| Unbundle the included samtools and SeqAn, and use system libraries. |
| See also: https://bugs.gentoo.org/show_bug.cgi?id=566494 |
| |
| Remove ancient ax_boost_base.m4 and ax_boost_thread.m4, and depend |
| on >=sys-devel/autoconf-archive-2016.09.16 in the ebuild instead. |
| See also: https://bugs.gentoo.org/show_bug.cgi?id=594810 |
| |
| --- a/configure.ac |
| +++ b/configure.ac |
| @@ -28,26 +28,15 @@ |
| AC_PROG_INSTALL |
| AM_PATH_PYTHON([2.4]) |
| |
| -m4_include([ax_boost_base.m4]) |
| -m4_include([ax_boost_thread.m4]) |
| # CXXFLAGS="$CXXFLAGS $threadLib" |
| AX_BOOST_BASE([1.38.0]) |
| +AX_BOOST_SYSTEM |
| AX_BOOST_THREAD |
| -if test -z "$BOOST_THREAD_LIBS"; then |
| +if test -z "$BOOST_THREAD_LIB"; then |
| AC_MSG_ERROR([boost.thread not found. Aborting.]) |
| fi |
| |
| |
| -# BAM related: |
| - ac_bam_path=samtools-0.1.18 |
| - BAM_LIB="-lbam" |
| - BAM_LDFLAGS="-L./$ac_bam_path" |
| - BAM_CPPFLAGS="-I./$ac_bam_path" |
| - AC_SUBST(BAM_CPPFLAGS) |
| - AC_SUBST(BAM_LDFLAGS) |
| - AC_SUBST(BAM_LIB) |
| - |
| - |
| # Checks for header files. |
| AC_CHECK_HEADERS([stdlib.h string.h unistd.h]) |
| |
| @@ -80,32 +69,23 @@ |
| # set CFLAGS and CXXFLAGS |
| #user_CFLAGS="${CXXFLAGS}" |
| user_CFLAGS=${CFLAGS} |
| -generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized" |
| +generic_CFLAGS="" |
| ext_CFLAGS="" |
| debug_CFLAGS="" |
| user_LDFLAGS="$LDFLAGS" |
| |
| -AC_ARG_ENABLE(intel64, [ --enable-intel64 optimize for Intel64 CPU such as Xeon and Core2], |
| - [ext_CFLAGS="${ext_CFLAGS} -mtune=nocona"], []) |
| - |
| AC_ARG_ENABLE([debug], |
| [AS_HELP_STRING([--enable-debug], |
| [enable debugging info (default is no)])], |
| [], [enable_debug=no]) |
| -AC_ARG_ENABLE([optim], |
| - [AS_HELP_STRING([--enable-optim@<:@=0|1|2|3@:>@], |
| - [set optimization level (default is 3)])], |
| - [if test "x$enable_optim" = xyes; then enable_optim=3; fi], |
| - [enable_optim=3]) |
| |
| -AS_IF([test "x$enable_optim" != xno], [ext_CFLAGS="$ext_CFLAGS -O$enable_optim"]) |
| AS_IF([test "x$enable_debug" = xyes], |
| [debug_CFLAGS="-DDEBUG"], |
| [debug_CFLAGS="-DNDEBUG"]) |
| |
| CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS}" |
| CXXFLAGS="$CFLAGS" |
| -CXXFLAGS="$CXXFLAGS $BAM_CPPFLAGS $BOOST_CPPFLAGS -I./SeqAn-1.4.2" |
| +CXXFLAGS="$CXXFLAGS $BAM_CPPFLAGS $BOOST_CPPFLAGS" |
| LDFLAGS="$BAM_LDFLAGS $BOOST_LDFLAGS $user_LDFLAGS" |
| |
| AM_INIT_AUTOMAKE([-Wall foreign tar-pax foreign]) |
| @@ -122,7 +102,7 @@ |
| -- ${PACKAGE_STRING} Configuration Results -- |
| C++ compiler: ${CXX} ${CXXFLAGS} |
| Linker flags: ${LDFLAGS} |
| - BOOST libraries: ${BOOST_THREAD_LIBS}" |
| + BOOST libraries: ${BOOST_THREAD_LIB}" |
| |
| if test x"${GCC}" = x"yes" ; then |
| gcc_version=`${CC} --version | head -n 1` |
| --- a/src/Makefile.am |
| +++ b/src/Makefile.am |
| @@ -683,17 +683,12 @@ |
| SeqAn-1.4.2/seqan/system/system_thread.h \ |
| SeqAn-1.4.2/seqan/version.h |
| |
| -SAMDIR = ./samtools-0.1.18 |
| -SAMLIB = libbam.a |
| -SAMPROG = samtools_0.1.18 |
| -BAM_LIB = -lbam |
| -BAM_CPPFLAGS = -I$(SAMDIR) |
| -BAM_LDFLAGS = -L$(SAMDIR) |
| +BAM_LIB = -lbam-0.1-legacy |
| +AM_CPPFLAGS = -I/usr/include/bam-0.1-legacy/ |
| |
| #-- progs to be installed in $prefix/bin |
| |
| bin_PROGRAMS = \ |
| - $(SAMPROG) \ |
| prep_reads \ |
| gtf_to_fasta \ |
| fix_map_ordering \ |
| @@ -722,9 +717,6 @@ |
| tophat2 \ |
| tophat |
| |
| -clean-local: |
| - cd $(SAMDIR) && make clean |
| - |
| tophat2: tophat2.sh |
| cp tophat2.sh tophat2 && chmod 755 tophat2 |
| |
| @@ -732,7 +724,7 @@ |
| sed -e 's|__VERSION__|$(VERSION)|' tophat.py > tophat && chmod 755 tophat |
| |
| #-- tophat library for linking convienence |
| -noinst_LIBRARIES = $(SAMLIB) libgc.a libtophat.a |
| +noinst_LIBRARIES = libgc.a libtophat.a |
| |
| noinst_HEADERS = \ |
| reads.h \ |
| @@ -801,11 +793,11 @@ |
| prep_reads_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) |
| |
| segment_juncs_SOURCES = segment_juncs.cpp |
| -segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB) |
| +segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) |
| segment_juncs_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS) |
| |
| long_spanning_reads_SOURCES = long_spanning_reads.cpp |
| -long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB) |
| +long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) |
| long_spanning_reads_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS) |
| |
| gtf_juncs_SOURCES = gtf_juncs.cpp |
| @@ -817,7 +809,7 @@ |
| juncs_db_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) |
| |
| tophat_reports_SOURCES = tophat_reports.cpp |
| -tophat_reports_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB) |
| +tophat_reports_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) |
| tophat_reports_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS) |
| |
| fix_map_ordering_SOURCES = fix_map_ordering.cpp |
| @@ -844,15 +836,5 @@ |
| gtf_to_fasta_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB) |
| gtf_to_fasta_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) |
| |
| - |
| -libbam_a_SOURCES = |
| -samtools_0_1_18_SOURCES = |
| - |
| -$(SAMPROG): $(SAMLIB) |
| - |
| - |
| -$(SAMLIB): |
| - cd $(SAMDIR) && make $(SAMPROG) && cp $(SAMLIB) $(SAMPROG) .. |
| - |
| install-data-hook: |
| cp -r intervaltree sortedcontainers $(DESTDIR)$(bindir) |
