diff options
Diffstat (limited to 'sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch')
| -rw-r--r-- | sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch | 162 |
1 files changed, 0 insertions, 162 deletions
diff --git a/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch b/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch deleted file mode 100644 index 9d0a2694051a..000000000000 --- a/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch +++ /dev/null @@ -1,162 +0,0 @@ -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) |