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