6 files changed, 0 insertions, 310 deletions
diff --git a/sci-biology/tophat/Manifest b/sci-biology/tophat/Manifest
deleted file mode 100644
index 05897bbf09e4..000000000000
--- a/sci-biology/tophat/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST tophat-2.1.1.tar.gz 2259554 BLAKE2B f01b08cc2046b7d143864d64aa3e34d3000c7c10d7e50a4e102d500556e8620996de03392463f9d08ae97858eaec85b2df3b5d5ee5b0b4f7a5c0ae06bb3d08e8 SHA512 e2e0943a6f3d34b83922e6e403b65a3bee480a2b2bb4bf2de0cae7e0ef5bb166b66fec923316c2b643e8550e43c842f0f1bcc2ca7249d20fbcf5a4733fbdeabc
diff --git a/sci-biology/tophat/files/tophat-2.1.1-fix-c++14.patch b/sci-biology/tophat/files/tophat-2.1.1-fix-c++14.patch
deleted file mode 100644
index e8168bb91438..000000000000
--- a/sci-biology/tophat/files/tophat-2.1.1-fix-c++14.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-Fix building with C++14, which errors out due to broken perfect forwarding signature.
-See also: https://bugs.gentoo.org/show_bug.cgi?id=594544
-
---- a/src/tophat_reports.cpp
-+++ b/src/tophat_reports.cpp
-@@ -2705,7 +2705,7 @@
- 				junction_stat.gtf_match = true;
- 				junction_stat.accepted = true;
- 
--				gtf_junctions.insert(make_pair<Junction, JunctionStats>(Junction(ref_id, left_coord, right_coord, antisense), junction_stat));
-+				gtf_junctions.insert(make_pair(Junction(ref_id, left_coord, right_coord, antisense), junction_stat));
- 			}
- 		}
- 		fprintf(stderr, "Loaded %d GFF junctions from %s.\n", (int)(gtf_junctions.size()), gtf_juncs.c_str());
diff --git a/sci-biology/tophat/files/tophat-2.1.1-python2-shebangs.patch b/sci-biology/tophat/files/tophat-2.1.1-python2-shebangs.patch
deleted file mode 100644
index 5c38bcc072ef..000000000000
--- a/sci-biology/tophat/files/tophat-2.1.1-python2-shebangs.patch
+++ /dev/null
@@ -1,42 +0,0 @@
-Make Python 2 explicit in python scripts
-
---- a/src/bed_to_juncs
-+++ b/src/bed_to_juncs
-@@ -1,4 +1,4 @@
--#!/usr/bin/env python
-+#!/usr/bin/env python2
- # encoding: utf-8
- """
- bed_to_juncs.py
---- a/src/contig_to_chr_coords
-+++ b/src/contig_to_chr_coords
-@@ -1,4 +1,4 @@
--#!/usr/bin/env python
-+#!/usr/bin/env python2
- # encoding: utf-8
- """
- contig_to_chr_coords.py
---- a/src/sra_to_solid
-+++ b/src/sra_to_solid
-@@ -1,4 +1,4 @@
--#!/usr/bin/env python
-+#!/usr/bin/env python2
- 
- """
- sra_to_solid.py
---- a/src/tophat-fusion-post
-+++ b/src/tophat-fusion-post
-@@ -1,4 +1,4 @@
--#!/usr/bin/env python
-+#!/usr/bin/env python2
- 
- 
- """
---- a/src/tophat.py
-+++ b/src/tophat.py
-@@ -1,4 +1,4 @@
--#!/usr/bin/env python
-+#!/usr/bin/env python2
- 
- # encoding: utf-8
- """
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)
diff --git a/sci-biology/tophat/metadata.xml b/sci-biology/tophat/metadata.xml
deleted file mode 100644
index 959160fe46b1..000000000000
--- a/sci-biology/tophat/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/tophat/tophat-2.1.1-r5.ebuild b/sci-biology/tophat/tophat-2.1.1-r5.ebuild
deleted file mode 100644
index 753188771381..000000000000
--- a/sci-biology/tophat/tophat-2.1.1-r5.ebuild
+++ /dev/null
@@ -1,83 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools eutils flag-o-matic python-single-r1 toolchain-funcs
-
-DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie2"
-HOMEPAGE="https://ccb.jhu.edu/software/tophat/"
-SRC_URI="https://ccb.jhu.edu/software/tophat/downloads/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}
-	dev-libs/boost:=[threads]
-	$(python_gen_cond_dep '
-		dev-python/intervaltree[${PYTHON_MULTI_USEDEP}]
-		dev-python/sortedcontainers[${PYTHON_MULTI_USEDEP}]
-	')
-	sci-biology/samtools:0.1-legacy
-	sci-biology/bowtie:2"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	sci-biology/seqan:1.4
-	>=sys-devel/autoconf-archive-2016.09.16"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-unbundle-seqan-samtools.patch
-	"${FILESDIR}"/${P}-fix-c++14.patch
-	"${FILESDIR}"/${P}-python2-shebangs.patch
-)
-
-src_prepare() {
-	default
-
-	# remove bundled libs
-	rm -rf src/samtools-0.1.18/ src/SeqAn-1.4.2/ || die
-
-	sed -e "s:samtools_0.1.18:${EPREFIX}/usr/bin/samtools-0.1-legacy/samtools:" \
-		-i src/tophat.py src/common.cpp || die
-
-	sed -e "s:/usr/include/bam-0.1-legacy/:${EPREFIX}/usr/include/bam-0.1-legacy/:" \
-		-e '/^samtools-0\.1\.18\//d' \
-		-e '/^SeqAn-1\.4\.2\//d' \
-		-e 's:sortedcontainers/sortedset.py \\:sortedcontainers/sortedset.py:' \
-		-e 's:\$(top_builddir)\/src\/::' \
-		-i src/Makefile.am || die
-	sed -e 's:\$(top_builddir)\/src\/::' -i src/Makefile.am || die
-
-	# innocuous non-security flags, prevent log pollution
-	append-cflags -Wno-unused-but-set-variable -Wno-unused-variable
-	append-cppflags "$($(tc-getPKG_CONFIG) --cflags seqan-1.4)"
-
-	# remove ancient autoconf archive macros, wreaking havoc,
-	# depend on sys-devel/autoconf-archive instead, bug #594810
-	rm {ax_boost_thread,ax_boost_base}.m4 || die
-
-	eautoreconf
-}
-
-src_configure() {
-	econf $(use_enable debug)
-}
-
-src_install() {
-	default
-
-	# delete bundled python modules
-	local i
-	for i in intervaltree sortedcontainers; do
-		rm -r "${ED%/}"/usr/bin/${i} || die
-	done
-}
-
-pkg_postinst() {
-	optfeature "ABI SOLiD colorspace reads" sci-biology/bowtie:1
-}