidx.c
+md5fa:md5.o md5fa.o md5.h ../kseq.h
+       $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz
+md5fa.o:md5.h md5fa.c
+       $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c
+md5sum-lite:md5sum-lite.o
+       $(CC) $(CFLAGS) -o $@ md5sum-lite.o
+md5sum-lite.o:md5.c md5.h
+       $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c
+maq2sam-short:maq2sam-short.o
+       $(CC) $(CFLAGS) -o $@ maq2sam-short.o -lz 
+maq2sam-short.o:maq2sam.c
+       $(CC) -c $(CFLAGS) -o $@ maq2sam.c 
+maq2sam-long:maq2sam-long.o
+       $(CC) $(CFLAGS) -o $@ maq2sam-long.o -lz 
+maq2sam-long.o:maq2sam.c
+       $(CC) -c $(CFLAGS) -DMAQ_LONGREADS -D_MAQ_LONGREADS -o $@ maq2sam.c