proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

11 files changed, 570 insertions, 0 deletions

diff --git a/sci-biology/tophat/Manifest b/sci-biology/tophat/Manifest
new file mode 100644
index 000000000000..2d7d1928582d
--- /dev/null
+++ b/sci-biology/tophat/Manifest
@@ -0,0 +1,6 @@
+DIST tophat-1.0.12.tar.gz 468781 SHA256 f67b3f89aa79c7e14b40bcdba87f5aba6d322f869ca4260503e64ffcd2b621b2
+DIST tophat-1.4.1.tar.gz 1420422 SHA256 97fd6e09e3cafa90b969dac152585ce5bab4c86f32a980ce2c8ecaac846cd937
+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
diff --git a/sci-biology/tophat/files/tophat-2.0.2-flags.patch b/sci-biology/tophat/files/tophat-2.0.2-flags.patch
new file mode 100644
index 000000000000..ac1ca62da254
--- /dev/null
+++ b/sci-biology/tophat/files/tophat-2.0.2-flags.patch
@@ -0,0 +1,124 @@
+ 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 = $(BAM_LDFLAGS)
diff --git a/sci-biology/tophat/files/tophat-2.0.8-flags.patch b/sci-biology/tophat/files/tophat-2.0.8-flags.patch
new file mode 100644
index 000000000000..604f657d4c42
--- /dev/null
+++ b/sci-biology/tophat/files/tophat-2.0.8-flags.patch
@@ -0,0 +1,105 @@
+ configure.ac    |  3 ++-
+ src/Makefile.am | 50 +++++++++++++++++++++++++-------------------------
+ 2 files changed, 27 insertions(+), 26 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 75e9218..98b05d2 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -68,7 +68,8 @@ AC_CANONICAL_HOST
+ # set CFLAGS and CXXFLAGS
+ #user_CFLAGS="${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 = $(BAM_LDFLAGS)
diff --git a/sci-biology/tophat/files/tophat-2.0.9-flags.patch b/sci-biology/tophat/files/tophat-2.0.9-flags.patch
new file mode 100644
index 000000000000..af89e72084bf
--- /dev/null
+++ b/sci-biology/tophat/files/tophat-2.0.9-flags.patch
@@ -0,0 +1,109 @@
+ configure.ac    |  3 ++-
+ src/Makefile.am | 50 +++++++++++++++++++++++++-------------------------
+ 2 files changed, 27 insertions(+), 26 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 75e9218..98b05d2 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -68,7 +68,8 @@ AC_CANONICAL_HOST
+ # set CFLAGS and CXXFLAGS
+ #user_CFLAGS="${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
new file mode 100644
index 000000000000..36cf4a138940
--- /dev/null
+++ b/sci-biology/tophat/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <use>
+    <flag name="bam">Compile support for the BAM format</flag>
+  </use>
+</pkgmetadata>
diff --git a/sci-biology/tophat/tophat-1.0.12.ebuild b/sci-biology/tophat/tophat-1.0.12.ebuild
new file mode 100644
index 000000000000..88870c93982b
--- /dev/null
+++ b/sci-biology/tophat/tophat-1.0.12.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+inherit 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/${P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86"
+
+DEPEND=""
+RDEPEND="sci-biology/bowtie"
+
+src_prepare() {
+	# fix missing includes
+	sed -i '/#include <string>/ a #include <stdio.h>' "${S}/src/gff_juncs.cpp" || die
+	sed -i \
+		-e '/#include <stdio.h>/ a #include <unistd.h>' \
+		"${S}/src/prep_reads.cpp" \
+		"${S}/src/extract_reads.cpp" || die
+	# fix parallel make race
+	sed -i -e 's/\$(top_builddir)\/src\///g' src/Makefile.am || die
+	# remove broken arch-dependent CFLAGS setting
+	perl -i -ne 'print unless /case "\${host_cpu}-\${host_os}" in/../^esac/' configure.ac || die
+	eautoreconf
+}
+
+src_install() {
+	einstall || die
+	dodoc AUTHORS NEWS THANKS
+}
diff --git a/sci-biology/tophat/tophat-1.4.1.ebuild b/sci-biology/tophat/tophat-1.4.1.ebuild
new file mode 100644
index 000000000000..3130c0d7c9c7
--- /dev/null
+++ b/sci-biology/tophat/tophat-1.4.1.ebuild
@@ -0,0 +1,32 @@
+# 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
new file mode 100644
index 000000000000..93159f65c773
--- /dev/null
+++ b/sci-biology/tophat/tophat-2.0.0.ebuild
@@ -0,0 +1,31 @@
+# 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
new file mode 100644
index 000000000000..7f68695af743
--- /dev/null
+++ b/sci-biology/tophat/tophat-2.0.2.ebuild
@@ -0,0 +1,31 @@
+# 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
new file mode 100644
index 000000000000..c20007cd6160
--- /dev/null
+++ b/sci-biology/tophat/tophat-2.0.8.ebuild
@@ -0,0 +1,40 @@
+# 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/${P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="debug"
+
+DEPEND="
+	dev-libs/boost
+	sci-biology/samtools
+	sci-biology/seqan"
+RDEPEND="${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
new file mode 100644
index 000000000000..91cc2d463330
--- /dev/null
+++ b/sci-biology/tophat/tophat-2.0.9.ebuild
@@ -0,0 +1,46 @@
+# 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/${P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="debug"
+
+DEPEND="
+	dev-libs/boost
+	sci-biology/samtools
+	sci-biology/seqan"
+RDEPEND="${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
+}