Updating liguros repo

26 files changed, 0 insertions, 1676 deletions

diff --git a/sci-biology/amos/Manifest b/sci-biology/amos/Manifest
deleted file mode 100644
index 1dcaaed1bb97..000000000000
--- a/sci-biology/amos/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST amos-3.1.0-fix-c++14.patch.bz2 8033 BLAKE2B 942248f64906253205392df71010bf41105d2985fc8112e7443975d776cc484a4e2b6cf34284d4c384145bf32601892c06f156a0b0ccf0f2ce721de242e02e9b SHA512 76e26ca48a009cbf637d9462878223633e9b21cbd12d58a19e9a561f2cf4805791becc0b5f7aaf81975ca1e02b263cdd9d5ff310c4594670922ea65885ad9634
-DIST amos-3.1.0.tar.gz 2094268 BLAKE2B b9fb80d4e7b7e9e7769081c2680a3cba26591f00a4d9fdb17ad602e581dea5e8e2add4b0d9d3821a7f8a4ec1a45dfd867037baf35ecd401584f030c86b2b0f83 SHA512 7a416b9a0438b47425355383b709491a58f38c8d834df29e43c942170e710c6ea7e3bc8c509a58421b1340ad6eece9ea2da357ce5cd1d41ce08375676ee30491
diff --git a/sci-biology/amos/amos-3.1.0-r4.ebuild b/sci-biology/amos/amos-3.1.0-r4.ebuild
deleted file mode 100644
index bef4452c9a49..000000000000
--- a/sci-biology/amos/amos-3.1.0-r4.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools flag-o-matic python-single-r1
-
-DESCRIPTION="A Modular, Open-Source whole genome assembler"
-HOMEPAGE="https://sourceforge.net/projects/amos/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz
-	https://dev.gentoo.org/~soap/distfiles/${PN}-3.1.0-fix-c++14.patch.bz2"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	${PYTHON_DEPS}
-	dev-perl/DBI
-	dev-perl/Statistics-Descriptive
-	sci-biology/mummer"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-gcc-4.7.patch
-	"${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch
-	"${WORKDIR}"/${P}-fix-c++14.patch
-	"${FILESDIR}"/${P}-qa-Wformat.patch
-	"${FILESDIR}"/${P}-fix-build-system.patch
-)
-
-src_prepare() {
-	default
-	eautoreconf
-
-	# prevent GCC 6 log pollution due
-	# to hash_map deprecation in C++11
-	append-cxxflags -Wno-cpp
-}
-
-src_configure() {
-	econf --with-qmake-qt4=no
-}
-
-src_install() {
-	default
-	python_fix_shebang "${ED%/}"/usr/bin/goBambus2
-}
diff --git a/sci-biology/amos/files/amos-3.1.0-fix-build-system.patch b/sci-biology/amos/files/amos-3.1.0-fix-build-system.patch
deleted file mode 100644
index 9c824dd2f122..000000000000
--- a/sci-biology/amos/files/amos-3.1.0-fix-build-system.patch
+++ /dev/null
@@ -1,116 +0,0 @@
-* Use proper AR and not just 'ar'
-* Fix build system to build in parallel
-
---- a/configure.ac
-+++ b/configure.ac
-@@ -34,6 +34,7 @@
- AC_PROG_INSTALL
- AC_PROG_LN_S
- AC_PROG_RANLIB
-+AM_PROG_AR
- AC_PROG_CPP
- AC_PATH_PROG(PERL, [perl], [:])
- AC_PATH_PROG(PYTHON, [python], [:])
---- a/src/Align/Makefile.am
-+++ b/src/Align/Makefile.am
-@@ -133,7 +133,7 @@
- 
- ##-- hash-overlap
- hash_overlap_LDADD = \
--	$(top_builddir)/src/Align/libAlign.a \
-+	libAlign.a \
- 	$(top_builddir)/src/CelMsg/libCelMsg.a \
- 	$(top_builddir)/src/Slice/libSlice.a \
- 	$(top_builddir)/src/Common/libCommon.a \
-@@ -172,7 +172,7 @@
- 
- ##-- make-consensus
- make_consensus_LDADD = \
--	$(top_builddir)/src/Align/libAlign.a \
-+	libAlign.a \
- 	$(top_builddir)/src/CelMsg/libCelMsg.a \
- 	$(top_builddir)/src/Slice/libSlice.a \
- 	$(top_builddir)/src/Common/libCommon.a \
-@@ -182,7 +182,7 @@
- 
- ##-- make-consensus_poly
- make_consensus_poly_LDADD = \
--	$(top_builddir)/src/Align/libAlign_poly.a \
-+	libAlign_poly.a \
- 	$(top_builddir)/src/CelMsg/libCelMsg.a \
- 	$(top_builddir)/src/Slice/libSlice.a \
- 	$(top_builddir)/src/Common/libCommon.a \
-@@ -192,7 +192,7 @@
- 
- ##-- maligntest
- maligntest_LDADD = \
--	$(top_builddir)/src/Align/libAlign.a \
-+	libAlign.a \
- 	$(top_builddir)/src/CelMsg/libCelMsg.a \
- 	$(top_builddir)/src/Slice/libSlice.a \
- 	$(top_builddir)/src/Common/libCommon.a \
-@@ -202,7 +202,7 @@
- 
- ##-- merge-contigs
- merge_contigs_LDADD = \
--	$(top_builddir)/src/Align/libAlign.a \
-+	libAlign.a \
- 	$(top_builddir)/src/CelMsg/libCelMsg.a \
- 	$(top_builddir)/src/Slice/libSlice.a \
- 	$(top_builddir)/src/Common/libCommon.a \
-@@ -235,7 +235,7 @@
- 
- ##-- show-ma-asm
- show_ma_asm_LDADD = \
--	$(top_builddir)/src/Align/libAlign.a \
-+	libAlign.a \
- 	$(top_builddir)/src/Common/libCommon.a \
- 	$(top_builddir)/src/AMOS/libAMOS.a
- show_ma_asm_SOURCES = \
-@@ -261,7 +261,7 @@
- 
- ##-- simple-overlap
- simple_overlap_LDADD = \
--	$(top_builddir)/src/Align/libAlign.a \
-+	libAlign.a \
- 	$(top_builddir)/src/CelMsg/libCelMsg.a \
- 	$(top_builddir)/src/Slice/libSlice.a \
- 	$(top_builddir)/src/Common/libCommon.a \
-@@ -272,7 +272,7 @@
- 
- ##-- test-align
- test_align_LDADD = \
--	$(top_builddir)/src/Align/libAlign.a \
-+	libAlign.a \
- 	$(top_builddir)/src/CelMsg/libCelMsg.a \
- 	$(top_builddir)/src/Slice/libSlice.a \
- 	$(top_builddir)/src/Common/libCommon.a \
---- a/src/Bambus/Bundler/Makefile.am
-+++ b/src/Bambus/Bundler/Makefile.am
-@@ -47,7 +47,7 @@
- 	clk.cc
- 
- MarkRepeats_LDADD = \
--	$(top_builddir)/src/Bambus/Bundler/libBundler.a \
-+	libBundler.a \
- 	$(top_builddir)/src/Common/libCommon.a \
- 	$(top_builddir)/src/AMOS/libAMOS.a \
- 	$(top_builddir)/src/GNU/libGNU.a
-@@ -55,7 +55,7 @@
- 	MarkRepeats.cc
- 
- OrientContigs_LDADD = \
--	$(top_builddir)/src/Bambus/Bundler/libBundler.a \
-+	libBundler.a \
- 	$(top_builddir)/src/Common/libCommon.a \
- 	$(top_builddir)/src/AMOS/libAMOS.a \
- 	$(top_builddir)/src/GNU/libGNU.a
-@@ -63,7 +63,7 @@
- 	OrientContigs.cc
- 
- FilterEdgesByCluster_LDADD = \
--	$(top_builddir)/src/Bambus/Bundler/libBundler.a \
-+	libBundler.a \
- 	$(top_builddir)/src/Common/libCommon.a \
- 	$(top_builddir)/src/AMOS/libAMOS.a \
- 	$(top_builddir)/src/GNU/libGNU.a
diff --git a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch
deleted file mode 100644
index de2a41184c52..000000000000
--- a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- src/Align/find-tandem.cc |    1 +
- 1 files changed, 1 insertions(+), 0 deletions(-)
-
-diff --git a/src/Align/find-tandem.cc b/src/Align/find-tandem.cc
-index ddf1cab..a29e21e 100644
---- a/src/Align/find-tandem.cc
-+++ b/src/Align/find-tandem.cc
-@@ -7,6 +7,7 @@
- #include <vector>
- #include <ctime>
- #include <sys/time.h>
-+#include <unistd.h>
- using namespace std;
- 
- const int OFFSET_TABLE_SIZE = 100;
diff --git a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch
deleted file mode 100644
index 97a8f59d0208..000000000000
--- a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch
+++ /dev/null
@@ -1,25 +0,0 @@
---- amos-3.1.0/src/Pipeline/goBambus2.py.orig	2013-09-11 01:05:29.850090457 +0200
-+++ amos-3.1.0/src/Pipeline/goBambus2.py	2013-09-11 01:07:03.250090701 +0200
-@@ -1,7 +1,7 @@
- #pipeline script for assembly + Bambus 2
- #contributed by Todd J Treangen
- 
--import string, sys, os, subprocess#, spincursor
-+import sys, os, subprocess#, spincursor
- 
- RED =    "\033[0;31m"
- GREEN =  "\033[0;32m"
-@@ -360,7 +360,7 @@
-                 print "\t\t%s...failed%s"%(RED,NONE)
-                 sys.exit(1)
- 
--       p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile)
-+        p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile)
- 
-         if xopt_dict["verbose"] == 1:
-             print "10) running OutputResults"
-@@ -388,4 +388,3 @@
-             else:
-                 print "\t\t%s...failed%s"%(RED,NONE)
-                 sys.exit(1)
--)
diff --git a/sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch b/sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch
deleted file mode 100644
index 13f4eeb247a1..000000000000
--- a/sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch
+++ /dev/null
@@ -1,136 +0,0 @@
-Fix QA warnings, due to using incorrect format specifiers in printf:
-* contig-cmp.cc:237:50: warning: format ‘%u’ expects argument of type ‘unsigned int’,
-* but argument 3 has type ‘std::vector<Contig_t>::size_type {aka long unsigned int}’ [-Wformat=]
-*     fprintf (stderr, "%u b contigs\n", b . size ());
-
---- a/src/Align/align.cc
-+++ b/src/Align/align.cc
-@@ -1936,7 +1936,7 @@
-    n = align . size ();
-    con = consensus . c_str ();
- 
--   fprintf (fp, "\nConsensus len = %d\n", consensus . length ());
-+   fprintf (fp, "\nConsensus len = %zu\n", consensus . length ());
- 
-    for  (i = 0;  i < n;  i ++)
-      {
-@@ -3936,7 +3936,7 @@
-         }
- 
-       // Array of sum of quality scores in the slice for A,C,G,T,- resp.
--      for (j = 0; j < 6; j ++)
-+      for (j = 0; j < 5; j ++)
-         qvsum [j] = 0;
- 
-       int nof_ambiguities = 0;
---- a/src/Align/align_poly.cc
-+++ b/src/Align/align_poly.cc
-@@ -1761,7 +1761,7 @@
-    n = align . size ();
-    con = consensus . c_str ();
- 
--   fprintf (fp, "\nConsensus len = %d\n", consensus . length ());
-+   fprintf (fp, "\nConsensus len = %zu\n", consensus . length ());
-    for  (i = 0;  i < n;  i ++)
-      {
-       fprintf (fp, "\nString #%d:\n", i);
---- a/src/Align/count-qmers.cc
-+++ b/src/Align/count-qmers.cc
-@@ -191,8 +191,8 @@
- 
-     PrintMers(mer_table, min_count);
- 
--    fprintf(stderr, "reporter:counter:asm,reads_total,%ld\n", COUNT);
--    fprintf(stderr, "reporter:counter:asm,reads_bp,%ld\n",    LEN);
-+    fprintf(stderr, "reporter:counter:asm,reads_total,%lld\n", COUNT);
-+    fprintf(stderr, "reporter:counter:asm,reads_bp,%lld\n",    LEN);
-   }
-   catch (Exception_t & e)
-   {
---- a/src/Align/kmer-cov.cc
-+++ b/src/Align/kmer-cov.cc
-@@ -485,7 +485,7 @@
-           Kmer_Len = s . length ();
-       else if  (Kmer_Len != int (s . length ()))
-           {
--           sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %d instead of %d",
-+           sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %zu instead of %d",
-                 s . c_str (), s . length (), Kmer_Len);
-            Clean_Exit (Clean_Exit_Msg_Line, __FILE__, __LINE__);
-           }
---- a/src/Align/kmer-cov-plot.cc
-+++ b/src/Align/kmer-cov-plot.cc
-@@ -316,7 +316,7 @@
-     }
-     else if  (Kmer_Len != int (s . length ()))
-     {
--      sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %d instead of %d",
-+      sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %zu instead of %d",
-                s . c_str (), s . length (), Kmer_Len);
-       Clean_Exit (Clean_Exit_Msg_Line, __FILE__, __LINE__);
-     }
---- a/src/Align/make-consensus.cc
-+++ b/src/Align/make-consensus.cc
-@@ -303,7 +303,7 @@
-             break;
-         }
- 
--        sprintf (sid, "%ld", ++layout_id);
-+        sprintf (sid, "%u", ++layout_id);
-         cid = string (sid);
-         ID_t lid = layout.getIID ();
-         if (lid == 0)
---- a/src/Align/make-consensus_poly.cc
-+++ b/src/Align/make-consensus_poly.cc
-@@ -279,7 +279,7 @@
- 		   break;
- 	       }
- 		 
--	       sprintf(sid, "%ld", ++layout_id);
-+	       sprintf(sid, "%u", ++layout_id);
- 	       cid = string(sid);
- 	       ID_t lid = layout.getIID();
- 	       if (lid == 0) {
---- a/src/Align/simple-overlap.cc
-+++ b/src/Align/simple-overlap.cc
-@@ -422,7 +422,7 @@
-            "Options:\n"
-            "  -a       Also show alignments of overlaps \n"
-            "  -E <x>   Maximum error rate for overlaps is <x>\n"
--           "           e.g., -E 0.06 for 6% error rate\n"
-+           "           e.g., -E 0.06 for 6%% error rate\n"
-            "  -F       Input is a fasta file\n"
-            "  -h       Print this usage message\n"
-            "  -o <n>   Set minimum overlap length to <n>\n"
---- a/src/Compare/contig-cmp.cc
-+++ b/src/Compare/contig-cmp.cc
-@@ -145,7 +145,7 @@
- 
-    fclose (fp);
- 
--   fprintf (stderr, "%u a contigs\n", a . size ());
-+   fprintf (stderr, "%zu a contigs\n", a . size ());
-    vector <Unitig_t>  a_contig (max_id + 1);
-    n = a . size ();
-    for  (i = 0;  i < n;  i ++)
-@@ -234,7 +234,7 @@
- 
-    fclose (fp);
- 
--   fprintf (stderr, "%u b contigs\n", b . size ());
-+   fprintf (stderr, "%zu b contigs\n", b . size ());
-    vector <Unitig_t>  b_contig (max_id + 1);
-    n = b . size ();
-    for  (i = 0;  i < n;  i ++)
---- a/src/Staden/progs/trace_convert.c
-+++ b/src/Staden/progs/trace_convert.c
-@@ -6,6 +6,9 @@
- #include "traceType.h"
- #include "seqIOABI.h"
- 
-+#include <fcntl.h>
-+#include <unistd.h>
-+
- static char fileIdentifier[] = "$Id$";
- 
- struct opts {
diff --git a/sci-biology/amos/metadata.xml b/sci-biology/amos/metadata.xml
deleted file mode 100644
index f1b37b35b889..000000000000
--- a/sci-biology/amos/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">amos</remote-id>
-  </upstream>
-	<origin>gentoo-staging</origin>
-</pkgmetadata>
diff --git a/sci-biology/embassy-meme/Manifest b/sci-biology/embassy-meme/Manifest
deleted file mode 100644
index 551af7aef93e..000000000000
--- a/sci-biology/embassy-meme/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST embassy-meme-4.7.660.tar.gz 622448 BLAKE2B 93bbbe3de085aa2cd843349f8397b2d1f547be62afdb7deb30eec90a891f7825c847b92754bd956388b1bfe0250cabcbc7ad68f7d0378748a7949001016d344c SHA512 0536531b198aac09a9fe6c17cf1c60c766789c94a7f83f743a90aaa65061c95534bf398c53611a34549b7ec1a4928fdc45fe0d2553f25f85eeda41f90c2e8c6f
diff --git a/sci-biology/embassy-meme/embassy-meme-4.7.660.ebuild b/sci-biology/embassy-meme/embassy-meme-4.7.660.ebuild
deleted file mode 100644
index 8752e78d8fc9..000000000000
--- a/sci-biology/embassy-meme/embassy-meme-4.7.660.ebuild
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-EBO_DESCRIPTION="MEME - Multiple Em for Motif Elicitation"
-
-EBO_EAUTORECONF=1
-
-inherit emboss-r2
-
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="sci-biology/meme"
-
-S="${WORKDIR}/MEME-4.7.650"
-PATCHES=( "${FILESDIR}"/${PN}-4.7.650_fix-build-system.patch )
diff --git a/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch b/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch
deleted file mode 100644
index 56f5814e1efa..000000000000
--- a/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch
+++ /dev/null
@@ -1,100 +0,0 @@
- configure.ac    | 49 +++++++------------------------------------------
- src/Makefile.am |  6 ++----
- 2 files changed, 9 insertions(+), 46 deletions(-)
-
-diff --git a/configure.ac b/configure.ac
-index 391989f..d921f25 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -635,33 +635,6 @@ AS_CASE([${host_os}],
- 
- 
- 
--dnl PCRE library definitions - see the MAJOR and MINOR values
--dnl to see which version's configure.in these lines come from
--
--dnl Provide the current PCRE version information. Do not use numbers
--dnl with leading zeros for the minor version, as they end up in a C
--dnl macro, and may be treated as octal constants. Stick to single
--dnl digits for minor numbers less than 10. There are unlikely to be
--dnl that many releases anyway.
--
--PCRE_MAJOR="7"
--PCRE_MINOR="9"
--PCRE_DATE="11-Apr-2009"
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
--
--dnl Default values for miscellaneous macros
--
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
--
--dnl Provide versioning information for libtool shared libraries that
--dnl are built by default on Unix systems.
--
--PCRE_LIB_VERSION="0:1:0"
--PCRE_POSIXLIB_VERSION="0:0:0"
--
--
--
--
- dnl FIXME: This does no longer seem required with Autoconf 2.67?
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place
- dnl AS_IF([test "x${with_x}" != "xno"],
-@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL
- 
- 
- 
--dnl "Export" these variables for PCRE
--
--AC_SUBST([HAVE_MEMMOVE])
--AC_SUBST([HAVE_STRERROR])
--AC_SUBST([PCRE_MAJOR])
--AC_SUBST([PCRE_MINOR])
--AC_SUBST([PCRE_DATE])
--AC_SUBST([PCRE_VERSION])
--AC_SUBST([PCRE_LIB_VERSION])
--AC_SUBST([PCRE_POSIXLIB_VERSION])
--AC_SUBST([POSIX_MALLOC_THRESHOLD])
--
--
--
--
- dnl Test if --enable-localforce given
- locallink="no"
- embprefix="/usr/local"
-@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs],
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
- 
- 
-+AS_IF([test "x${enable_systemlibs}" = "xyes"],
-+[
-+dnl using system libraries
-+  PKG_CHECK_MODULES([PLPLOT], [plplotd],
-+  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
-+  )
-+])
- 
- 
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
-diff --git a/src/Makefile.am b/src/Makefile.am
-index 1600399..9f28162 100644
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \
- 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
- 	-I../../../ajax/acd -I../../../plplot
- else
--AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
--	$(NLINCLUDES) \
--	-I${embprefix}/include/epcre
-+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
- endif
- 
- if ISSHARED
-@@ -60,5 +58,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
- 	$(XLIB)
- else
- LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
--        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
-+        -lajax $(NLADD) $(XLIB)
- endif
diff --git a/sci-biology/embassy-meme/metadata.xml b/sci-biology/embassy-meme/metadata.xml
deleted file mode 100644
index d385a3ebce1c..000000000000
--- a/sci-biology/embassy-meme/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">emboss</remote-id>
-  </upstream>
-	<origin>gentoo-staging</origin>
-</pkgmetadata>
diff --git a/sci-biology/meme/Manifest b/sci-biology/meme/Manifest
deleted file mode 100644
index fd161837618b..000000000000
--- a/sci-biology/meme/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST meme_4.11.2.tar.gz 18004930 BLAKE2B accacc7d2422ff6ea3411ff43ea664c94f5d6ba320e1cfec642a88cb6ea5303b2fe8c99a6c35d865c377560118402ab11f869930fd108f02eeaa06321db21655 SHA512 c97c3815e71e2fb5491548152f00688cdfbf4365f6027657e0ffc68e5d96cdd10a4708e0882ab7a5a61d78d93113c925cf5bb300fbe93fa4b2961becef497894
diff --git a/sci-biology/meme/files/meme-4.11.2_p2-fix-build-system.patch b/sci-biology/meme/files/meme-4.11.2_p2-fix-build-system.patch
deleted file mode 100644
index b548de5a39a5..000000000000
--- a/sci-biology/meme/files/meme-4.11.2_p2-fix-build-system.patch
+++ /dev/null
@@ -1,346 +0,0 @@
-Fix and modernise build system
-* Remove all *FLAGS setting, just append to the user-supplied ones
-* Add --enable-doc and --enable-examples configure flags
-* Install documentation and examples in correct directories
-* Discover libxml2 and libxslt dependencies using PKG_CHECK_MODULES
-* Install python and perl modules correctly
-
---- a/configure.ac
-+++ b/configure.ac
-@@ -76,61 +76,10 @@
- AM_CONDITIONAL(WANT_STRLCPY, test ["$have_strlcpy" = no])
- 
- # Check for compiler-specific settings
--LARGE_FILE_SUPPORT=`getconf LFS_CFLAGS`
--if test "${GCC}" = "yes"; then
--  ac_cc_opt="-O3"
--  ac_cc_debug_opt="-O0"
--  ac_cc_warn="-Wall -Wno-unused"
--  ac_cc_debug="-ggdb"
--  # Check for OS X llvm (clang) compiler
--  if `gcc --version |grep llvm >/dev/null`; then
--    ac_cc_debug="-g"
--  fi
--  CFLAGS="-std="gnu89" $ac_cc_warn -DUNIX -D__USE_FIXED_PROTOTYPES__ $LARGE_FILE_SUPPORT"
--else
--  ac_cc_opt="-O"
--  ac_cc_debug_opt=""
--  ac_cc_warn=""
--  ac_cc_debug="-g"
--  CFLAGS="$ac_cc_warn -DUNIX -D__USE_FIXED_PROTOTYPES__ $LARGE_FILE_SUPPORT"
--fi
--
--# Set up default libxml2 settings
--# check for installed copy of libxml2
--build_libxml2="yes"
--if test -n "$XML2_CONFIG"; then
--  # Require at least version 2.6
--  required_libxml2_version="2006000"
--  LIBXML2_VERSION="`$XML2_CONFIG --version | \
--    awk 'BEGIN { FS = "."; } { printf "%d", ($1 * 1000 + $2) * 1000 + $3;}'`"
--  if test -n "$LIBXML2_VERSION" && \
--     test "$LIBXML2_VERSION"  -ge "$required_libxml2_version"; then 
--    build_libxml2="no"
--    LIBXML2_LIBS="`$XML2_CONFIG --libs`"
--    LIBXML2_CFLAGS="`$XML2_CONFIG --cflags`"
--  fi
--fi
--if test -z "$LIBXML2_LIBS"; then
--  AC_MSG_WARN([libxml2 library not found])
--  LIBXML2_LIBS="\${top_builddir}/src/libxml2/libxml2.la"
--  LIBXML2_CFLAGS="-I\${top_srcdir}/src/libxml2/include"
--fi
--
--# Set up default libxslt settings
--# check for installed copy of libxslt
--build_libxslt="yes"
--if test -n "$XSLT_CONFIG"; then
--  build_libxslt="no"
--  LIBXSLT_LIBS="`$XSLT_CONFIG --libs` -lexslt"
--  LIBXSLT_CFLAGS="`$XSLT_CONFIG --cflags`"
--fi
--if test -z "$LIBXSLT_LIBS"; then
--  AC_MSG_WARN([libxslt library not found])
--  LIBEXSLT_LIBS="\${top_builddir}/src/libexslt/libexslt.la"
--  LIBXSLT_LIBS="\${top_builddir}/src/libxslt/libxslt.la"
--  LIBEXSLT_CFLAGS="-I\${top_srcdir}/src/libexslt"
--  LIBXSLT_CFLAGS="-I\${top_srcdir}/src/"
--fi
-+AC_PROG_MKDIR_P
-+AC_SYS_LARGEFILE
-+CFLAGS="-std=gnu89 -Wall -Wno-unused ${CFLAGS}"
-+CPPFLAGS="-DUNIX -D__USE_FIXED_PROTOTYPES__ ${CPPFLAGS}"
- 
- # who is installing 
- USER=`whoami`
-@@ -279,6 +227,16 @@
- AM_CONDITIONAL(PARALLEL, test ["$parallel" != no])
- AM_CONDITIONAL(PARALLEL_IS_LAM, test -n ["$lammpi"]) 
- 
-+dnl Documentation
-+AC_ARG_ENABLE([doc],
-+	AS_HELP_STRING([--enable-doc], [Enable installation of documentation]))
-+AM_CONDITIONAL([ENABLE_DOC], [test "x$enable_doc" = "xyes"])
-+
-+dnl Examples
-+AC_ARG_ENABLE([examples],
-+	AS_HELP_STRING([--enable-examples], [Enable installation of examples]))
-+AM_CONDITIONAL([ENABLE_EXAMPLES], [test "x$enable_examples" = "xyes"])
-+
- AC_ARG_ENABLE(
-     webservice,
-     [  --enable-webservice=deploy_dir       Deploy the MEME service on an existing Opal 2.5+ installation],
-@@ -309,24 +267,35 @@
- AM_CONDITIONAL(WEBEITHER, test ["x$OPAL_DEPLOY" != "x" -o "x$OPAL_URL" != "xno"])
- 
- # enable building of included libxml2
--AC_ARG_ENABLE(
--    build_libxml2,
--    [  --enable-build-libxml2     Build included version of libxml2. Default is to use pre-existing locally installed copy.],
--    build_libxml2=$enableval; \
--    LIBXML2_LIBS="\${top_builddir}/src/libxml2/libxml2.la"; \
--    LIBXML2_CFLAGS="-I\${top_srcdir}/src/libxml2/include" , )
--AM_CONDITIONAL(BUILD_LIBXML2, test ["$build_libxml2" = yes])
-+AC_ARG_ENABLE([build-libxml2],
-+	AS_HELP_STRING([--enable-build-libxml2], [Build included version of libxml2. Default is to use pre-existing locally installed copy.]))
-+AS_IF([test "x$enable_build_libxml2" = "xyes"], [
-+	dnl Enable building of bundled libs
-+	LIBXML2_CFLAGS="-I\${top_srcdir}/src/libxml2/include"
-+	LIBXML2_LIBS="\${top_builddir}/src/libxml2/libxml2.la"
-+	],[
-+	dnl Use system libraries
-+	PKG_CHECK_MODULES([LIBXML2], [libxml-2.0 >= 2.6])
-+])
-+AM_CONDITIONAL([BUILD_LIBXML2], [test "x$enable_build_libxml2" = "xyes"])
-+
- 
- # enable building of included libxslt
--AC_ARG_ENABLE(
--    build_libxslt,
--    [  --enable-build-libxslt     Build included version of libxslt. Default is to use pre-existing locally installed copy.],
--    build_libxslt=$enableval; \
--    LIBEXSLT_LIBS="\${top_builddir}/src/libexslt/libexslt.la"; \
--    LIBXSLT_LIBS="\${top_builddir}/src/libxslt/libxslt.la"; \
--    LIBEXSLT_CFLAGS="-I\${top_srcdir}/src/libexslt"; \
--    LIBXSLT_CFLAGS="-I\${top_srcdir}/src/" , )
--AM_CONDITIONAL(BUILD_LIBXSLT, test ["$build_libxslt" = yes])
-+AC_ARG_ENABLE([build-libxslt],
-+	AS_HELP_STRING([--enable-build-libxslt], [Build included version of libxslt. Default is to use pre-existing locally installed copy.]))
-+AS_IF([test "x$enable_build_libxslt" = "xyes"], [
-+	dnl Enable building of bundled libs
-+	LIBXSLT_CFLAGS="-I\${top_srcdir}/src/"
-+	LIBXSLT_LIBS="\${top_builddir}/src/libxslt/libxslt.la"
-+
-+	LIBEXSLT_CFLAGS="-I\${top_srcdir}/src/libexslt"
-+	LIBEXSLT_LIBS="\${top_builddir}/src/libexslt/libexslt.la"
-+	],[
-+	dnl Use system libraries
-+	PKG_CHECK_MODULES([LIBXSLT], [libxslt])
-+	PKG_CHECK_MODULES([LIBEXSLT], [libexslt])
-+])
-+AM_CONDITIONAL([BUILD_LIBXSLT], [test "x$enable_build_libxslt" = "xyes"])
- 
- # set website url
- AC_ARG_WITH(
-@@ -427,13 +396,13 @@
-     [AC_PATH_PROG(PERL, perl)])
- AC_DEFINE_UNQUOTED(PERL, "$PERL", [Path to Perl] )
- 
-+AC_ARG_WITH([perl-dir],
-+	AS_HELP_STRING([--with-perl-dir], [Perl modules directory]), [perlmoddir="$with_perl_dir"], [perlmoddir="lib/perl"])
-+AC_SUBST([perlmoddir])
-+
-+
- # set path to Python
--AC_ARG_WITH(
--    python,
--    [  --with-python=NAME     Set path to Python. Default is to take from user's PATH.],
--    [PYTHON=$withval],
--    [AC_PATH_PROG(PYTHON, python)])
--AC_DEFINE_UNQUOTED(PYTHON, "$PYTHON", [Path to Python] )
-+AM_PATH_PYTHON
- 
- # set path to convert utility
- AC_ARG_WITH(
-@@ -586,13 +555,15 @@
-         Configuration parameters
-         ========================
- 
--  Install path:               ${prefix}
-+  Install path (prefix):      ${prefix}
-   Install UID:                ${MEME_USER}
-   Version:                    ${VERSION}
--  C compiler:                 ${CC}
--  C compiler flags:           ${CFLAGS}
--  Linker:                     ${LD}
--  Special Libs:               ${LIBS}
-+  C compiler (CC):            ${CC}
-+  C compiler flags (CFLAGS):  ${CFLAGS}
-+  C preproc flags (CPPFLAGS): ${CPPFLAGS}
-+  Linker (LD):                ${LD}
-+  Linker flags (LDFLAGS):     ${LDFLAGS}
-+  Special Libs (LIBS):        ${LIBS}
-   MPICC                       ${MPICC}
-   MPIRUN                      ${MPIRUN}
-   MPI_CMD                     ${MPI_CMD}
---- a/doc/css/Makefile.am
-+++ b/doc/css/Makefile.am
-@@ -5,7 +5,7 @@
- 
- EXTRA_DIST = $(NORMAL_FILES)
- 
--if ! WEBSITE
--doccssdir = $(prefix)/doc/css
-+if ENABLE_DOC
-+doccssdir = $(htmldir)/css
- doccss_DATA =  $(NORMAL_FILES)
- endif
---- a/doc/examples/compute_prior_dist_example_output_files/Makefile.am
-+++ b/doc/examples/compute_prior_dist_example_output_files/Makefile.am
-@@ -7,8 +7,8 @@
- EXAMPLES = \
-   prior.dist.txt
- 
--if ! WEBSITE
--exdir = $(prefix)/doc/examples/compute_prior_dist_example_output_files
-+if ENABLE_EXAMPLES
-+exdir = $(docdir)/examples/compute_prior_dist_example_output_files
- ex_DATA = $(EXAMPLES)
- endif
- 
---- a/doc/examples/Makefile.am
-+++ b/doc/examples/Makefile.am
-@@ -22,8 +22,8 @@
- # load the EXAMPLE_OUTPUT_FILES variable
- include examples.mk
- 
--if ! WEBSITE
--exdir = $(prefix)/doc/examples
-+if ENABLE_EXAMPLES
-+exdir = $(docdir)/examples
- nobase_dist_ex_DATA = $(EXAMPLES) $(EXAMPLE_OUTPUT_FILES)
- endif
- 
---- a/doc/examples/sample_opal_scripts/Makefile.am
-+++ b/doc/examples/sample_opal_scripts/Makefile.am
-@@ -15,8 +15,8 @@
-   MemeClient.pl \
-   MemeClient.py
- 
--if ! WEBSITE
--exdir = $(prefix)/doc/examples/sample_opal_scripts
-+if ENABLE_EXAMPLES
-+exdir = $(docdir)/examples/sample_opal_scripts
- ex_DATA = $(EXAMPLES)
- endif
- 
---- a/doc/images/Makefile.am
-+++ b/doc/images/Makefile.am
-@@ -30,8 +30,8 @@
- 
- MEME_IMAGES = $(PROGRAM_ICONS) $(OTHER_IMAGES)
- 
--if ! WEBSITE
--memeimgdir = $(prefix)/doc/images
-+if ENABLE_DOC
-+memeimgdir = $(htmldir)/images
- memeimg_DATA = $(MEME_IMAGES)
- endif
- 
---- a/doc/js/Makefile.am
-+++ b/doc/js/Makefile.am
-@@ -41,8 +41,8 @@
- 
- BUILT_SOURCES = $(BUILT_FILES)
- 
--if ! WEBSITE
--docjsdir = $(prefix)/doc/js
-+if ENABLE_DOC
-+docjsdir = $(htmldir)/js
- docjs_DATA =  $(NORMAL_FILES) $(BUILT_FILES) $(SYMLINK_FILES)
- endif
- 
---- a/doc/Makefile.am
-+++ b/doc/Makefile.am
-@@ -129,8 +129,8 @@
-   update-sequence-db.html \
-   ismb94.pdf
- 
--if ! WEBSITE
--memedocdir = $(prefix)/doc
-+if ENABLE_DOC
-+memedocdir = $(htmldir)
- memedoc_DATA =  $(NORMAL_FILES)
- endif
- 
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -52,7 +52,7 @@
- endif
- 
- dbdir:
--	mkdir -p $(MEME_DB)
-+	$(MKDIR_P) $(DESTDIR)/$(MEME_DB)
- 
- all-local:
- if WEBSITE
-@@ -64,8 +64,8 @@
- endif
- 
- install-data-local:
--	mkdir -p $(MEME_LOGS)
--	chmod a+w $(MEME_LOGS)
-+	$(MKDIR_P) $(DESTDIR)/$(MEME_LOGS)
-+	chmod a+w $(DESTDIR)/$(MEME_LOGS)
- 
- distdir = $(PACKAGE)_$(VERSION)
- 
---- a/scripts/Makefile.am
-+++ b/scripts/Makefile.am
-@@ -22,8 +22,8 @@
-   -e 's%@WHICHJAVA@%$(JAVA)%' \
-   -e 's%@WHICHCONVERT@%$(CONVERT)%' \
-   -e 's%@WHICHGHOSTSCRIPT@%$(GHOSTSCRIPT)%' \
--  -e 's%@PERLLIBDIR@%$(libdir)/perl%' \
--  -e 's%@PYTHONLIBDIR@%$(libdir)/python%' \
-+  -e 's%@PERLLIBDIR@%$(perlmoddir)%' \
-+  -e 's%@PYTHONLIBDIR@%$(pythondir)%' \
-   -e 's%@JAVALIBDIR@%$(libdir)/java%' \
-   -e 's%@LAM_BIN@%$(LAMBIN)%' \
-   -e 's%@APPCONFIGDIR@%$(sysconfdir)%' \
-@@ -62,7 +62,7 @@
-   DiffXML.pm \
-   HypergeometricDynProg.pm
- 
--perlmoddir=$(libdir)/perl
-+perlmoddir = $(exec_prefix)/@perlmoddir@
- perlmod_SCRIPTS = \
-   $(BUILT_PERL_MOD) \
-   $(NORMAL_PERL_MOD)
-@@ -76,8 +76,7 @@
-   hypergeometric.py \
-   sequence.py
- 
--pythonlibdir=$(libdir)/python
--pythonlib_SCRIPTS = \
-+python_PYTHON = \
-   $(BUILT_PYTHON_LIB) \
-   $(NORMAL_PYTHON_LIB)
- 
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -19,7 +19,13 @@
- ARCHIVE_REVISION = $(shell cat ../ARCHIVE_REVISION)
- ARCHIVE_DATE = $(shell cat ../ARCHIVE_DATE)
- 
--SUBDIRS = filters libxml2 libxslt libexslt . parallel
-+SUBDIRS = filters . parallel
-+if BUILD_LIBXML2
-+SUBDIRS += libxml2
-+endif
-+if BUILD_LIBXSLT
-+SUBDIRS += libxslt libexslt
-+endif
- 
- BUILT_SOURCES = dir.h projrel.h
- 
diff --git a/sci-biology/meme/files/meme-4.11.2_p2-patch1.patch b/sci-biology/meme/files/meme-4.11.2_p2-patch1.patch
deleted file mode 100644
index 30a182f8f43a..000000000000
--- a/sci-biology/meme/files/meme-4.11.2_p2-patch1.patch
+++ /dev/null
@@ -1,383 +0,0 @@
---- a/doc/alphabet-format.html
-+++ b/doc/alphabet-format.html
-@@ -233,7 +233,7 @@
-           providing a reference on the meaning of the symbols used. If present, the
-           symbol name must be the second field.</p>
-           <p>The &quot;<span class="pdat">name</span>&quot; follows the rules of
--          <a href="qstr">quoted text</a>.</p>
-+          <a href="#qstr">quoted text</a>.</p>
-         </div>
-         <h5>color</h5>
-         <div class="indent">
---- a/doc/release-notes.html
-+++ b/doc/release-notes.html
-@@ -14,8 +14,26 @@
-       <h2>Motif-based sequence analysis tools</h2>
-     </div>
-     <h2>MEME Suite Release Notes</h2>
-+    <hr>
-+      <b>MEME version 4.11.2 patch 1 -- June 16, 2016</b>
-+      <ul>
-+        <li>
-+            <b>Bug fixes</b>
-+            <ul>
-+              <li>
-+              Fixed bug in MCAST 4.11.2 that caused it to prematurely truncate
-+              reading the sequence file.
-+              </li>
-+              <li>
-+              Modified MEME to fall back to a simple Dirichlet prior when
-+              using DNA or a custom alphabet with a prior that requires
-+              a prior library, but no prior libray is specified.
-+              </li>
-+            </ul
-+        </li>
-+      </ul>
-+      <p>
-       <hr>
--      <p>
-         <b>MEME version 4.11.2 -- May 5 2016</b>
-       </p>
-       <ul>
---- a/src/fasta-io.c
-+++ b/src/fasta-io.c
-@@ -14,6 +14,7 @@
- #include "alphabet.h"
- #include "fasta-io.h"
- #include "io.h"
-+#include "seq-reader-from-fasta.h"
- #include "prior-reader-from-psp.h"
- #include "seq.h"
- 
-@@ -159,61 +160,6 @@
- }
- 
- /****************************************************************************
-- * Read raw sequence until a new sequence is encountered or too many letters
-- * are read.  The new sequence is appended to the end of the given
-- * sequence.
-- *
-- * Return: Was the sequence read completely?
-- ****************************************************************************/
--static BOOLEAN_T read_raw_sequence_from_reader(
--   DATA_BLOCK_READER_T *fasta_reader, // Sequence source
--   char* name, // Sequence ID (used in error messages).
--   ALPH_T* alph, // Alphabet in use
--   unsigned int offset, // Current position in raw_sequence.
--   unsigned int max_chars, // Maximum chars in raw_sequence.
--   char* raw_sequence // Pre-allocated sequence.
--) {
--  // tlb; change a_char to integer so it will compile on SGI
--  int a_char;
--  int start_update;
--  BOOLEAN_T return_value = TRUE;
--
--  // Start at the end of the given sequence.
--  assert(offset < max_chars);
--
--  DATA_BLOCK_T *seq_block = new_sequence_block(max_chars - offset);
--  return_value = !fasta_reader->get_next_block(fasta_reader, seq_block);
--
--  char *seq_buffer = get_sequence_from_data_block(seq_block);
--  size_t seq_buffer_size = get_num_read_into_data_block(seq_block);
--  int i;
--  for (i = 0; i < seq_buffer_size; ++i) {
--    a_char = seq_buffer[i];
--    // Skip non-alphabetic characters.
--    if (!isalnum(a_char) && a_char != '-' && a_char != '*' && a_char != '.') {
--      if ((a_char != ' ') && (a_char != '\t') && (a_char != '\n') && (a_char != '\r')) {
--        fprintf(stderr, "Warning: Skipping character %c in sequence %s.\n",
--                a_char, name);
--      }
--    } else {
--      // skip check if unknown alph
--      if (alph != NULL && !alph_is_known(alph, a_char)) {
--        fprintf(stderr, "Warning: Converting illegal character %c to %c ",
--                a_char, alph_wildcard(alph));
--        fprintf(stderr, "in sequence %s.\n", name);
--        a_char = alph_wildcard(alph);
--      }
--      raw_sequence[offset] = (char) a_char;
--      ++offset;
--    }
--  }
--
--  raw_sequence[offset] = '\0';
--  free_data_block(seq_block);
--  return(return_value);
--}
--
--/****************************************************************************
-  * Read one sequence from a file in Fasta format.
-  *
-  * Return: Was a sequence successfully read?
-@@ -320,44 +266,6 @@
- }
- 
- /****************************************************************************
-- * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder
-- * and copy them in to the raw sequence in the SEQ_T object starting at the
-- * given buffer offset. 
-- ****************************************************************************/
--void read_one_fasta_segment_from_reader(
--   DATA_BLOCK_READER_T *fasta_reader,
--   size_t max_size,
--   size_t buffer_offset,
--   SEQ_T *sequence
--) {
--
--  assert(sequence != NULL);
--  assert(get_seq_length(sequence) <= max_size);
--
--  // Get the raw sequence buffer from the SEQ_T
--  char *raw_sequence = get_raw_sequence(sequence);
--  if (raw_sequence == NULL) {
--    // Allocate space for raw sequence if not done yet.
--    raw_sequence = mm_malloc(sizeof(char) * max_size + 1);
--    raw_sequence[0] = 0;
--  }
--
--  // Read a block of sequence charaters into the
--  // raw sequence buffer for the SEQ_T.
--  char *name = get_seq_name(sequence);
--  BOOLEAN_T is_complete = read_raw_sequence_from_reader(
--    fasta_reader,
--    name,
--    NULL, //FIXME this is dodgy, need a proper way of getting the alphabet. The fasta_reader has it but it is not accessable!
--    buffer_offset,
--    max_size,
--    raw_sequence
--  );
--  set_raw_sequence(raw_sequence, is_complete, sequence);
--
--}
--
--/****************************************************************************
-  * Read all the sequences from a FASTA file at once.
-    Multiple files can be appended by calling this more than once.
-  ****************************************************************************/
---- a/src/fasta-io.h
-+++ b/src/fasta-io.h
-@@ -43,19 +43,6 @@
- );
- 
- /****************************************************************************
-- * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder
-- * and copy them in to the raw sequence in the SEQ_T object starting at the
-- * given buffer offset. 
-- ****************************************************************************/
--void read_one_fasta_segment_from_reader(
--  DATA_BLOCK_READER_T *fasta_reader,
--  size_t max_size,
--  size_t buffer_offset,
--  SEQ_T* sequence
--);
--
--
--/****************************************************************************
-  * Read all the sequences from a file in Fasta format.
-  ****************************************************************************/
- void read_many_fastas
---- a/src/init.c
-+++ b/src/init.c
-@@ -767,10 +767,16 @@
-       if (alph_is_builtin_protein(alph)) { // default mixture prior for proteins
-         plib_name = make_path_to_file(get_meme_etc_dir(), PROTEIN_PLIB);
-       } else {
--        fprintf(stderr, "The prior library must be specified for DNA or custom "
--            "alphabets when specifiying a prior type of 'dmix', 'mega' "
--            "or 'megap'.");
--        exit(1);
-+        fprintf(
-+          stderr, 
-+          "WARNING: When using DNA or a custom alphabet, "
-+          "and specifiying a prior type of\n"
-+          "'dmix', 'mega' or 'megap', a prior library must be provided.\n"
-+          "No prior library was provided, so a simple Dirichlet prior will be used.\n"
-+        );
-+        prior = "dirichlet";
-+        ptype = Dirichlet;
-+        if (beta <= 0) beta = 0.01; // default b = 0.01 for simple Dirichlet
-       }
-     }
-   }
---- a/src/seq-reader-from-fasta.c
-+++ b/src/seq-reader-from-fasta.c
-@@ -639,11 +639,140 @@
-   return fasta_reader->current_position;
- }
- 
-+
-+/****************************************************************************
-+ * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder
-+ * and copy them in to the raw sequence in the SEQ_T object starting at the
-+ * given buffer offset. 
-+ ****************************************************************************/
-+void read_one_fasta_segment_from_reader(
-+   DATA_BLOCK_READER_T *fasta_reader,
-+   size_t max_size,
-+   size_t offset,
-+   SEQ_T *sequence
-+) {
-+
-+
-+  assert(sequence != NULL);
-+  assert(offset < max_size);
-+
-+  // Get the raw sequence buffer from the SEQ_T
-+  char *raw_sequence = get_raw_sequence(sequence);
-+  if (raw_sequence == NULL) {
-+    // Allocate space for raw sequence if not done yet.
-+    raw_sequence = mm_malloc(sizeof(char) * max_size + 1);
-+    raw_sequence[0] = 0;
-+  }
-+
-+  // Read a block of sequence charaters into the
-+  // raw sequence buffer for the SEQ_T, starting at offset.
-+  BOOLEAN_T is_complete = read_raw_sequence_from_reader(
-+    fasta_reader,
-+    max_size - offset,
-+    raw_sequence + offset
-+  );
-+  set_raw_sequence(raw_sequence, is_complete, sequence);
-+}
-+
-+/****************************************************************************
-+ * Read raw sequence until a new sequence is encountered or too many letters
-+ * are read.
-+ *
-+ * Return: Was the sequence read completely?
-+ ****************************************************************************/
-+BOOLEAN_T read_raw_sequence_from_reader(
-+   DATA_BLOCK_READER_T *reader, // Sequence source
-+   unsigned int max_chars, // Maximum chars in raw_sequence.
-+   char* raw_sequence // Pre-allocated sequence buffer.
-+) {
-+
-+  SEQ_READER_FROM_FASTA_T *fasta_reader 
-+    = (SEQ_READER_FROM_FASTA_T *) get_data_block_reader_data(reader);
-+
-+  // Read sequence into temp. buffer from the sequence file.
-+  char buffer[max_chars];
-+  long start_file_pos = ftell(fasta_reader->fasta_file);
-+  size_t seq_index = 0;
-+  size_t total_read = 0;
-+  while (seq_index < max_chars) {
-+
-+    size_t num_char_read = fread(
-+      buffer,
-+      sizeof(char), 
-+      max_chars - seq_index,
-+      fasta_reader->fasta_file
-+    );
-+    fasta_reader->current_position += num_char_read;
-+    total_read += num_char_read;
-+
-+    if (feof(fasta_reader->fasta_file)) {
-+       fasta_reader->at_end_of_file = TRUE;
-+    }
-+    else if (num_char_read < (max_chars - seq_index)) {
-+      die(
-+        "Error while reading sequence from file:%s.\nError message: %s\n", 
-+        fasta_reader->filename,
-+        strerror(ferror(fasta_reader->fasta_file))
-+      );
-+    }
-+
-+    size_t i;
-+    for(i = 0; i < num_char_read; ++i) {
-+      char c = buffer[i];
-+      assert(c != 0);
-+      if (isspace(c)) {
-+        // Skip over white space
-+        fasta_reader->at_start_of_line = (c == '\n');
-+      }
-+      else if (c == '>' && fasta_reader->at_start_of_line == TRUE) {
-+        // We found the start of a new sequence while trying
-+        // to fill the buffer. Leave the buffer incomplete.
-+        // and wind back the file
-+        fseek(fasta_reader->fasta_file, start_file_pos + i - 1, SEEK_SET);
-+        fasta_reader->current_position = start_file_pos + i - 1;
-+        fasta_reader->at_end_of_seq = TRUE;
-+        fasta_reader->at_start_of_line = FALSE;
-+        fasta_reader->at_end_of_file = FALSE;
-+        break;
-+      }
-+      else {
-+        fasta_reader->at_start_of_line = FALSE;
-+        // Check that character is legal in alphabet. 
-+        // If not, replace with wild card character.
-+        if (alph_is_known(fasta_reader->alphabet, c)) {
-+          raw_sequence[seq_index] = c;
-+        }
-+        else {
-+          raw_sequence[seq_index] = alph_wildcard(fasta_reader->alphabet);
-+          fprintf(
-+            stderr, 
-+            "Warning: %c is not a valid character in %s alphabet.\n"
-+            "         Converting %c to %c.\n",
-+            c,
-+            alph_name(fasta_reader->alphabet),
-+            c,
-+            raw_sequence[i]
-+          );
-+        }
-+        ++seq_index;
-+      }
-+    }
-+    if (fasta_reader->at_end_of_seq | fasta_reader->at_end_of_file) {
-+      break;
-+    }
-+  }
-+
-+  raw_sequence[seq_index] = '\0';
-+  return(fasta_reader->at_end_of_seq | fasta_reader->at_end_of_file);
-+}
-+
- /******************************************************************************
-- * Fills in the next data block for the sequence. 
-- * During the first call for the sequence it fills in the full data block.
-- * On successive calls, shifts the sequence in the block down one position
-- * and reads one more character.
-+ * Populates the data block for the with the next block of sequence. 
-+ *
-+ * During the first call for the sequence it fills in a buffer from a file,
-+ * The sequence pointer in the data block is set to point at the start of the buffer.
-+ * On successive calls, the sequence pointer in the block is shifted down one position
-+ * in the buffer. When the end of the buffer is reached, it is filled again from the file.
-  * 
-  * Returns TRUE if it was able to completely fill the block, FALSE if 
-  * the next sequence or EOF was reached before the block was filled.
---- a/src/seq-reader-from-fasta.h
-+++ b/src/seq-reader-from-fasta.h
-@@ -37,5 +37,30 @@
-   int * end_ptr           // end position of sequence (chr:\d+-(\d+))
- );
- 
-+/****************************************************************************
-+ * Read raw sequence until a new sequence is encountered or too many letters
-+ * are read.
-+ *
-+ * Return: Was the sequence read completely?
-+ ****************************************************************************/
-+BOOLEAN_T read_raw_sequence_from_reader(
-+   DATA_BLOCK_READER_T *fasta_reader, // Sequence source
-+   unsigned int max_chars, // Maximum chars in raw_sequence.
-+   char* raw_sequence // Pre-allocated sequence.
-+);
-+
-+/****************************************************************************
-+ * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder
-+ * and copy them in to the raw sequence in the SEQ_T object starting at the
-+ * given buffer offset. 
-+ ****************************************************************************/
-+void read_one_fasta_segment_from_reader(
-+   DATA_BLOCK_READER_T *reader,
-+   size_t max_size,
-+   size_t offset,
-+   SEQ_T *sequence
-+);
-+
-+
- size_t get_current_pos_from_seq_reader_from_fasta(DATA_BLOCK_READER_T *reader);
- #endif
diff --git a/sci-biology/meme/files/meme-4.11.2_p2-patch2.patch b/sci-biology/meme/files/meme-4.11.2_p2-patch2.patch
deleted file mode 100644
index 498d1df7b664..000000000000
--- a/sci-biology/meme/files/meme-4.11.2_p2-patch2.patch
+++ /dev/null
@@ -1,54 +0,0 @@
---- a/doc/release-notes.html
-+++ b/doc/release-notes.html
-@@ -15,6 +15,21 @@
-     </div>
-     <h2>MEME Suite Release Notes</h2>
-     <hr>
-+      <b>MEME version 4.11.2 patch 2 -- October 24, 2016</b>
-+      <ul>
-+        <li>
-+            <b>Bug fixes</b>
-+            <ul>
-+              <li>
-+              Fixed bug in handling of RNA-like custom alphabets.
-+              </li>
-+              <li>
-+              Fixed bug in MAST -comp option.
-+              </li>
-+            </ul
-+        </li>
-+      </ul>
-+      <hr>
-       <b>MEME version 4.11.2 patch 1 -- June 16, 2016</b>
-       <ul>
-         <li>
---- a/src/alph-in.c
-+++ b/src/alph-in.c
-@@ -1044,7 +1044,7 @@
-           lookup[0] = sym->complement;
-           comp2 = (ALPH_SYM_T*)rbtree_get(reader->merged, lookup);
-         }
--        if (comp1 != comp2) {
-+        if (comp1 && (comp1 != comp2)) {
-           add_msg(reader, parmsg_create(SEVERITY_ERROR, -1, -1, -1, 
-                 "not like %s alphabet as %c complement rules are incorrect",
-                 ext_name, req_syms[i]));
---- a/src/mast-util.c
-+++ b/src/mast-util.c
-@@ -740,14 +740,14 @@
- 
-   // create the frequency array  
-   alph = xlate ? xlate_dest_alph(xlate) : alph;
--  freq = allocate_array(alph_size_core(alph));
-+  freq = allocate_array(alph_size_full(alph));
-   init_array(0, freq);
- 
-   // count the number of letters of each type 
-   if (xlate) {
-     for (n=0; sequence[n]; n++) {
-       i = xlate_index(xlate, false, sequence+n);
--      if (i > 0 && i < alph_size_core(alph)) incr_array_item(i, 1, freq);
-+      if (i > 0 && i < alph_size_full(alph)) incr_array_item(i, 1, freq);
-     }
-   } else {
-     for (n=0; sequence[n]; n++) {
diff --git a/sci-biology/meme/meme-4.11.2_p2.ebuild b/sci-biology/meme/meme-4.11.2_p2.ebuild
deleted file mode 100644
index 9487f7a9789c..000000000000
--- a/sci-biology/meme/meme-4.11.2_p2.ebuild
+++ /dev/null
@@ -1,109 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools perl-functions python-single-r1 versionator
-
-MY_PV=$(get_version_component_range 1-3)
-MY_P=${PN}_${MY_PV}
-
-DESCRIPTION="The MEME/MAST system - Motif discovery and search"
-HOMEPAGE="https://meme-suite.org/tools/meme"
-SRC_URI="http://meme-suite.org/meme-software/${MY_PV}/${MY_P}.tar.gz"
-
-LICENSE="meme"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug doc examples mpi"
-
-RDEPEND="
-	${PYTHON_DEPS}
-	app-shells/tcsh
-	dev-libs/libxml2:2
-	dev-libs/libxslt
-	sys-libs/zlib
-	app-text/ghostscript-gpl
-	media-gfx/imagemagick
-	dev-lang/perl:=
-	dev-perl/HTML-Parser
-	dev-perl/HTML-Template
-	dev-perl/Log-Log4perl
-	dev-perl/Math-CDF
-	dev-perl/XML-Compile-SOAP
-	dev-perl/XML-Compile-WSDL11
-	dev-perl/XML-Parser
-	dev-perl/XML-Simple
-	virtual/perl-Data-Dumper
-	virtual/perl-Exporter
-	virtual/perl-File-Path
-	virtual/perl-File-Spec
-	virtual/perl-File-Temp
-	virtual/perl-Getopt-Long
-	virtual/perl-Scalar-List-Utils
-	virtual/perl-Time-HiRes
-	mpi? ( virtual/mpi )"
-DEPEND="${RDEPEND}"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-S="${WORKDIR}/${MY_P}"
-PATCHES=(
-	"${FILESDIR}"/${PN}-4.11.2_p2-patch1.patch
-	"${FILESDIR}"/${PN}-4.11.2_p2-patch2.patch
-	"${FILESDIR}"/${PN}-4.11.2_p2-fix-build-system.patch
-)
-
-pkg_setup() {
-	python-single-r1_pkg_setup
-	perl_set_version
-}
-
-src_prepare() {
-	default
-	eautoreconf
-}
-
-src_configure() {
-	econf \
-		--sysconfdir="${EPREFIX}"/etc/${PN} \
-		--with-logs="${EPREFIX}"/var/log/${PN} \
-		--with-perl=perl \
-		--with-convert=convert \
-		--with-gs=gs \
-		--disable-build-libxml2 \
-		--disable-build-libxslt \
-		$(use_enable debug) \
-		$(use_enable doc) \
-		$(use_enable examples) \
-		$(use_enable !mpi serial) \
-		--with-perl-dir="${VENDOR_LIB#${EPREFIX}/usr}" \
-		PYTHON="${EPYTHON}"
-
-	# delete bundled libs, just to be sure. These need
-	# to be removed after econf, else AC_OUTPUT will fail
-	rm -r src/{libxml2,lib{,e}xslt} || die
-}
-
-src_test() {
-	# bug #297070
-	emake -j1 test
-}
-
-src_install() {
-	default
-	docompress -x /usr/share/doc/${PF}/examples
-
-	# prefix all binaries with 'meme-', in order
-	# to prevent collisions, bug 455010
-	cd "${ED%/}"/usr/bin/ || die
-	local i
-	for i in *; do
-		if [[ $i != meme-* ]]; then
-			mv {,meme-}"${i}" || die
-		fi
-	done
-
-	keepdir /var/log/meme
-}
diff --git a/sci-biology/meme/metadata.xml b/sci-biology/meme/metadata.xml
deleted file mode 100644
index b9f3a66d9198..000000000000
--- a/sci-biology/meme/metadata.xml
+++ /dev/null
@@ -1,9 +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>
-	<origin>gentoo-staging</origin>
-</pkgmetadata>
diff --git a/sci-biology/shrimp/Manifest b/sci-biology/shrimp/Manifest
deleted file mode 100644
index 5be68cd79e21..000000000000
--- a/sci-biology/shrimp/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST SHRiMP_2_2_3.src.tar.gz 4596867 BLAKE2B 64e485b8e2524062c11c581bbcac426800c9f42f61da467378dbfd3add63f721a9da9c04df61bde3704e654a20395e799e89fc5e47129b1d3f5bc93f960470fa SHA512 029179aeeb317194b998c29aa91d1d2ce5ccbc6f9ad4a1043d1e5fc75d3344c2f39500ab07e8389c09fa179f0c9b59afee22691bc4eb5d396777f4e0fe25f2d5
diff --git a/sci-biology/shrimp/metadata.xml b/sci-biology/shrimp/metadata.xml
deleted file mode 100644
index b9f3a66d9198..000000000000
--- a/sci-biology/shrimp/metadata.xml
+++ /dev/null
@@ -1,9 +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>
-	<origin>gentoo-staging</origin>
-</pkgmetadata>
diff --git a/sci-biology/shrimp/shrimp-2.2.3.ebuild b/sci-biology/shrimp/shrimp-2.2.3.ebuild
deleted file mode 100644
index 17501c8bb96a..000000000000
--- a/sci-biology/shrimp/shrimp-2.2.3.ebuild
+++ /dev/null
@@ -1,82 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit flag-o-matic python-single-r1 toolchain-funcs
-
-MY_PV=${PV//./_}
-
-DESCRIPTION="SHort Read Mapping Package"
-HOMEPAGE="https://compbio.cs.toronto.edu/shrimp/"
-SRC_URI="http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_${MY_PV}.src.tar.gz"
-
-LICENSE="shrimp"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="custom-cflags +cpu_flags_x86_sse2"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-# file collision on /usr/bin/utils #453044
-DEPEND="!sci-mathematics/cado-nfs"
-RDEPEND="${DEPEND}
-	${PYTHON_DEPS}"
-
-S=${WORKDIR}/SHRiMP_${MY_PV}
-
-pkg_pretend() {
-	use cpu_flags_x86_sse2 || die "This package needs sse2 support in your CPU"
-}
-
-pkg_setup() {
-	if [[ ${CC} == *gcc* ]] &&	! tc-has-openmp; then
-		elog "Please set CC to an OPENMP capable compiler (e.g. gcc[openmp] or icc"
-		die "C compiler lacks OPENMP support"
-	fi
-	python-single-r1_pkg_setup
-}
-
-src_prepare() {
-	sed \
-		-e '1 a #include <stdint.h>' \
-		-i common/dag_glue.cpp || die
-	# respect LDFLAGS wrt 331823
-	sed \
-		-e "s/LDFLAGS/LIBS/" \
-		-e "s/\$(LD)/& \$(LDFLAGS)/" \
-		-e 's/-static//' \
-		-i Makefile || die
-
-	append-flags -fopenmp
-	if ! use custom-cflags; then
-		append-flags -O3
-		replace-flags -O* -O3
-	fi
-	tc-export CXX
-
-	cd utils || die
-	sed -e '/^#!/d' -i *py || die
-	sed -e '1i#!/usr/bin/python' -i *py || die
-}
-
-src_compile() {
-	emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}"
-}
-
-src_install() {
-	local i
-	newdoc bin/README README.bin && rm bin/README
-	dobin bin/* utils/split-contigs utils/temp-sink
-	dodoc HISTORY README TODO SPLITTING_AND_MERGING SCORES_AND_PROBABILITES
-
-	pushd utils > /dev/null
-
-	python_doscript *py
-
-	rm *.py *.o *.c split-contigs temp-sink || die
-	insinto /usr/share/${PN}
-	doins -r *
-}
diff --git a/sci-biology/vienna-rna/Manifest b/sci-biology/vienna-rna/Manifest
deleted file mode 100644
index 8acf7884e034..000000000000
--- a/sci-biology/vienna-rna/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST ViennaRNA-2.1.8.tar.gz 5464683 BLAKE2B ed2086461b37c90de11638852680507c823495abacec1e797c589c22d07dc48b4833d8d6916e5c95083bb9b970c659bbfb14ca45e155486333a915593c4caf01 SHA512 84f9db1247ff7a77aa6550b6285d9bed31fa6ce179aab26eef798c65a07f5cbd89f944630dfa5d29a43401b12a439324b57ee69047a3985e3a4f1e88dffca60e
diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch
deleted file mode 100644
index de457f318e8e..000000000000
--- a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- Readseq/readseq.c | 1 +
- 1 file changed, 1 insertion(+)
-
-diff --git a/Readseq/readseq.c b/Readseq/readseq.c
-index 8af7b39..56a25ae 100644
---- a/Readseq/readseq.c
-+++ b/Readseq/readseq.c
-@@ -171,6 +171,7 @@ link -w -o readseq -t MPST -c 'MPS ' 
- #include <stdio.h>
- #include <string.h>
- #include <ctype.h>
-+#include <stdlib.h>
- 
- #include "ureadseq.h"
- 
diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch
deleted file mode 100644
index ee4aef5c3308..000000000000
--- a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch
+++ /dev/null
@@ -1,30 +0,0 @@
- Readseq/Makefile | 6 +++---
- 1 file changed, 3 insertions(+), 3 deletions(-)
-
-diff --git a/Readseq/Makefile b/Readseq/Makefile
-index f073aaa..05f2edd 100644
---- a/Readseq/Makefile
-+++ b/Readseq/Makefile
-@@ -6,11 +6,11 @@
- #
- 
- # pick an ANSI C compiler (the default Sun CC is not ANSI)
--CC=gcc  # Gnu C Compiler
-+CC?=gcc  # Gnu C Compiler
- #CC=cc  # SGI Irix
- #CC=vcc # some DEC Ultrix
- 
--CFLAGS=
-+CFLAGS?=
- #CFLAGS= -DSMALLCHECKSUM  # if you prefer to use a GCG-standard 13 bit checksum
- #    instead of a full 32 bit checksum. This may enhance compatibility w/ GCG software
- 
-@@ -40,7 +40,7 @@ all: build test
- 
- build: $(SOURCES)
- 	@echo "Compiling readseq..."
--	$(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c ureadasn.c
- 
- # if using NCBI, uncomment these lines in place of build: above
- #build: $(SOURCES)
diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch
deleted file mode 100644
index e54dff95b485..000000000000
--- a/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch
+++ /dev/null
@@ -1,10 +0,0 @@
-diff --git a/Utils/Makefile.am b/Utils/Makefile.am
-index f42ebf4..d84a0f1 100644
---- a/Utils/Makefile.am
-+++ b/Utils/Makefile.am
-@@ -1,4 +1,4 @@
--pkgbindir = $(pkgdatadir)/bin
-+pkgbindir = $(prefix)/bin
- pkgbin_PROGRAMS = b2ct popt ct2db
- 
- pscript = b2mt.pl ct2b.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl colorrna.pl coloraln.pl refold.pl switch.pl
diff --git a/sci-biology/vienna-rna/metadata.xml b/sci-biology/vienna-rna/metadata.xml
deleted file mode 100644
index 7fbaca57cac1..000000000000
--- a/sci-biology/vienna-rna/metadata.xml
+++ /dev/null
@@ -1,26 +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>
-	<longdescription>
-		The Vienna RNA Package consists of a C code library and several
-		stand-alone programs for the prediction and comparison of RNA secondary
-		structures. RNA secondary structure prediction through energy
-		minimization is the most used function in the package. We provide three
-		kinds of dynamic programming algorithms for structure prediction: the
-		minimum free energy algorithm of (Zuker and Stiegler 1981) which yields a
-		single optimal structure, the partition function algorithm of
-		(McCaskill 1990) which calculates base pair probabilities in the
-		thermodynamic ensemble, and the suboptimal folding algorithm of
-		(Wuchty et.al 1999) which generates all suboptimal structures within a
-		given energy range of the optimal energy. For secondary structure
-		comparison, the package contains several measures of distance
-		(dissimilarities) using either string alignment or tree-editing
-		(Shapiro and Zhang 1990). Finally, we provide an algorithm to design
-		sequences with a predefined structure (inverse folding).
-	</longdescription>
-	<origin>gentoo-staging</origin>
-</pkgmetadata>
diff --git a/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild b/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild
deleted file mode 100644
index a1d52a8d5365..000000000000
--- a/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild
+++ /dev/null
@@ -1,112 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-DISTUTILS_OPTIONAL=true
-AUTOTOOLS_AUTORECONF=true
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
-inherit autotools-utils distutils-r1 multilib perl-module toolchain-funcs
-
-DESCRIPTION="RNA secondary structure prediction and comparison"
-HOMEPAGE="https://www.tbi.univie.ac.at/~ivo/RNA/"
-SRC_URI="http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-${PV}.tar.gz"
-
-SLOT="0"
-LICENSE="vienna-rna"
-KEYWORDS="~amd64 ~ppc ~x86"
-IUSE="doc openmp python static-libs"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="
-	dev-lang/perl
-	media-libs/gd
-	doc? ( dev-texlive/texlive-latex )
-	python? ( ${PYTHON_DEPS} )"
-DEPEND="${RDEPEND}
-	python? ( dev-lang/swig:0 )"
-
-S="${WORKDIR}/ViennaRNA-${PV}"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-bindir.patch
-	"${FILESDIR}"/${PN}-2.1.1-prll.patch
-	"${FILESDIR}"/${PN}-2.1.1-impl-decl.patch
-)
-
-src_prepare() {
-	sed -i 's/ getline/ v_getline/' Readseq/ureadseq.c || die
-	sed -i 's/@PerlCmd@ Makefile.PL/& INSTALLDIRS=vendor/' interfaces/Perl/Makefile.am || die
-
-	autotools-utils_src_prepare
-
-	if use python; then
-		cd interfaces/Python || die
-		local PATCHES=()
-		distutils-r1_src_prepare
-	fi
-}
-
-src_configure() {
-	local myeconfargs=(
-		--with-cluster
-		$(use_enable openmp)
-	)
-
-	use doc || \
-		myeconfargs+=(
-			--without-doc-pdf
-			--without-doc-html
-			--without-doc
-			)
-	autotools-utils_src_configure
-	sed \
-		-e "s:CC=gcc:CC=$(tc-getCC):" \
-		-e "s:^CFLAGS=:CFLAGS=${CFLAGS}:" \
-		-i Readseq/Makefile || die
-	if use python; then
-		cd interfaces/Python || die
-		distutils-r1_src_configure
-	fi
-}
-
-src_compile() {
-	autotools-utils_src_compile
-	autotools-utils_src_compile -C Readseq build CC=$(tc-getCC)
-
-	# TODO: Add (optional?) support for the NCBI toolkit.
-	if use python; then
-		cd interfaces/Python || die
-		emake RNA_wrap.c
-		distutils-r1_src_compile
-	fi
-}
-
-src_test() {
-	autotools-utils_src_compile -C interfaces/Perl check
-	use python && autotools-utils_src_compile -C interfaces/Python check
-	autotools-utils_src_compile -C Readseq test
-}
-
-src_install() {
-	autotools-utils_src_install
-
-	if ! use static-libs; then
-		rm -f "${ED}"/usr/$(get_libdir)/*.a || die
-	fi
-
-	newbin Readseq/readseq readseq-vienna
-	dodoc Readseq/Readseq.help
-	newdoc Readseq/Readme README.readseq
-	newdoc Readseq/Formats Formats.readseq
-
-	# remove perlocal.pod to avoid file collisions (see #240358)
-	perl_delete_localpod || die "Failed to remove perlocal.pod"
-	if use python; then
-		cd interfaces/Python || die
-		distutils-r1_src_install
-	fi
-}