sci-biology/tophat: Remove old and broken

Package-Manager: portage-2.2.28

10 files changed, 0 insertions, 526 deletions

diff --git a/sci-biology/tophat/Manifest b/sci-biology/tophat/Manifest
index b269f5d56f90..2bf812108794 100644
--- a/sci-biology/tophat/Manifest
+++ b/sci-biology/tophat/Manifest
@@ -1,7 +1,2 @@
 DIST tophat-1.0.12.tar.gz 468781 SHA256 f67b3f89aa79c7e14b40bcdba87f5aba6d322f869ca4260503e64ffcd2b621b2 SHA512 275e14cb6fb5f7a0874adcf843aabfda6c6868f835faa2d03e6561646ca1fc80804fe1887c51a375125f2f5ed6242e304f97ff12774a7d676b4964614d4a5bf1 WHIRLPOOL ea62ce14aae28dc0cc2b18fde870a0d3c021d9fb0c2ffb728b02b008b5f5bd416f29176fe81ed2ad8b1a41014f8a7114e2b8032426e2767effe9cc6933417cee
-DIST tophat-1.4.1.tar.gz 1420422 SHA256 97fd6e09e3cafa90b969dac152585ce5bab4c86f32a980ce2c8ecaac846cd937 SHA512 f3f3823d7780cd7159c97d7dca38e4f8c599377a15d8ce4b9db804df2c619c050d3cc6a182e6aa21d2ff03af6a436ff0f2bd26c48c280360f205b1cd4e13539e WHIRLPOOL 0279af557ca2e473582068f8a2229b509ebaa5baedc3b60f89a63bee622f681b0dfcc8996c32fbf3df45e32b38a6d91446558bdc7d992da5874a4c2936e3ff7a
-DIST tophat-2.0.0.tar.gz 1750811 SHA256 1c45812225906fd014ed9671a3696727c6ed0cc5be8f330b3c5ec39a9234be97 SHA512 5bd1dcc79c301dc0b464dd95d6da2b2ed69c4e003bc1f9c5cb556a7974bcdb86cbe6f7d8912856691ca89e9a5a10cbe10fa7391c4bbdc163408e1e57afed7295 WHIRLPOOL ace795553630bcd1e9966cae2ed2c42195dea2f3845fe778d591ad0214afef28ca389f32f0bd53ad01d1e3a520be140e77305313992be16259c111a9aa5e8514
-DIST tophat-2.0.2.tar.gz 1759933 SHA256 f9e40ae123dab24d2f2d6896ebf191c8ae3c05c80da6d4d965defe7579d553e0 SHA512 8341d406bfc2b86323932a151ad60469c6d50031bace433c5e3b6678a92eaed3516744fb9077d0e8944018275642050e2e9aca0126b4dd69423754c3dc9ae83c WHIRLPOOL 45a52fc96b258f4ae0b5b7a4d1dc4c22885e0b9230891dde1db85671deeceb3213008de02878cc3b1f9dc6af68b40bc897f691a1835bd4abf29d1a2bde42e1c2
-DIST tophat-2.0.8.tar.gz 1757036 SHA256 07d323d295effc99d4e261439c5ba2e10d5530af078e5de97c1a7bf1cbdd0da1 SHA512 c69360cc2f558c37d14b6a0e006f2483771ce5cdb42dc8397dd15a944a61d762843158adbf7c2bc89c2d4db46d9a02633dbd2721bf3376ef5d3ae6fb153db100 WHIRLPOOL a97ad6d47be23089605578a6f8ff9434afcb27a9fa58118b5b923af1d79530614af9fcaf5ebda2043603bf2dd8b10c2b7636e7b14662b9ab4f6e2059da4cb2b2
-DIST tophat-2.0.9.tar.gz 1766681 SHA256 9b506bbfdbb14b296d804557a50f41cc167480dfeed66a31c33e2ffb580afd38 SHA512 a81b801ee6c1f643d1fa507c2372d43ccdf4922d3f7ab76a34442c96aee78a3afc4a47ba164d46c6b6b6451aeae78b711c44c118e584da742940f74af7bc9610 WHIRLPOOL a67392251e592df62deb3fe58dcc4eadd0d0b1fe0a09389e48f1f30a7c591343794d1e1b2a27467c0a0f5a0e84dd5a5fbdef538a5bcf1b80ba8972e6ec02fbcf
 DIST tophat-2.1.1.tar.gz 2259554 SHA256 37840b96f3219630082b15642c47f5ef95d14f6ee99c06a369b08b3d05684da5 SHA512 e2e0943a6f3d34b83922e6e403b65a3bee480a2b2bb4bf2de0cae7e0ef5bb166b66fec923316c2b643e8550e43c842f0f1bcc2ca7249d20fbcf5a4733fbdeabc WHIRLPOOL 1e0d2bc4031eaa56a3b77ca5966c2ed439a85c9b05f028f69f4477d517e51371156bbe73d499536148eb42d60641af7f294641ee79bc855fcc4df74d70dae26c
diff --git a/sci-biology/tophat/files/tophat-2.0.2-flags.patch b/sci-biology/tophat/files/tophat-2.0.2-flags.patch
deleted file mode 100644
index ac1ca62da254..000000000000
--- a/sci-biology/tophat/files/tophat-2.0.2-flags.patch
+++ /dev/null
@@ -1,124 +0,0 @@
- configure.ac    |    6 +++---
- src/Makefile.am |   30 +++++++++++++++---------------
- 2 files changed, 18 insertions(+), 18 deletions(-)
-
-diff --git a/configure.ac b/configure.ac
-index 314a78e..f6933e6 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -68,7 +68,8 @@ AC_CANONICAL_HOST
- # set CFLAGS and CXXFLAGS
- #user_CFLAGS="${CXXFLAGS}"
- user_CFLAGS=${CFLAGS}
--generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized"
-+#generic_CFLAGS="-Wall -Wno-strict-aliasing -Wuninitialized"
-+generic_CFLAGS=""
- ext_CFLAGS=""
- debug_CFLAGS=""
- AC_ARG_ENABLE(intel64,      [  --enable-intel64        optimize for Intel64 CPU such as Xeon and Core2],
-@@ -84,7 +85,7 @@ AC_ARG_ENABLE([optim],
-               [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$enable_optim" != xno], [ext_CFLAGS="$ext_CFLAGS -O$enable_optim"])	
- AS_IF([test "x$enable_debug" = xyes],
-       [debug_CFLAGS="-DDEBUG"],
-       [debug_CFLAGS="-DNDEBUG"])
-@@ -92,7 +93,6 @@ AS_IF([test "x$enable_debug" = xyes],
- CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS}"
- CXXFLAGS="$CFLAGS"
- CXXFLAGS="$CXXFLAGS $BOOST_CPPFLAGS $BAM_CPPFLAGS -I./SeqAn-1.3"
--LDFLAGS="$ext_LDFLAGS"
- 
- AM_INIT_AUTOMAKE([-Wall foreign tar-pax foreign])
- 
-diff --git a/src/Makefile.am b/src/Makefile.am
-index aa17841..42f9c0c 100644
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -2,7 +2,7 @@
- 
- #SUBDIRS = samtools
- 
--#AM_CXXFLAGS = -I$(top_srcdir)/src/SeqAn-1.3
-+AM_CXXFLAGS = -I$(top_srcdir)/src/SeqAn-1.3
- 
- # Generated with 
- # find SeqAn-1.3 -type f -print | grep -v ".svn" | sed 's/$/ \\/g'
-@@ -550,7 +550,7 @@ CLEANFILES = \
- 	tophat2
- 
- tophat2: tophat2.in
--	sed -e 's|__PREFIX__|$(prefix)|' tophat2.in > tophat2
-+	sed -e 's|__PREFIX__|$(prefix)|' $(top_srcdir)/src/tophat2.in > tophat2
- 
- #SUFFIXES = .py
- #.py:
-@@ -621,53 +621,53 @@ libgc_a_SOURCES = \
- #-- program sources
- 
- prep_reads_SOURCES = prep_reads.cpp
--prep_reads_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
-+prep_reads_LDADD = libtophat.a $(BAM_LIB)
- prep_reads_LDFLAGS = $(BAM_LDFLAGS)
- 
- segment_juncs_SOURCES = segment_juncs.cpp
--segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BAM_LIB)
-+segment_juncs_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BAM_LIB)
- segment_juncs_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
- 
- long_spanning_reads_SOURCES = long_spanning_reads.cpp
--long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BAM_LIB)
-+long_spanning_reads_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BAM_LIB)
- long_spanning_reads_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
- 
- gtf_juncs_SOURCES = gtf_juncs.cpp
--gtf_juncs_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
-+gtf_juncs_LDADD = libtophat.a libgc.a $(BAM_LIB)
- gtf_juncs_LDFLAGS = $(BAM_LDFLAGS)
- 
- juncs_db_SOURCES = juncs_db.cpp
--juncs_db_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
-+juncs_db_LDADD = libtophat.a $(BAM_LIB)
- juncs_db_LDFLAGS = $(BAM_LDFLAGS)
- 
- tophat_reports_SOURCES = tophat_reports.cpp
--tophat_reports_LDADD = $(top_builddir)/src/libtophat.a  $(BOOST_THREAD_LIB) $(BAM_LIB)
-+tophat_reports_LDADD = libtophat.a  $(BOOST_THREAD_LIB) $(BAM_LIB)
- tophat_reports_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
- 
- fix_map_ordering_SOURCES = fix_map_ordering.cpp
--fix_map_ordering_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
-+fix_map_ordering_LDADD = libtophat.a $(BAM_LIB)
- fix_map_ordering_LDFLAGS = $(BAM_LDFLAGS)
- 
- bam2fastx_SOURCES = bam2fastx.cpp
--bam2fastx_LDADD = $(top_builddir)/src/libgc.a $(BAM_LIB)
-+bam2fastx_LDADD = libgc.a $(BAM_LIB)
- bam2fastx_LDFLAGS = $(BAM_LDFLAGS)
- 
- bam_merge_SOURCES = bam_merge.cpp
--bam_merge_LDADD = $(top_builddir)/src/libtophat.a $(top_builddir)/src/libgc.a $(BAM_LIB)
-+bam_merge_LDADD = libtophat.a libgc.a $(BAM_LIB)
- bam_merge_LDFLAGS = $(BAM_LDFLAGS)
- 
- closure_juncs_SOURCES = closures.cpp
--closure_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
-+closure_juncs_LDADD = libtophat.a $(BAM_LIB)
- closure_juncs_LDFLAGS = $(BAM_LDFLAGS)
- 
- sam_juncs_SOURCES = sam_juncs.cpp
--sam_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
-+sam_juncs_LDADD = libtophat.a $(BAM_LIB)
- sam_juncs_LDFLAGS = $(BAM_LDFLAGS)
- 
- map2gtf_SOURCES = map2gtf.cpp
--map2gtf_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
-+map2gtf_LDADD = libtophat.a libgc.a $(BAM_LIB)
- map2gtf_LDFLAGS = $(BAM_LDFLAGS)
- 
- gtf_to_fasta_SOURCES = GTFToFasta.cpp FastaTools.cpp
--gtf_to_fasta_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
-+gtf_to_fasta_LDADD = libtophat.a libgc.a $(BAM_LIB)
- gtf_to_fasta_LDFLAGS = $(BAM_LDFLAGS)
diff --git a/sci-biology/tophat/files/tophat-2.0.8-flags.patch b/sci-biology/tophat/files/tophat-2.0.8-flags.patch
deleted file mode 100644
index 604f657d4c42..000000000000
--- a/sci-biology/tophat/files/tophat-2.0.8-flags.patch
+++ /dev/null
@@ -1,105 +0,0 @@
- configure.ac    |  3 ++-
- src/Makefile.am | 50 +++++++++++++++++++++++++-------------------------
- 2 files changed, 27 insertions(+), 26 deletions(-)
-
-diff --git a/configure.ac b/configure.ac
-index 75e9218..98b05d2 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -68,7 +68,8 @@ AC_CANONICAL_HOST
- # set CFLAGS and CXXFLAGS
- #user_CFLAGS="${CXXFLAGS}"
- user_CFLAGS=${CFLAGS}
--generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized"
-+#generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized"
-+generic_CFLAGS=""
- ext_CFLAGS=""
- debug_CFLAGS=""
- user_LDFLAGS="$LDFLAGS"
-diff --git a/src/Makefile.am b/src/Makefile.am
-index dde692e..ebb9fcd 100644
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -545,7 +545,7 @@ CLEANFILES = \
- 	tophat2
- 
- tophat2: tophat2.in
--	sed -e 's|__PREFIX__|$(prefix)|' tophat2.in > tophat2
-+	sed -e 's|__PREFIX__|$(prefix)|' $(top_srcdir)/src/tophat2.in > tophat2
- 
- #SUFFIXES = .py
- #.py:
-@@ -617,49 +617,49 @@ libgc_a_SOURCES = \
- #-- program sources
- 
- prep_reads_SOURCES = prep_reads.cpp
--prep_reads_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
--prep_reads_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) 
-+prep_reads_LDADD = libtophat.a $(BAM_LIB)
-+prep_reads_LDFLAGS = $(BAM_LDFLAGS) 
- 
- segment_juncs_SOURCES = segment_juncs.cpp
--segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
--segment_juncs_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
-+segment_juncs_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
-+segment_juncs_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
- 
- long_spanning_reads_SOURCES = long_spanning_reads.cpp
--long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
--long_spanning_reads_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
-+long_spanning_reads_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
-+long_spanning_reads_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
- 
- gtf_juncs_SOURCES = gtf_juncs.cpp
--gtf_juncs_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
--gtf_juncs_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
-+gtf_juncs_LDADD = libtophat.a libgc.a $(BAM_LIB)
-+gtf_juncs_LDFLAGS = $(BAM_LDFLAGS)
- 
- juncs_db_SOURCES = juncs_db.cpp
--juncs_db_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
--juncs_db_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
-+juncs_db_LDADD = libtophat.a $(BAM_LIB)
-+juncs_db_LDFLAGS = $(BAM_LDFLAGS)
- 
- tophat_reports_SOURCES = tophat_reports.cpp
--tophat_reports_LDADD = $(top_builddir)/src/libtophat.a  $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
--tophat_reports_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
-+tophat_reports_LDADD = libtophat.a  $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
-+tophat_reports_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
- 
- fix_map_ordering_SOURCES = fix_map_ordering.cpp
--fix_map_ordering_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
--fix_map_ordering_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
-+fix_map_ordering_LDADD = libtophat.a $(BAM_LIB)
-+fix_map_ordering_LDFLAGS = $(BAM_LDFLAGS)
- 
- bam2fastx_SOURCES = bam2fastx.cpp
--bam2fastx_LDADD = $(top_builddir)/src/libgc.a $(BAM_LIB)
--bam2fastx_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
-+bam2fastx_LDADD = libgc.a $(BAM_LIB)
-+bam2fastx_LDFLAGS = $(BAM_LDFLAGS)
- 
- bam_merge_SOURCES = bam_merge.cpp
--bam_merge_LDADD = $(top_builddir)/src/libtophat.a $(top_builddir)/src/libgc.a $(BAM_LIB)
--bam_merge_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
-+bam_merge_LDADD = libtophat.a libgc.a $(BAM_LIB)
-+bam_merge_LDFLAGS = $(BAM_LDFLAGS)
- 
- sam_juncs_SOURCES = sam_juncs.cpp
--sam_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
--sam_juncs_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
-+sam_juncs_LDADD = libtophat.a $(BAM_LIB)
-+sam_juncs_LDFLAGS = $(BAM_LDFLAGS)
- 
- map2gtf_SOURCES = map2gtf.cpp
--map2gtf_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
--map2gtf_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
-+map2gtf_LDADD = libtophat.a libgc.a $(BAM_LIB)
-+map2gtf_LDFLAGS = $(BAM_LDFLAGS)
- 
- gtf_to_fasta_SOURCES = GTFToFasta.cpp FastaTools.cpp
--gtf_to_fasta_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
--gtf_to_fasta_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
-+gtf_to_fasta_LDADD = libtophat.a libgc.a $(BAM_LIB)
-+gtf_to_fasta_LDFLAGS = $(BAM_LDFLAGS)
diff --git a/sci-biology/tophat/files/tophat-2.0.9-flags.patch b/sci-biology/tophat/files/tophat-2.0.9-flags.patch
deleted file mode 100644
index af89e72084bf..000000000000
--- a/sci-biology/tophat/files/tophat-2.0.9-flags.patch
+++ /dev/null
@@ -1,109 +0,0 @@
- configure.ac    |  3 ++-
- src/Makefile.am | 50 +++++++++++++++++++++++++-------------------------
- 2 files changed, 27 insertions(+), 26 deletions(-)
-
-diff --git a/configure.ac b/configure.ac
-index 75e9218..98b05d2 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -68,7 +68,8 @@ AC_CANONICAL_HOST
- # set CFLAGS and CXXFLAGS
- #user_CFLAGS="${CXXFLAGS}"
- user_CFLAGS=${CFLAGS}
--generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized"
-+#generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized"
-+generic_CFLAGS=""
- ext_CFLAGS=""
- debug_CFLAGS=""
- user_LDFLAGS="$LDFLAGS"
-diff --git a/src/Makefile.am b/src/Makefile.am
-index dde692e..ebb9fcd 100644
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -545,10 +545,10 @@ CLEANFILES = \
- 	tophat2
- 
- tophat2: tophat2.in
--	sed -e 's|__PREFIX__|$(prefix)|' tophat2.in > tophat2
-+	sed -e 's|__PREFIX__|$(prefix)|' $(top_srcdir)/src/tophat2.in > tophat2
- 
- tophat: tophat.py
--	sed -e 's|__VERSION__|$(VERSION)|' tophat.py > tophat
-+	sed -e 's|__VERSION__|$(VERSION)|' $(top_srcdir)/src/tophat.py > tophat
- 
- #SUFFIXES = .py
- #.py:
-@@ -617,49 +617,49 @@ libgc_a_SOURCES = \
- #-- program sources
- 
- prep_reads_SOURCES = prep_reads.cpp
--prep_reads_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
--prep_reads_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) 
-+prep_reads_LDADD = libtophat.a $(BAM_LIB)
-+prep_reads_LDFLAGS = $(BAM_LDFLAGS) 
- 
- segment_juncs_SOURCES = segment_juncs.cpp
--segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
--segment_juncs_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
-+segment_juncs_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
-+segment_juncs_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
- 
- long_spanning_reads_SOURCES = long_spanning_reads.cpp
--long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
--long_spanning_reads_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
-+long_spanning_reads_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
-+long_spanning_reads_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
- 
- gtf_juncs_SOURCES = gtf_juncs.cpp
--gtf_juncs_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
--gtf_juncs_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
-+gtf_juncs_LDADD = libtophat.a libgc.a $(BAM_LIB)
-+gtf_juncs_LDFLAGS = $(BAM_LDFLAGS)
- 
- juncs_db_SOURCES = juncs_db.cpp
--juncs_db_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
--juncs_db_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
-+juncs_db_LDADD = libtophat.a $(BAM_LIB)
-+juncs_db_LDFLAGS = $(BAM_LDFLAGS)
- 
- tophat_reports_SOURCES = tophat_reports.cpp
--tophat_reports_LDADD = $(top_builddir)/src/libtophat.a  $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
--tophat_reports_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
-+tophat_reports_LDADD = libtophat.a  $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
-+tophat_reports_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
- 
- fix_map_ordering_SOURCES = fix_map_ordering.cpp
--fix_map_ordering_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
--fix_map_ordering_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
-+fix_map_ordering_LDADD = libtophat.a $(BAM_LIB)
-+fix_map_ordering_LDFLAGS = $(BAM_LDFLAGS)
- 
- bam2fastx_SOURCES = bam2fastx.cpp
--bam2fastx_LDADD = $(top_builddir)/src/libgc.a $(BAM_LIB)
--bam2fastx_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
-+bam2fastx_LDADD = libgc.a $(BAM_LIB)
-+bam2fastx_LDFLAGS = $(BAM_LDFLAGS)
- 
- bam_merge_SOURCES = bam_merge.cpp
--bam_merge_LDADD = $(top_builddir)/src/libtophat.a $(top_builddir)/src/libgc.a $(BAM_LIB)
--bam_merge_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
-+bam_merge_LDADD = libtophat.a libgc.a $(BAM_LIB)
-+bam_merge_LDFLAGS = $(BAM_LDFLAGS)
- 
- sam_juncs_SOURCES = sam_juncs.cpp
--sam_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
--sam_juncs_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
-+sam_juncs_LDADD = libtophat.a $(BAM_LIB)
-+sam_juncs_LDFLAGS = $(BAM_LDFLAGS)
- 
- map2gtf_SOURCES = map2gtf.cpp
--map2gtf_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
--map2gtf_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
-+map2gtf_LDADD = libtophat.a libgc.a $(BAM_LIB)
-+map2gtf_LDFLAGS = $(BAM_LDFLAGS)
- 
- gtf_to_fasta_SOURCES = GTFToFasta.cpp FastaTools.cpp
--gtf_to_fasta_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
--gtf_to_fasta_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
-+gtf_to_fasta_LDADD = libtophat.a libgc.a $(BAM_LIB)
-+gtf_to_fasta_LDFLAGS = $(BAM_LDFLAGS)
diff --git a/sci-biology/tophat/metadata.xml b/sci-biology/tophat/metadata.xml
index 63e216a7b3ec..959160fe46b1 100644
--- a/sci-biology/tophat/metadata.xml
+++ b/sci-biology/tophat/metadata.xml
@@ -5,7 +5,4 @@
     <email>sci-biology@gentoo.org</email>
     <name>Gentoo Biology Project</name>
   </maintainer>
-  <use>
-    <flag name="bam">Compile support for the BAM format</flag>
-  </use>
 </pkgmetadata>
diff --git a/sci-biology/tophat/tophat-1.4.1.ebuild b/sci-biology/tophat/tophat-1.4.1.ebuild
deleted file mode 100644
index 3130c0d7c9c7..000000000000
--- a/sci-biology/tophat/tophat-1.4.1.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit flag-o-matic autotools
-
-DESCRIPTION="A fast splice junction mapper for RNA-Seq reads"
-HOMEPAGE="http://tophat.cbcb.umd.edu/"
-SRC_URI="http://tophat.cbcb.umd.edu/downloads/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-IUSE="+bam"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="bam? ( sci-biology/samtools )"
-RDEPEND="${DEPEND}
-	sci-biology/bowtie"
-
-MAKEOPTS="${MAKEOPTS} -j1"
-
-src_prepare() {
-	filter-ldflags -Wl,--as-needed
-	eautoreconf
-}
-
-src_configure() {
-	econf \
-		$(use_with bam)
-}
diff --git a/sci-biology/tophat/tophat-2.0.0.ebuild b/sci-biology/tophat/tophat-2.0.0.ebuild
deleted file mode 100644
index 93159f65c773..000000000000
--- a/sci-biology/tophat/tophat-2.0.0.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-AUTOTOOLS_AUTORECONF=yes
-
-inherit autotools-utils
-
-DESCRIPTION="A fast splice junction mapper for RNA-Seq reads"
-HOMEPAGE="http://tophat.cbcb.umd.edu/"
-SRC_URI="http://tophat.cbcb.umd.edu/downloads/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="+bam debug"
-
-DEPEND="
-	dev-libs/boost
-	bam? ( sci-biology/samtools )"
-RDEPEND="${DEPEND}
-	sci-biology/bowtie"
-
-PATCHES=( "${FILESDIR}"/${PN}-2.0.2-flags.patch )
-
-src_configure() {
-	local myeconfargs=( $(use_enable debug) )
-	autotools-utils_src_configure
-}
diff --git a/sci-biology/tophat/tophat-2.0.2.ebuild b/sci-biology/tophat/tophat-2.0.2.ebuild
deleted file mode 100644
index 7f68695af743..000000000000
--- a/sci-biology/tophat/tophat-2.0.2.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-AUTOTOOLS_AUTORECONF=yes
-
-inherit autotools-utils
-
-DESCRIPTION="A fast splice junction mapper for RNA-Seq reads"
-HOMEPAGE="http://tophat.cbcb.umd.edu/"
-SRC_URI="http://tophat.cbcb.umd.edu/downloads/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="+bam debug"
-
-DEPEND="
-	dev-libs/boost
-	bam? ( sci-biology/samtools )"
-RDEPEND="${DEPEND}
-	sci-biology/bowtie"
-
-PATCHES=( "${FILESDIR}"/${P}-flags.patch )
-
-src_configure() {
-	local myeconfargs=( $(use_enable debug) )
-	autotools-utils_src_configure
-}
diff --git a/sci-biology/tophat/tophat-2.0.8.ebuild b/sci-biology/tophat/tophat-2.0.8.ebuild
deleted file mode 100644
index 4a99dfdd784f..000000000000
--- a/sci-biology/tophat/tophat-2.0.8.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=yes
-
-inherit autotools-utils
-
-DESCRIPTION="A fast splice junction mapper for RNA-Seq reads"
-HOMEPAGE="http://tophat.cbcb.umd.edu/"
-SRC_URI="http://tophat.cbcb.umd.edu/downloads/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug"
-
-DEPEND="
-	dev-libs/boost
-	sci-biology/samtools
-	~sci-biology/seqan-1.3.1"
-RDEPEND="${DEPEND}
-	sci-biology/bowtie"
-
-PATCHES=( "${FILESDIR}"/${P}-flags.patch )
-
-src_prepare() {
-	rm -rf src/SeqAn* || die
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	local myeconfargs=(
-		--disable-optim
-		$(use_enable debug)
-	)
-	autotools-utils_src_configure
-}
diff --git a/sci-biology/tophat/tophat-2.0.9.ebuild b/sci-biology/tophat/tophat-2.0.9.ebuild
deleted file mode 100644
index d362ebe42002..000000000000
--- a/sci-biology/tophat/tophat-2.0.9.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=yes
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools-utils python-single-r1
-
-DESCRIPTION="A fast splice junction mapper for RNA-Seq reads"
-HOMEPAGE="http://tophat.cbcb.umd.edu/"
-SRC_URI="http://tophat.cbcb.umd.edu/downloads/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug"
-
-DEPEND="
-	dev-libs/boost
-	sci-biology/samtools
-	~sci-biology/seqan-1.3.1"
-RDEPEND="${DEPEND}
-	sci-biology/bowtie"
-
-PATCHES=( "${FILESDIR}"/${P}-flags.patch )
-
-src_prepare() {
-	rm -rf src/SeqAn* || die
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	local myeconfargs=(
-		--disable-optim
-		$(use_enable debug)
-	)
-	autotools-utils_src_configure
-}
-
-src_install() {
-	autotools-utils_src_install
-	python_fix_shebang "${ED}"/usr/bin/tophat
-}