gentoo resync : 16.09.2020

29 files changed, 26 insertions, 1026 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index fb1ebe38a141..cf12f63f683b 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
index 0141c7450dbb..963e867595db 100644
--- a/sci-biology/biopython/Manifest
+++ b/sci-biology/biopython/Manifest
@@ -1,3 +1,3 @@
 DIST biopython-1.77.tar.gz 16837021 BLAKE2B b5586f0ea3e476b11801dcc98039d5eea7b191e11d390192c0cf348018ded005fe2ad5dc9ba71c83aebc9cdde20c97244905dcc3aeb5436a97588da9f8c79c3e SHA512 6f4b03d46c591e1f49dd1e76bcc4ac5c9aaa2bf748c9dd37ffc5de5a613fbeed38f89b418c01601dd99c65b13b2e294bc8d81ffafc42a9ff1b309c84f840d0d5
-EBUILD biopython-1.77.ebuild 1855 BLAKE2B 739e5cc4a954ac9cc5fe0640ac5f418ad1ee1aadb66570a41996e8e260dc75c8c4373c94b53b0d147d1b661169c1aa3352b9367ab0e37cfd8bd05c220186ac92 SHA512 e2dd1ef79804c779645162410e6890d0618d080ac20195cae0097fe3a42c204d270321949e8d5056b85f9e9a5ed598e05c20f2869178dd16ea86ea105167271a
+EBUILD biopython-1.77.ebuild 1859 BLAKE2B 84f27ea48f70afb396f0670f41606e646872e0b4ed1596141bdc51c5432f048b75300e9ec74b430255eacea118cf717287294cb67e34faa82757d00793ceeb5f SHA512 0de36036de4e246f7c9dbde30c14c7a29016cc6ae28e8809ee1c95a150add413a19ab84c6ba1fc7b9344f900db4e93c040a90989ccce9c5f10ea9f426bffd189
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/biopython/biopython-1.77.ebuild b/sci-biology/biopython/biopython-1.77.ebuild
index 486e9fe694d1..a25abc9312c6 100644
--- a/sci-biology/biopython/biopython-1.77.ebuild
+++ b/sci-biology/biopython/biopython-1.77.ebuild
@@ -5,7 +5,7 @@ EAPI=7
 
 PYTHON_COMPAT=( python3_{6..9} )
 
-inherit distutils-r1 eutils
+inherit distutils-r1 optfeature
 
 DESCRIPTION="Python modules for computational molecular biology"
 HOMEPAGE="https://www.biopython.org/ https://pypi.org/project/biopython/"
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index bbf916477036..f9a42acddbb3 100644
--- a/sci-biology/bowtie/Manifest
+++ b/sci-biology/bowtie/Manifest
@@ -1,14 +1,4 @@
-AUX bowtie-1.1.2-_ContextLss-1.1-1.4.patch 601 BLAKE2B 36de166ef2f22d6a6cf9a5773d62f74bd69241b2a788f376108f847f09be0811b4c0156e8a5ded0e0f724cdffa77ed0b79ade064c0268b91ff966319ac2c0d0d SHA512 e39ec6323cc6fee49a6ecf3565066d9cb8f8001af2701de292025f268d57dcfa3d4c35f3e2aed56b7e3835a955e5bfb595214ac232309fcc46c6d51f83cd9f2e
-AUX bowtie-1.1.2-fix-setBegin-call.patch 1269 BLAKE2B 3bfa4fca8a94c600f6d405c4824cc83ac5838c0353f3e36417bdb1e88222902f786fe6f8e3e5099f577ca5044b2caf5d9eaf64876311ea9df4a5d4314bd22f03 SHA512 8838a0d8b35c9ceb4be1ef3439eab5e3478dcfe11c5e59e327717676eceab413b07ec97dbda9fb3527ab61653a8a6e2d651b5bb4c24114288d3b07922348c5d3
-AUX bowtie-1.1.2-seqan-popcount.patch 566 BLAKE2B 6d9d109fbbba2b85d22c923959ca0726cb9bb2da950b0b0b9aa84106c9b74c24d5bf997d1339273f92cffc5bf42c9852bf376dce260c1374c3374f8f230e395d SHA512 07b70a1941b98033967b8a7303fab94aa3a047bd5da9355f58f03af04f4515903cbf2698700fb3e987546998ebb28225672aa8fbfc65dd8bc202be8a26290838
-AUX bowtie-1.1.2-seqan-rename-ChunkPool.patch 11618 BLAKE2B bc4e9610bdde7dba741c7963c59f0361cca43e6224d1c4f2448d53111cbb0ac2d0cbd45a8d90948689bf0af1c511f180839a0b981c1588dda2f52f3a2e06a0d6 SHA512 3d05ea37c753c780163123ab8fdf8d149f0daddf4c52fcf81b1380951f132edf312b13505ea9afc2ff34ee4f3188b5251beb9e71e3c78f2eeabfadd4ab1ae5a1
-AUX bowtie-1.1.2-seqan-rename-fill-to-resize.patch 3280 BLAKE2B 00815454c116bc8b64a96668508fdddbf9909aefea84353031524eef479e60a540ed74512ca7c4e62d41e6bea4bed60cf102621390070b4f45bc63abcb2b20dd SHA512 e0a96c870670c6c38b48da0c0e0f3dc4f5e9b0654ecb1d55c22484472192cc926168a333625a582c470e2781f6e062d6704723feb29d7f32f2a19eb229622aa0
-AUX bowtie-1.1.2-spelling.patch 4157 BLAKE2B 2a48f2da1e68df166230fe35f9858b34b86962d97ec7d36a9bc0b19615961623ff2403dc630dae4cb2d4ade439b4b487762ac7be32efb7947dee3b2bb919d7a1 SHA512 1679ecdaffa55adb2c1e206a77eba6052e4d9e65e476f73df795bf1fc9e323d34c20f4673a285701b067c65477b3804cd44a4c30b36ae5502f534a4cf191af18
-AUX bowtie-1.1.2-tbb-tinythread-missing.patch 554 BLAKE2B 745629aa93f2e74191b944345b95b4d2e4e399a9e5c5a0f48690d3abe411076e4f71603333ff70050af8c63c2a9dcb753d1e9ceb1fa2ec066b9002a7f71ea96f SHA512 04cc9dad3a6c2598bde41975604a75ca5f0b1490144d2a9f91c049b04b8af80d95e8842aaf1b551ec3d9ca842981e72aa692f00b80971c067d7464776c1e78c9
-AUX bowtie-1.1.2-unbundle-seqan.patch 751 BLAKE2B d9689b298f21f4619dbbed96b58d8ae7fc5f646539ae33291222d282153b545ad6fb3e30fe1ba5f0f452e2f3e7e9706b6761f5d4184dcd5ad96a55ccc7b246be SHA512 9a68ccc98774a2c9ddb8f45b5ed009230d14d3e29837c6dd8aac34e298f57208361ef45d0e7d9d074495f3465b58f08606cced9e4fccb549785591ff954cb2b8
 AUX bowtie-2.2.9-fix-c++14.patch 687 BLAKE2B a75f473f429379789a97142d7820fb19fc1a64b764236c6fa1c068cefb03e37a58b41b0a515a62d42e85b3131f0dfe8f2bb856126528099277394674a0e53248 SHA512 3aa6e7a30fdf93ae564091ce9b87338ab9feccbd0c873f4130af71dc94fd3b27527b42a93f13471a2613bad44dbacd639d17515000f03856695a0021ce14dfc5
-DIST bowtie-1.1.2-src.zip 7713258 BLAKE2B ac10aca905099b5a70d3fab6f90e2dc4713bf7b460d027abf89a6ef6103979724e70b2915a86ffa571b59dcd9df768c80be1846cccd08f7f85dd402ce64c0cb0 SHA512 3d3d69bc3a865bb577b5a91440215d0d5b606c7a8751d565e606e36adbfbdef695b1718ae81cd3e2682a39ca7784c4d00976441e7618264ad99b04c7f53c36e8
 DIST bowtie2-2.2.9-source.zip 5734235 BLAKE2B ec48e09fe05403d1085bb4e0c6ef1325b8912da0a8c942061c34f3381c6dd7ccdcc64c4bcdbb18c1da84ac57e1e34cc866fe79809c33c2769a8d75ecde7d0846 SHA512 ead8f7641f3231638d986f9e500bc4ec7afe1e542048465bfcc2e93e2b2d2e499f0dd8aa5c1e3e21df285c9d195b187682eb7e12be4a408f6c50fb97c0e0a205
-EBUILD bowtie-1.1.2-r1.ebuild 1643 BLAKE2B 81f79b8b8d9b9a56061bf92df193a21e2db03bdacb6290020e8fb2426e3e1cf9e5a6a802cb6fa5f5f68be8d7f92f749e14c0c3528ebad5825d3927bcf33ca483 SHA512 8b5c22f29aafb5977313ea002fcd654ac991015f7808f02f8e02c2105dd9a6fa77b5f5342e82d38b07674c93dbe397333be78f6d1ca9a24a60531d6a40efe382
 EBUILD bowtie-2.2.9.ebuild 1277 BLAKE2B b9cf9edc34af3f01eb1cde1510637bbcbaf7206d9a24135d859d14dcefe793abd0b78dd19dbcd1835840514e754061aee86a79d5992ca68d316c64c98bb4891c SHA512 40e22698d5df241b8b98c601f8ed22276d39f4c9818bb23afec0a39b625fd38a0fdb3f4b4d6f8c01b458e2b6b3464a7ee8a135bd446f3488354eeca9934daa85
 MISC metadata.xml 528 BLAKE2B 310fb406a0dbe56b194ae13cf521264e105f9d849b09e10d5d7e556c7d00a9cc7a0f9546a91e43f30344c9ec14a76e0d8a3f037fb4cb91bba68999d9f45b69e0 SHA512 1eb83cbd7d7e747bc94021051ba6ae0bf22411091287b754851a9f6824b263b6ca83c9a0d055c0b6ab24963ceea9b32d76bf1b343f48a3ee4bd322fec539b301
diff --git a/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild b/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild
deleted file mode 100644
index d8b607f870fc..000000000000
--- a/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit flag-o-matic toolchain-funcs
-
-DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/"
-SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
-
-LICENSE="Artistic"
-SLOT="1"
-KEYWORDS="~amd64 ~x86 ~x64-macos"
-
-IUSE="examples +tbb"
-
-RDEPEND="tbb? ( dev-cpp/tbb )"
-DEPEND="${RDEPEND}
-	sci-biology/seqan:1.4
-	app-arch/unzip"
-
-DOCS=( AUTHORS NEWS TUTORIAL doc/README )
-HTML_DOCS=( doc/{manual.html,style.css} )
-
-PATCHES=(
-	"${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch"
-	"${FILESDIR}/${P}-fix-setBegin-call.patch"
-	"${FILESDIR}/${P}-seqan-popcount.patch"
-	"${FILESDIR}/${P}-seqan-rename-ChunkPool.patch"
-	"${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch"
-	"${FILESDIR}/${P}-spelling.patch"
-	"${FILESDIR}/${P}-tbb-tinythread-missing.patch"
-	"${FILESDIR}/${P}-unbundle-seqan.patch"
-)
-
-src_prepare() {
-	default
-
-	# remove bundled libraries, use system seqan 1.4
-	rm -rf SeqAn-1.1/ third_party/ || die
-
-	# innocuous non-security flags, prevent log pollution
-	append-cxxflags \
-		-Wno-unused-local-typedefs \
-		-Wno-unused-but-set-variable \
-		-Wno-unused-variable
-}
-
-src_compile() {
-	emake \
-		CC="$(tc-getCC)" \
-		CPP="$(tc-getCXX)" \
-		CFLAGS="" \
-		CXXFLAGS="" \
-		EXTRA_FLAGS="${LDFLAGS}" \
-		RELEASE_FLAGS="${CXXFLAGS}" \
-		WITH_TBB="$(usex tbb 1 0)"
-}
-
-src_install() {
-	dobin ${PN} ${PN}-*
-
-	exeinto /usr/libexec/${PN}
-	doexe scripts/*
-
-	newman MANUAL ${PN}.1
-	einstalldocs
-
-	if use examples; then
-		insinto /usr/share/${PN}
-		doins -r genomes indexes
-	fi
-}
diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch b/sci-biology/bowtie/files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch
deleted file mode 100644
index 78b9c01a0462..000000000000
--- a/sci-biology/bowtie/files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-Description: Change class name of _Context_LSS
- New version 1.4 of SeQan uses a different name of the class. 
-Forwarded: no
-Author: Gert Wollny <gw.fossdev@gmail.com>
-Last-Update: 2014-100-06
-
---- a/diff_sample.h
-+++ b/diff_sample.h
-@@ -856,7 +856,7 @@ void DifferenceCoverSample<TStr>::build(
- 	{
- 		Timer timer(cout, "  Invoking Larsson-Sadakane on ranks time: ", this->verbose());
- 		VMSG_NL("  Invoking Larsson-Sadakane on ranks");
--		_Context_LSS<TIndexOff> c;
-+		ContextLss_<TIndexOff> c;
- 		c.suffixsort(
- 			(TIndexOff*)begin(_isaPrime, Standard()),
- 			(TIndexOff*)begin(sPrime, Standard()),
diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-fix-setBegin-call.patch b/sci-biology/bowtie/files/bowtie-1.1.2-fix-setBegin-call.patch
deleted file mode 100644
index af7f7f61cd5e..000000000000
--- a/sci-biology/bowtie/files/bowtie-1.1.2-fix-setBegin-call.patch
+++ /dev/null
@@ -1,42 +0,0 @@
-Description: Proper type-casting in using seqan::_setBegin().
- Required by newer versions of GCC.
-Forwarded: no
-Author: Ognyan Kulev <ogi@debian.org>
-Last-Update: 2013-04-18
-
---- a/pat.h
-+++ b/pat.h
-@@ -82,20 +82,20 @@ struct ReadBuf {
- 	~ReadBuf() {
- 		clearAll(); reset();
- 		// Prevent seqan from trying to free buffers
--		_setBegin(patFw, NULL);
--		_setBegin(patRc, NULL);
--		_setBegin(qual, NULL);
--		_setBegin(patFwRev, NULL);
--		_setBegin(patRcRev, NULL);
--		_setBegin(qualRev, NULL);
--		_setBegin(name, NULL);
-+		_setBegin(patFw, (Dna5*)NULL);
-+		_setBegin(patRc, (Dna5*)NULL);
-+		_setBegin(qual, (char*)NULL);
-+		_setBegin(patFwRev, (Dna5*)NULL);
-+		_setBegin(patRcRev, (Dna5*)NULL);
-+		_setBegin(qualRev, (char*)NULL);
-+		_setBegin(name, (char*)NULL);
- 		for(int j = 0; j < 3; j++) {
--			_setBegin(altPatFw[j], NULL);
--			_setBegin(altPatFwRev[j], NULL);
--			_setBegin(altPatRc[j], NULL);
--			_setBegin(altPatRcRev[j], NULL);
--			_setBegin(altQual[j], NULL);
--			_setBegin(altQualRev[j], NULL);
-+			_setBegin(altPatFw[j], (Dna5*)NULL);
-+			_setBegin(altPatFwRev[j], (Dna5*)NULL);
-+			_setBegin(altPatRc[j], (Dna5*)NULL);
-+			_setBegin(altPatRcRev[j], (Dna5*)NULL);
-+			_setBegin(altQual[j], (char*)NULL);
-+			_setBegin(altQualRev[j], (char*)NULL);
- 		}
- 	}
- 
diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-popcount.patch b/sci-biology/bowtie/files/bowtie-1.1.2-seqan-popcount.patch
deleted file mode 100644
index 52cb4f496521..000000000000
--- a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-popcount.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-Description: Use SeqAn 1.4's seqan::popCount() function instead of own function
-Author: Ognyan Kulev <ogi@debian.org>
-Last-Update: 2014-03-08
----
-This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- a/diff_sample.h
-+++ b/diff_sample.h
-@@ -476,6 +476,8 @@ static String<T> getDeltaMap(T v, const
- 	return amap;
- }
- 
-+// Debian: Use seqan::popCount
-+#if 0
- /**
-  * Return population count (count of all bits set to 1) of i.
-  */
-@@ -488,6 +490,7 @@ static unsigned int popCount(T i) {
- 	}
- 	return cnt;
- }
-+#endif
- 
- /**
-  * Calculate log-base-2 of i
diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-ChunkPool.patch b/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-ChunkPool.patch
deleted file mode 100644
index 171f9bab8fae..000000000000
--- a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-ChunkPool.patch
+++ /dev/null
@@ -1,382 +0,0 @@
-Description: Renamed ChunkPool class to bowtieChunkPool.
- SeqAn has a class with the same name and fatal name collision happens.
-Forwarded: no
-Author: Ognyan Kulev <ogi@debian.org>
-Last-Update: 2013-04-18
-
---- a/aligner.h
-+++ b/aligner.h
-@@ -337,7 +337,7 @@ public:
- 		bool verbose,
- 		bool quiet,
- 		int maxBts,
--		ChunkPool *pool,
-+		bowtieChunkPool *pool,
- 		int *btCnt = NULL,
- 		AlignerMetrics *metrics = NULL) :
- 		Aligner(true, rangeMode),
-@@ -544,7 +544,7 @@ protected:
- 	bool quiet_; // don't print informational/warning info
- 
- 	const int maxBts_;
--	ChunkPool *pool_;
-+	bowtieChunkPool *pool_;
- 	int *btCnt_;
- 	AlignerMetrics *metrics_;
- };
-@@ -585,7 +585,7 @@ public:
- 		bool verbose,
- 		bool quiet,
- 		int maxBts,
--		ChunkPool *pool,
-+		bowtieChunkPool *pool,
- 		int *btCnt) :
- 		Aligner(true, rangeMode),
- 		refs_(refs),
-@@ -1358,7 +1358,7 @@ protected:
- 	bool quiet_;
- 
- 	int maxBts_;
--	ChunkPool *pool_;
-+	bowtieChunkPool *pool_;
- 	int *btCnt_;
- 
- 	// Range-finding state for first mate
-@@ -1482,7 +1482,7 @@ public:
- 		bool verbose,
- 		bool quiet,
- 		int maxBts,
--		ChunkPool *pool,
-+		bowtieChunkPool *pool,
- 		int *btCnt) :
- 		Aligner(true, rangeMode),
- 		refs_(refs),
-@@ -2035,7 +2035,7 @@ protected:
- 	TDriver* driver_;
- 
- 	// Pool for distributing chunks of best-first path descriptor memory
--	ChunkPool *pool_;
-+	bowtieChunkPool *pool_;
- 
- 	bool verbose_;
- 	bool quiet_;
---- a/aligner_0mm.h
-+++ b/aligner_0mm.h
-@@ -32,7 +32,7 @@ public:
- 			RangeCache* cacheFw,
- 			RangeCache* cacheBw,
- 			uint32_t cacheLimit,
--			ChunkPool *pool,
-+			bowtieChunkPool *pool,
- 			BitPairReference* refs,
- 			vector<String<Dna5> >& os,
- 			bool maqPenalty,
-@@ -124,7 +124,7 @@ private:
- 	RangeCache *cacheFw_;
- 	RangeCache *cacheBw_;
- 	const uint32_t cacheLimit_;
--	ChunkPool *pool_;
-+	bowtieChunkPool *pool_;
- 	BitPairReference* refs_;
- 	vector<String<Dna5> >& os_;
- 	bool maqPenalty_;
-@@ -164,7 +164,7 @@ public:
- 			RangeCache* cacheFw,
- 			RangeCache* cacheBw,
- 			uint32_t cacheLimit,
--			ChunkPool *pool,
-+			bowtieChunkPool *pool,
- 			BitPairReference* refs,
- 			vector<String<Dna5> >& os,
- 			bool reportSe,
-@@ -366,7 +366,7 @@ private:
- 	RangeCache *cacheFw_;
- 	RangeCache *cacheBw_;
- 	const uint32_t cacheLimit_;
--	ChunkPool *pool_;
-+	bowtieChunkPool *pool_;
- 	BitPairReference* refs_;
- 	vector<String<Dna5> >& os_;
- 	const bool reportSe_;
---- a/aligner_1mm.h
-+++ b/aligner_1mm.h
-@@ -32,7 +32,7 @@ public:
- 			RangeCache *cacheFw,
- 			RangeCache *cacheBw,
- 			uint32_t cacheLimit,
--			ChunkPool *pool,
-+			bowtieChunkPool *pool,
- 			BitPairReference* refs,
- 			vector<String<Dna5> >& os,
- 			bool maqPenalty,
-@@ -161,7 +161,7 @@ private:
- 	RangeCache *cacheFw_;
- 	RangeCache *cacheBw_;
- 	const uint32_t cacheLimit_;
--	ChunkPool *pool_;
-+	bowtieChunkPool *pool_;
- 	BitPairReference* refs_;
- 	vector<String<Dna5> >& os_;
- 	const bool maqPenalty_;
-@@ -201,7 +201,7 @@ public:
- 			RangeCache *cacheFw,
- 			RangeCache *cacheBw,
- 			uint32_t cacheLimit,
--			ChunkPool *pool,
-+			bowtieChunkPool *pool,
- 			BitPairReference* refs,
- 			vector<String<Dna5> >& os,
- 			bool reportSe,
-@@ -478,7 +478,7 @@ private:
- 	RangeCache *cacheFw_;
- 	RangeCache *cacheBw_;
- 	const uint32_t cacheLimit_;
--	ChunkPool *pool_;
-+	bowtieChunkPool *pool_;
- 	BitPairReference* refs_;
- 	vector<String<Dna5> >& os_;
- 	const bool reportSe_;
---- a/aligner_23mm.h
-+++ b/aligner_23mm.h
-@@ -33,7 +33,7 @@ public:
- 			RangeCache *cacheFw,
- 			RangeCache *cacheBw,
- 			uint32_t cacheLimit,
--			ChunkPool *pool,
-+			bowtieChunkPool *pool,
- 			BitPairReference* refs,
- 			vector<String<Dna5> >& os,
- 			bool maqPenalty,
-@@ -231,7 +231,7 @@ private:
- 	RangeCache *cacheFw_;
- 	RangeCache *cacheBw_;
- 	const uint32_t cacheLimit_;
--	ChunkPool *pool_;
-+	bowtieChunkPool *pool_;
- 	BitPairReference* refs_;
- 	vector<String<Dna5> >& os_;
- 	const bool maqPenalty_;
-@@ -273,7 +273,7 @@ public:
- 			RangeCache *cacheFw,
- 			RangeCache *cacheBw,
- 			uint32_t cacheLimit,
--			ChunkPool *pool,
-+			bowtieChunkPool *pool,
- 			BitPairReference* refs,
- 			vector<String<Dna5> >& os,
- 			bool reportSe,
-@@ -675,7 +675,7 @@ private:
- 	RangeCache *cacheFw_;
- 	RangeCache *cacheBw_;
- 	const uint32_t cacheLimit_;
--	ChunkPool *pool_;
-+	bowtieChunkPool *pool_;
- 	BitPairReference* refs_;
- 	vector<String<Dna5> >& os_;
- 	const bool reportSe_;
---- a/aligner_seed_mm.h
-+++ b/aligner_seed_mm.h
-@@ -37,7 +37,7 @@ public:
- 			RangeCache* cacheFw,
- 			RangeCache* cacheBw,
- 			uint32_t cacheLimit,
--			ChunkPool *pool,
-+			bowtieChunkPool *pool,
- 			BitPairReference* refs,
- 			vector<String<Dna5> >& os,
- 			bool maqPenalty,
-@@ -554,7 +554,7 @@ private:
- 	RangeCache *cacheFw_;
- 	RangeCache *cacheBw_;
- 	const uint32_t cacheLimit_;
--	ChunkPool *pool_;
-+	bowtieChunkPool *pool_;
- 	BitPairReference* refs_;
- 	vector<String<Dna5> >& os_;
- 	bool strandFix_;
-@@ -598,7 +598,7 @@ public:
- 			RangeCache* cacheFw,
- 			RangeCache* cacheBw,
- 			uint32_t cacheLimit,
--			ChunkPool *pool,
-+			bowtieChunkPool *pool,
- 			BitPairReference* refs,
- 			vector<String<Dna5> >& os,
- 			bool reportSe,
-@@ -1375,7 +1375,7 @@ private:
- 	RangeCache *cacheFw_;
- 	RangeCache *cacheBw_;
- 	const uint32_t cacheLimit_;
--	ChunkPool *pool_;
-+	bowtieChunkPool *pool_;
- 	BitPairReference* refs_;
- 	vector<String<Dna5> >& os_;
- 	const bool reportSe_;
---- a/ebwt_search.cpp
-+++ b/ebwt_search.cpp
-@@ -111,7 +111,7 @@ static bool strandFix;  // attempt to fi
- static bool randomizeQuals; // randomize quality values
- static bool stats; // print performance stats
- static int chunkPoolMegabytes;    // max MB to dedicate to best-first search frames per thread
--static int chunkSz;    // size of single chunk disbursed by ChunkPool
-+static int chunkSz;    // size of single chunk disbursed by bowtieChunkPool
- static bool chunkVerbose; // have chunk allocator output status messages?
- static bool recal;
- static int recalMaxCycle;
-@@ -223,7 +223,7 @@ static void resetOptions() {
- 	randomizeQuals			= false; // randomize quality values
- 	stats					= false; // print performance stats
- 	chunkPoolMegabytes		= 64;    // max MB to dedicate to best-first search frames per thread
--	chunkSz					= 256;   // size of single chunk disbursed by ChunkPool (in KB)
-+	chunkSz					= 256;   // size of single chunk disbursed by bowtieChunkPool (in KB)
- 	chunkVerbose			= false; // have chunk allocator output status messages?
- 	recal					= false;
- 	recalMaxCycle			= 64;
-@@ -1201,7 +1201,7 @@ static void exactSearchWorkerStateful(vo
- 	PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid);
- 	HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink);
- 
--	ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
-+	bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
- 	UnpairedExactAlignerV1Factory alSEfact(
- 			ebwt,
- 			NULL,
-@@ -1385,7 +1385,7 @@ static void mismatchSearchWorkerFullStat
- 	// Global initialization
- 	PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid);
- 	HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink);
--	ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
-+	bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
- 
- 	Unpaired1mmAlignerV1Factory alSEfact(
- 			ebwtFw,
-@@ -1687,7 +1687,7 @@ static void twoOrThreeMismatchSearchWork
- 	PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid);
- 	HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink);
- 
--	ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
-+	bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
- 	Unpaired23mmAlignerV1Factory alSEfact(
- 			ebwtFw,
- 			&ebwtBw,
-@@ -2156,7 +2156,7 @@ static void seededQualSearchWorkerFullSt
- 	// Global initialization
- 	PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid);
- 	HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink);
--	ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
-+	bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
- 
- 	AlignerMetrics *metrics = NULL;
- 	if(stats) {
---- a/ebwt_search_backtrack.h
-+++ b/ebwt_search_backtrack.h
-@@ -2724,7 +2724,7 @@ public:
- 			bool verbose,
- 			bool quiet,
- 			bool mate1,
--			ChunkPool* pool,
-+			bowtieChunkPool* pool,
- 			int *btCnt) :
- 			SingleRangeSourceDriver<EbwtRangeSource>(
- 					params, rs, fw, sink, sinkPt, os, verbose,
-@@ -2927,7 +2927,7 @@ public:
- 			bool verbose,
- 			bool quiet,
- 			bool mate1,
--			ChunkPool* pool,
-+			bowtieChunkPool* pool,
- 			int *btCnt = NULL) :
- 			params_(params),
- 			rs_(rs),
-@@ -2986,7 +2986,7 @@ protected:
- 	bool verbose_;
- 	bool quiet_;
- 	bool mate1_;
--	ChunkPool* pool_;
-+	bowtieChunkPool* pool_;
- 	int *btCnt_;
- };
- 
---- a/pool.h
-+++ b/pool.h
-@@ -19,13 +19,13 @@
-  * is set at construction time.  Heap memory is only allocated at
-  * construction and deallocated at destruction.
-  */
--class ChunkPool {
-+class bowtieChunkPool {
- public:
- 	/**
- 	 * Initialize a new pool with an initial size of about 'bytes'
- 	 * bytes.  Exit with an error message if we can't allocate it.
- 	 */
--	ChunkPool(uint32_t chunkSz, uint32_t totSz, bool verbose_) :
-+	bowtieChunkPool(uint32_t chunkSz, uint32_t totSz, bool verbose_) :
- 		verbose(verbose_), patid(0), pool_(NULL), cur_(0),
- 		chunkSz_(chunkSz), totSz_(totSz), lim_(totSz/chunkSz),
- 		bits_(lim_), exhaustCrash_(false),
-@@ -38,7 +38,7 @@ public:
- 			}
- 		} catch(std::bad_alloc& e) {
- 			ThreadSafe _ts(&gLock);
--			std::cerr << "Error: Could not allocate ChunkPool of "
-+			std::cerr << "Error: Could not allocate bowtieChunkPool of "
- 			          << totSz << " bytes" << std::endl;
- 			exhausted();
- 			throw 1; // Exit if we haven't already
-@@ -48,7 +48,7 @@ public:
- 	/**
- 	 * Delete all the pools.
- 	 */
--	~ChunkPool() {
-+	~bowtieChunkPool() {
- 		if(pool_ != NULL) delete[] pool_;
- 	}
- 
-@@ -189,7 +189,7 @@ public:
- 	 * Initialize a new pool with an initial size of about 'bytes'
- 	 * bytes.  Exit with an error message if we can't allocate it.
- 	 */
--	AllocOnlyPool(ChunkPool* pool, const char *name) :
-+	AllocOnlyPool(bowtieChunkPool* pool, const char *name) :
- 		pool_(pool), name_(name), curPool_(0), cur_(0)
- 	{
- 		assert(pool != NULL);
-@@ -388,7 +388,7 @@ protected:
- 		lastCurInPool_.pop_back();
- 	}
- 
--	ChunkPool*      pool_;
-+	bowtieChunkPool*      pool_;
- 	const char     *name_;
- 	std::vector<T*> pools_; /// the memory pools
- 	uint32_t        curPool_; /// pool we're current allocating from
---- a/range_source.h
-+++ b/range_source.h
-@@ -1388,7 +1388,7 @@ class PathManager {
- 
- public:
- 
--	PathManager(ChunkPool* cpool_, int *btCnt, bool verbose, bool quiet) :
-+	PathManager(bowtieChunkPool* cpool_, int *btCnt, bool verbose, bool quiet) :
- 		branchQ_(verbose, quiet),
- 		cpool(cpool_),
- 		bpool(cpool, "branch"),
-@@ -1637,7 +1637,7 @@ protected:
- 
- public:
- 
--	ChunkPool *cpool; // pool for generic chunks of memory
-+	bowtieChunkPool *cpool; // pool for generic chunks of memory
- 	AllocOnlyPool<Branch> bpool; // pool for allocating Branches
- 	AllocOnlyPool<RangeState> rpool; // pool for allocating RangeStates
- 	AllocOnlyPool<Edit> epool; // pool for allocating Edits
-@@ -1811,7 +1811,7 @@ public:
- 		bool quiet,
- 		bool mate1,
- 		uint32_t minCostAdjustment,
--		ChunkPool* pool,
-+		bowtieChunkPool* pool,
- 		int *btCnt) :
- 		RangeSourceDriver<TRangeSource>(true, minCostAdjustment),
- 		len_(0), mate1_(mate1),
diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch b/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch
deleted file mode 100644
index 38664aeee989..000000000000
--- a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch
+++ /dev/null
@@ -1,85 +0,0 @@
-Description: Renamed seqan::fill function calls to use seqan::resize.
- SeqAn 1.3 renamed seqan::fill() to seqan::resize().
- SeqAn ticket: http://trac.seqan.de/ticket/77
-Forwarded: no
-Author: Ognyan Kulev <ogi@debian.org>
-Last-Update: 2014-08-13
-
---- a/blockwise_sa.h
-+++ b/blockwise_sa.h
-@@ -456,8 +456,8 @@ void KarkkainenBlockwiseSA<TStr>::buildS
- 		try {
- 			// Allocate and initialize containers for holding bucket
- 			// sizes and representatives.
--			fill(bucketSzs, numBuckets, 0, Exact());
--			fill(bucketReps, numBuckets, OFF_MASK, Exact());
-+			resize(bucketSzs, numBuckets, 0, Exact());
-+			resize(bucketReps, numBuckets, OFF_MASK, Exact());
- 		} catch(bad_alloc &e) {
- 			if(this->_passMemExc) {
- 				throw e; // rethrow immediately
-@@ -816,7 +816,7 @@ void KarkkainenBlockwiseSA<TStr>::nextBl
- 				// Not the last bucket
- 				assert_lt(_cur, length(_sampleSuffs));
- 				hi = _sampleSuffs[_cur];
--				fill(zHi, _dcV, 0, Exact());
-+				resize(zHi, _dcV, 0, Exact());
- 				assert_eq(zHi[0], 0);
- 				calcZ(t, hi, zHi, this->verbose(), this->sanityCheck());
- 			}
-@@ -825,7 +825,7 @@ void KarkkainenBlockwiseSA<TStr>::nextBl
- 				assert_gt(_cur, 0);
- 				assert_leq(_cur, length(_sampleSuffs));
- 				lo = _sampleSuffs[_cur-1];
--				fill(zLo, _dcV, 0, Exact());
-+				resize(zLo, _dcV, 0, Exact());
- 				assert_gt(_dcV, 3);
- 				assert_eq(zLo[0], 0);
- 				calcZ(t, lo, zLo, this->verbose(), this->sanityCheck());
---- a/diff_sample.h
-+++ b/diff_sample.h
-@@ -452,7 +452,7 @@ static String<T> getDeltaMap(T v, const
- 	// Declare anchor-map-related items
- 	String<T> amap;
- 	size_t amapEnts = 1;
--	fill(amap, v, 0xffffffff, Exact());
-+	resize(amap, v, 0xffffffff, Exact());
- 	amap[0] = 0;
- 	// Print out difference cover (and optionally calculate
- 	// anchor map)
-@@ -532,7 +532,7 @@ public:
- 		assert_gt(_d, 0);
- 		assert_eq(1, popCount(_v)); // must be power of 2
- 		// Build map from d's to idx's
--		fill(_dInv, _v, 0xffffffff, Exact());
-+		resize(_dInv, _v, 0xffffffff, Exact());
- 		uint32_t lim = (uint32_t)length(_ds);
- 		for(uint32_t i = 0; i < lim; i++) {
- 			_dInv[_ds[i]] = i;
-@@ -656,7 +656,7 @@ void DifferenceCoverSample<TStr>::doBuil
- 	VMSG_NL("  Doing sanity check");
- 	TIndexOffU added = 0;
- 	String<TIndexOffU> sorted;
--	fill(sorted, length(_isaPrime), OFF_MASK, Exact());
-+	resize(sorted, length(_isaPrime), OFF_MASK, Exact());
- 	for(size_t di = 0; di < this->d(); di++) {
- 		uint32_t d = _ds[di];
- 		size_t i = 0;
-@@ -717,7 +717,7 @@ void DifferenceCoverSample<TStr>::buildS
- 	assert_eq(length(_doffs), d+1);
- 	// Size sPrime appropriately
- 	reserve(sPrime, sPrimeSz+1, Exact()); // reserve extra slot for LS
--	fill(sPrime, sPrimeSz, OFF_MASK, Exact());
-+	resize(sPrime, sPrimeSz, OFF_MASK, Exact());
- 	// Slot suffixes from text into sPrime according to the mu
- 	// mapping; where the mapping would leave a blank, insert a 0
- 	TIndexOffU added = 0;
-@@ -823,7 +823,7 @@ void DifferenceCoverSample<TStr>::build(
- 		// arrays back into sPrime.
- 		VMSG_NL("  Allocating rank array");
- 		reserve(_isaPrime, length(sPrime)+1, Exact());
--		fill(_isaPrime, length(sPrime), OFF_MASK, Exact());
-+		resize(_isaPrime, length(sPrime), OFF_MASK, Exact());
- 		assert_gt(length(_isaPrime), 0);
- 		{
- 			Timer timer(cout, "  Ranking v-sort output time: ", this->verbose());
diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-spelling.patch b/sci-biology/bowtie/files/bowtie-1.1.2-spelling.patch
deleted file mode 100644
index ff484dfa3ebb..000000000000
--- a/sci-biology/bowtie/files/bowtie-1.1.2-spelling.patch
+++ /dev/null
@@ -1,48 +0,0 @@
-Author: Andreas Tille <tille@debian.org>
-Last-Update: Thu, 01 Oct 2015 09:47:23 +0200
-Description: Fix spelling
-
---- a/MANUAL
-+++ b/MANUAL
-@@ -544,7 +544,7 @@ The `bowtie`, `bowtie-build` and `bowtie
- actually wrapper scripts that call binary programs as appropriate. The
- wrappers shield users from having to distinguish between "small" and
- "large" index formats, discussed briefly in the following section. The
--appropiate index type is selected based on the input size.
-+appropriate index type is selected based on the input size.
- 
- It is recommended that you always run the bowtie wrappers and not run
- the binaries directly.
---- a/MANUAL.markdown
-+++ b/MANUAL.markdown
-@@ -559,7 +559,7 @@ The `bowtie`, `bowtie-build` and `bowtie
- actually wrapper scripts that call binary programs as appropriate. The
- wrappers shield users from having to distinguish between "small" and
- "large" index formats, discussed briefly in the following section. The
--appropiate index type is selected based on the input size.
-+appropriate index type is selected based on the input size.
- 
- It is recommended that you always run the bowtie wrappers and not run
- the binaries directly.
---- a/doc/manual.html
-+++ b/doc/manual.html
-@@ -201,7 +201,7 @@ T2302111203131231130300111123220
- <p>Like other platforms, SOLiD supports generation of paired-end reads. When colorspace alignment is enabled, the default paired-end orientation setting is <a href="#bowtie-options-fr"><code>--ff</code></a>. This is because most SOLiD datasets have that orientation.</p>
- <p>Note that SOLiD-generated read files can have &quot;orphaned&quot; mates; i.e. mates without a correpsondingly-named mate in the other file. To avoid problems due to orphaned mates, SOLiD paired-end output should first be converted to <code>.csfastq</code> files with unpaired mates omitted. This can be accomplished using, for example, [Galaxy]'s conversion tool (click &quot;NGS: QC and manipulation&quot;, then &quot;SOLiD-to-FASTQ&quot; in the left-hand sidebar).</p>
- <h2 id="wrapper-scripts">Wrapper scripts</h2>
--<p>The <code>bowtie</code>, <code>bowtie-build</code> and <code>bowtie-inspect</code> executables are actually wrapper scripts that call binary programs as appropriate. The wrappers shield users from having to distinguish between &quot;small&quot; and &quot;large&quot; index formats, discussed briefly in the following section. The appropiate index type is selected based on the input size.</p>
-+<p>The <code>bowtie</code>, <code>bowtie-build</code> and <code>bowtie-inspect</code> executables are actually wrapper scripts that call binary programs as appropriate. The wrappers shield users from having to distinguish between &quot;small&quot; and &quot;large&quot; index formats, discussed briefly in the following section. The appropriate index type is selected based on the input size.</p>
- <p>It is recommended that you always run the bowtie wrappers and not run the binaries directly.</p>
- <h2 id="small-and-large-indexes">Small and large indexes</h2>
- <p><code>bowtie-build</code> can index reference genomes of any size. For genomes less than about 4 billion nucleotides in length, <code>bowtie-build</code> builds a &quot;small&quot; index using 32-bit numbers in various parts of the index. When the genome is longer, <code>bowtie-build</code> builds a &quot;large&quot; index using 64-bit numbers. Small indexes are stored in files with the <code>.ebwt</code> extension, and large indexes are stored in files with the <code>.ebwtl</code> extension. The user need not worry about whether a particular index is small or large; the wrapper scripts will automatically build and use the appropriate index.</p>
---- a/ref_read.cpp
-+++ b/ref_read.cpp
-@@ -263,7 +263,7 @@ fastaRefReadSizes(vector<FileBuf*>& in,
- 				     << "reference into smaller chunks and index each independently." << endl;
- #else
- 				cerr << "Error: Reference sequence has more than 2^32-1 characters!  Please try to" << endl
--				     << "build a large index instead using the appropiate options." << endl;
-+				     << "build a large index instead using the appropriate options." << endl;
- #endif
- 				throw 1;
- 			}
diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch b/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch
deleted file mode 100644
index bc0f1d09557d..000000000000
--- a/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-Fixes missing tinythread.cpp when using TBB:
-
-ebwt_search.cpp:(.text+0x91bb): undefined reference to `tthread::thread::join()'
-
---- bowtie-1.1.2/Makefile
-+++ bowtie-1.1.2/Makefile
-@@ -106,10 +106,7 @@
- endif
- 
- OTHER_CPPS = ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp \
--             edit.cpp ebwt.cpp
--ifneq (1,$(WITH_TBB))
--	OTHER_CPPS += tinythread.cpp
--endif
-+             edit.cpp ebwt.cpp tinythread.cpp
- 
- SEARCH_CPPS = qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp \
-               log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp \
diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-unbundle-seqan.patch b/sci-biology/bowtie/files/bowtie-1.1.2-unbundle-seqan.patch
deleted file mode 100644
index 54391ae415a3..000000000000
--- a/sci-biology/bowtie/files/bowtie-1.1.2-unbundle-seqan.patch
+++ /dev/null
@@ -1,27 +0,0 @@
-Description: Use Debian packaged SeqAn library instead of copy in upstream source
-Author: Andreas Tille <tille@debian.org>
-Date: 2011-01-30
-Last-Update: 2013-04-18
-Reviewed-by: Ognyan Kulev <ogi@debian.org>
-
---- a/Makefile
-+++ b/Makefile
-@@ -5,9 +5,7 @@
- prefix = /usr/local
- bindir = $(prefix)/bin
- 
--SEQAN_DIR = SeqAn-1.1
--SEQAN_INC = -I $(SEQAN_DIR)
--INC = $(SEQAN_INC) -I third_party
-+INC = `pkg-config --cflags seqan-1.4`
- CPP = g++
- CXX = $(CPP)
- CC = gcc
-@@ -168,7 +166,6 @@
-                $(wildcard genomes/NC_008253.fna) \
-                $(wildcard reads/e_coli_1000.*) \
-                $(wildcard reads/e_coli_1000_*) \
--               SeqAn-1.1 \
-                bowtie \
-                bowtie-build \
-                bowtie-inspect \
diff --git a/sci-biology/embassy/Manifest b/sci-biology/embassy/Manifest
index 634ffefa74ec..742fc01f8c04 100644
--- a/sci-biology/embassy/Manifest
+++ b/sci-biology/embassy/Manifest
@@ -1,2 +1,2 @@
-EBUILD embassy-6.6.0-r1.ebuild 965 BLAKE2B 736fb94d1774dfa22a0b7b9ea4809389cb65ed1e79ac44b908eb76c0fc348f1ebed4a41dd7c9d19f7b4118509055309f0e0351b8067872c1a461029d96249c10 SHA512 8dd638ed450b83656c3848bd014f2429a9e269f3e3dea5c16e370becbdb1473f2eec261fbfe2b4bc5675262ac6d9ce871fc287045f777a5d0f85a3f05bbf795b
+EBUILD embassy-6.6.0-r2.ebuild 929 BLAKE2B 378e0757280f2e0bc04d673892f79ce0139100790e84618697c4e55d23f4bcb193c075cca1a5ca9aa67eacb0412250be1186e3b32eeff28306358b753852e32d SHA512 1f17adca5f631bea36776135ae545411a35f3d575eb4e059bde004fa3616447ee3eb5f1b867c5c4debfc95a5d6d476b3d2c1a80b2a8bb429c3ce4db83b0f1e4d
 MISC metadata.xml 347 BLAKE2B 2368d452e759747738601ae0e5e5e7181167badeaa28ed89aa8e07b55ebc9d2f1dbcd351cd5569a4548c307cfaa23b26756d88778c078685848db72dd9b094e7 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e
diff --git a/sci-biology/embassy/embassy-6.6.0-r1.ebuild b/sci-biology/embassy/embassy-6.6.0-r2.ebuild
index b30223eda805..c0777d1aac70 100644
--- a/sci-biology/embassy/embassy-6.6.0-r1.ebuild
+++ b/sci-biology/embassy/embassy-6.6.0-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -20,7 +20,6 @@ RDEPEND="
 	>=sci-biology/embassy-esim4-1.0.0.660
 	>=sci-biology/embassy-hmmer-2.3.2.660
 	>=sci-biology/embassy-iprscan-4.3.1.660
-	>=sci-biology/embassy-meme-4.7.660
 	>=sci-biology/embassy-mse-3.0.0.660
 	>=sci-biology/embassy-phylipnew-3.69.660
 	>=sci-biology/embassy-signature-0.1.660
diff --git a/sci-biology/exonerate/Manifest b/sci-biology/exonerate/Manifest
index edfda5895233..1ffc0cd9c93a 100644
--- a/sci-biology/exonerate/Manifest
+++ b/sci-biology/exonerate/Manifest
@@ -1,4 +1,4 @@
 AUX exonerate-2.2.0-asneeded.patch 362 BLAKE2B 57bb7d7d57bf2347fc0cb20f650cd0a452bd70ed8ed46a87d132cf8d68e152438ec2c4e877129feb91748f5ca43021cc0010cf2f50b3bdb8eed60218d904eb27 SHA512 7c08fe7ee520ab7198557f5ac7f99f0bae53da77d46949d6bac78a3330fc9023a4aece085e060ad6a40303475999654dcfe5311d3a78f1d1be0d461cefbfcfb0
 DIST exonerate-2.2.0.tar.gz 509870 BLAKE2B 58b12338ef7d819a8e33ab87d72afe807ca219581a8f35ae38951860915a676bb9ba34a481f685e970948d9272be3e5f28d6b63c14f4d5facf35c4be52530d3b SHA512 c0aec4df83fbf6bcd1b27242397349769211ab88d71e2d081e20cb5453a03acd805807535a69841e991cf543d99fcd458cbd22d60b21f0fc6ce813eac45b838c
 EBUILD exonerate-2.2.0-r2.ebuild 967 BLAKE2B 27a48f5dc4e1040f4296152ae445ba6bb2dc29132605b6cce240c40d2719d16c0c7d80103d2b9f8440fb7d5bb8fec3e8ba0385f6f87b9196b443dd14ae1a6310 SHA512 1d5be70396afabf08489501cba460bb47a7bfe9efead75226b07707ed00813f0dcd69611b75e3135444ee100ceeaf2cd492cd79ffc5f3d01e6f5d808ce84f2e1
-MISC metadata.xml 438 BLAKE2B ae3dbc6cf8628225e3238076ec24fbadffd60818cb051cfc153c37af4cadbce7070697f0a2f21219a5a32aa9ebe8e4518fb2e4eb0e147959965f468fb0629b2d SHA512 e77d02d4d9664234895ef29ffc633e2e8ae49ac8c324fe0e82ac6ec3ac416570443f4a9831838d2eceb420398dfb5c5872b562861002974fa8754b2d846cf777
+MISC metadata.xml 326 BLAKE2B 51316d3ba2a93eeda2dc044ff76245b49ab71781bd822dbd52e790c738e866c899b4efd47daf298a6cad7258091ee1163778fae39c7cd27cf5a64408dc559d39 SHA512 226349d3fc3368937b974630a4251d2f6ac067a92325a376c278570beca0d316c8749e7026bd6d337f7c1cf9abd9d760499e6a7d8d85f00822a10575978e8973
diff --git a/sci-biology/exonerate/metadata.xml b/sci-biology/exonerate/metadata.xml
index 7851377e083e..b64950792715 100644
--- a/sci-biology/exonerate/metadata.xml
+++ b/sci-biology/exonerate/metadata.xml
@@ -5,9 +5,6 @@
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>
 	</maintainer>
-	<longdescription lang="en">
-		exonerate is a generic tool for pairwise sequence comparison
-	</longdescription>
 	<use>
 		<flag name="utils">Install all utilities</flag>
 	</use>
diff --git a/sci-biology/finchtv/Manifest b/sci-biology/finchtv/Manifest
index 385708b89211..1eb48ad0f1f3 100644
--- a/sci-biology/finchtv/Manifest
+++ b/sci-biology/finchtv/Manifest
@@ -1,4 +1,4 @@
 DIST finchtv_1_3_1.tar.gz 6706911 BLAKE2B 5aea60c2a107dc0d1d878b0416011f57bfcdb73b6e7c0da80be5b485ec5824aae7c610235057b74002765f5ab5e7bd250efec2a04a471b55abd046afc560ea38 SHA512 813217a6d44cbd60fff061da94f70adadcc803b77352b278246711bf1b952b592a0fdb6bfc9d74264d896cb816078e809bdc633981d4009c422f59f74aca5bc8
 EBUILD finchtv-1.3.1-r2.ebuild 610 BLAKE2B 4c58fdc546782232ea8c1fc5937ab83ba36000bbea56b83d813a9afd52cdc9caff0b946235f9d452c2ee287d11a228697c8a972e2bbbdaa94c640e4ac40c82eb SHA512 693cc060e91d2ed1ca9d4bc6ff6baaa9a3afe1a876d83d79e3cc3d4c416f8e7ddc878696e890e0b4e660ed5c017c0402bb8247e1b4d6d819f567292b5aa168a7
 EBUILD finchtv-1.3.1-r3.ebuild 694 BLAKE2B ede749140addd096bd6ab449b94af6f204b8970b4978d49971ff1c46d3cde1bd225a8792ea76b68272ca080ac08b8d989e8cf704b09797b3b5d5bad0ec0c47e3 SHA512 0772745c5d1d529def77475c8fdc90321c029dbd0b87ea5b65db65cf29485a8e59b2c0aa2003e6c8d0b7b2bffdb5b988d1452da7a7d32775b539dd2676f59a96
-MISC metadata.xml 374 BLAKE2B 1aeffa98b6c6a1ebf19451781a691992a8662bb1de184ab26bac1455d3dbd5ea182f7a7d44b8dd7b943dd400af365f70ee0693921a5216783f201078e61157f3 SHA512 5e1e1540a94ba73446163db04367641e83cc222dec5e062ff8159b9a16a256729fecf19ee19c9980a2a88da6b39e4d21334d7bbba8526c34e05d22c1e578b16d
+MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/finchtv/metadata.xml b/sci-biology/finchtv/metadata.xml
index a46ebf47e871..959160fe46b1 100644
--- a/sci-biology/finchtv/metadata.xml
+++ b/sci-biology/finchtv/metadata.xml
@@ -5,7 +5,4 @@
     <email>sci-biology@gentoo.org</email>
     <name>Gentoo Biology Project</name>
   </maintainer>
-  <longdescription lang="en">
-A cross-platform graphical viewer for chromatogram files.
-</longdescription>
 </pkgmetadata>
diff --git a/sci-biology/libgtextutils/Manifest b/sci-biology/libgtextutils/Manifest
index dc3c8bb842ae..74b2ae8850e5 100644
--- a/sci-biology/libgtextutils/Manifest
+++ b/sci-biology/libgtextutils/Manifest
@@ -2,4 +2,4 @@ AUX libgtextutils-0.6.1-fix-build-system.patch 1719 BLAKE2B 993f1e68f960853a264d
 AUX libgtextutils-0.6.1-gcc6.patch 724 BLAKE2B 14ebd0ab5ec4685688caa922dacccdaad9101af0814a93b08f0c9ba5e50ac6a02291528b6ad3d61b48a2f29a25b63e421690f19109351f4472cc118886ca0e10 SHA512 74ec8fafc699cadc5d40f5284cd42cfb8c949744b7a16bbf8142c8db71ad6c921551da03f260e82bfe84b69dd5fbd2261031fe22aee6b3396515b1f66576a530
 DIST libgtextutils-0.6.1.tar.bz2 273459 BLAKE2B 81b1e9b467287ed9551fc53abddf5757efb2dd1c98f0388e2128535fbe70b706badd5702a5b5c3cb19a34c26ffa218c9c41caf9f17770a015b09fc13fabe4d53 SHA512 0bc392385f9e6c345dff82b3fb04f322e8aceca769e15a3a87da6c718b6e9a7e1de082940d4bb0339a4c3a86f706fde0de047df459682aa9ea216d6e5c17eab6
 EBUILD libgtextutils-0.6.1.ebuild 623 BLAKE2B 5bd2ff34a6898b662e6e624a77682a358b9340c6b94b9dfa40bec0637d4074ec648ca6146ee870f9cf5a8141028d23aedc55407aea04fbf2b69d62699d69d547 SHA512 e72eaddb48422afe71140394825964e6778a339ea182d614178061eb294dada1b81e7b5221a1a19d9d2ac720200f6eb4a7eab09f6ef1b7425ce7dda491add449
-MISC metadata.xml 379 BLAKE2B b5f42185a237d0dd1dcbf6c5ae9e007f0a2f875ab0e7c4e6bb8cca07b6f24248d449541e0f455687a0876d7286bc8fbd08e72df88cffc69d255d22788fbadc05 SHA512 9b77656bd047462678494259c168f2214238c909e4dd19ff822cf182e442ce385a3375158fcc0a1be53303a4828e6339ea379f9de60851c894b8d57c0a099aea
+MISC metadata.xml 370 BLAKE2B 01c5f6253c80b7fc48e8c7980c62366fd38643da25fdd999cef041558b7d559cb45a22a6125d222569104443c75045e6169f133bc46871ab9f567bdf3f3ae3dc SHA512 b9a044abc657680f9c8fdc80d318b5a9891c5c532eb0831f00bf2f774391c885cf568f6ec3376617da2a5d4d8f9b87283384d595086b3ae57defbc988e96f1c1
diff --git a/sci-biology/libgtextutils/metadata.xml b/sci-biology/libgtextutils/metadata.xml
index 138cb7705c0a..38108be67e14 100644
--- a/sci-biology/libgtextutils/metadata.xml
+++ b/sci-biology/libgtextutils/metadata.xml
@@ -2,7 +2,7 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
+		<email>mmokrejs@gmail.com</email>
 		<name>Martin Mokrejs</name>
 	</maintainer>
 	<maintainer type="project">
diff --git a/sci-biology/seqan/Manifest b/sci-biology/seqan/Manifest
index 12365d2c556e..5ce9c67f4212 100644
--- a/sci-biology/seqan/Manifest
+++ b/sci-biology/seqan/Manifest
@@ -1,13 +1,6 @@
-AUX seqan-1.4.2-buildsystem.patch 870 BLAKE2B 2b3e32e4bea47caf6165e1c0ab89cdadf1e4d4756bb3ddd77b943b89a9366fb28d49dfdc22d69d5c431f78a83fc73b20c486085804a153c987020b3e28120b20 SHA512 d769eb4137c8c0ddb7137ecfdb0673ba8648ae720673848cbb473a0c80d479b6e5c564c12f1a9dd01953d955605eb2f273e04808ae50058c565e997381c3f748
-AUX seqan-1.4.2-include.patch 552 BLAKE2B f8d67014e59751616227471995254684b3edfacacfb455099f99c719f5602c88f0d106df01354921557d3324f77e03934606f698801516bc8432837c6211b67e SHA512 b02ab4fe49a511494134e44855d865f0ff210392810970834deb304499b5017764ed1c04d8f8dbfb513c333ac302946e5c72c9160cd38a5ef5ad095a865cb6d0
-AUX seqan-1.4.2-shared.patch 974 BLAKE2B e46b6b61c4927ca36c53e68e39c77eb5d983221dd074040a8911a7d7dfb04d2fb4c4ded0f3c9b6d90082a26f704654daa1d2b70e547b9ad657cc48bb96fc435b SHA512 a509c243244b6b40b26700a73be267558ceb17c4e0079f3eca606835ecfe8d1417b88fd37719ca9cf226e6d2d33ee3e22790b20e39a86a300f722eb186cabaad
 AUX seqan-2.4.0-fix-pthread.patch 541 BLAKE2B 16d42c72d6ea0654ba6727ce1007b89d3fc76141320f5a71cfd0fe102b8e511ccb36d48e021baf0928ac8857e97f6addde3f15f4f0577c531285027f23f5eea8 SHA512 f8a3df0892a81a65562dbd85f0945e5722df524e07b9949f860df4e0f07c285df3a48a112c8e1e5dca28a97c219dc9feed677e803ec5d3964216f7052b6f431b
 AUX seqan.pc.in 263 BLAKE2B ffd2a2c1ac74af7bc6b33c5959792551447ee61fe87fbb8bc6966ad44c33ae5bd512e836bc67175a3bf1895554364e48fcfea207f94f18ef72b7eae74fbe82d5 SHA512 bde1c89624284a37dac1a8717049a3b14340a2543003d9cf8406bddf4033541b65b617b802b18c80b2c7733d55ad9d7484bd85fdc927582363885da6d0210af7
-DIST seqan-src-1.4.2.tar.gz 120601994 BLAKE2B 62de2f961ba3c7c564090d746877d2b0b94ec7967c56f28786a286160770e66f0a8f08aacbe76d828cf429f92f0aa640ab29f5220297686979df9b7e9f9a0408 SHA512 dbb56167c507b70111619a414054d9e70f1db42507bbfdf9e40c5dcbbe9489ad4187d882e638a675e96551c860c08f8203c929c4c9a558b19ea7d6059f50492a
-DIST seqan-src-2.2.0.tar.gz 110936119 BLAKE2B be41f266e140ec5992f7e9e507659dc7902aad0e0dd17e6a8c6c9ef0b11f690454a771ba10a5998ccf70e2e50ef9b24904ebf537d982b2cbc68963c004097614 SHA512 1097372976ec9c86baa3787ac38aa4fde3a3e153d81c22435e6a12df87d8063165f27406de33851bffadd904b0ac4ea579a28625cff6257fe8c14d906f408421
 DIST seqan-v2.4.0.tar.gz 109626901 BLAKE2B a10b5ee9a95667f560a8c2aec3808131f5f838f3c07d56584f4b29e9622912bf3d00b958b02db7c9d62dd52d9d08a171abcccef7f50cddf0407538168cf2c592 SHA512 f92cfc97304581920850c5d49fe4336f7c3855e99c3bcb035b6172fa7307e08e6f06fb06d1cd8f5b447c3220fc7f669684fbfe25641b43e9f6953999cf9ddd4b
-EBUILD seqan-1.4.2-r1.ebuild 1997 BLAKE2B 7e7934e70e17b65cc3557dc2f9e7c7d16db4f57bee1b0238d211ed57039e47cc03f495dc068e94d5d4502983c0d0e3b4cca21c0e88ff6c63a9e4d1496ba2850d SHA512 b1ba7611fe3de91484b05e06e4313eb7422bf38d5987c164e9ae7b788b4e7c3cdc0cd5702c215bd6747d2dd94f305f9ae8ea359699e5c32114e8a03514007bfd
-EBUILD seqan-2.2.0-r1.ebuild 2703 BLAKE2B e56cdb3ad4cf674e2349a8d380b49c58b68b528ae28e7b52066a24cf09efbc262855d51f8f3a6ae8111e46b3f95bcec8eaa117a43a895c5bca59963769300307 SHA512 e9524b59db85d13554f99b01c681e2d9137d8971a7df628c2a0b7f5774f8ea324191b3ed6bf0c51b8023b7b1947586adad22709c959656cf1fda58c92c3d89a6
-EBUILD seqan-2.4.0.ebuild 1917 BLAKE2B c53b1c51fd7b8a1c1498f5b2072f26a7829545f626fef177e0e64bc488784f7b9273c2f101db4c045203b3198aa6f37fa6f3226c633575815fbb95174ed5d30a SHA512 6f17b5d2d3be7a19fadcad798f0328fe467bc811d0a931c7b43df87fe23d17ebf2fb48aa197b838c9756bf9f3af7eaa04d346b0b5a05b03b28d03e4e80400c71
-EBUILD seqan-9999.ebuild 1860 BLAKE2B 745e69b7a80868f3faf45a6dfc9727835c8482737b3902a9e0f809a456ce5b3335d821d1106579da01fa495bc3df1caf222f425e41e172479b7de4e4a6e6a2b4 SHA512 3da317388c84933b817705825385c20c3673208c9a3fa1867078f7aea6a9959c6db3b8463cc3713d728180e30093cb1e30220072866305ac58f7b3de6b412f83
+EBUILD seqan-2.4.0.ebuild 1624 BLAKE2B e2b8d8c2e7f87abc063255e0c6c826a57e4da29b063eb3fc82d143593e06d8cbbf5744cd6e39e9cc1b2623c010d181e4361665946a8489ad454f3e1fb9a33c88 SHA512 1d39216baa3877df91b19f36519103114a6858b4600d5bfe3ba01e5619bcfb2543d208e7d5af2806a5c964ebcb8399a8244ca65f4e7ecf169e02827e055545d3
+EBUILD seqan-9999.ebuild 1567 BLAKE2B b171570acf62243121541b771c26fd7ef86e4be86878c060050af2cd665973182e2498f9ba9c336e8a382768b71aa3547edde927682dcdd844c6fd0ed9e2cd99 SHA512 b91b532d3655de47c0cfb9f243e46c120d5259f9166be4e41d7b0dd02a6f681e714fd5941aadb54b6ee89a0f5a4aa10628157c9b25bfd8074178dc36b70e5944
 MISC metadata.xml 372 BLAKE2B d620401f1aab9be80ddb6dc7abe737fd3e6322c560136e2c3b33d9246beca2986b4d91225b506e8c3035550994c3f714a11c0d8b17efd30c29278002d4eb7a12 SHA512 ae6c49e7e45c0ce4dd4fe27d21c5376c6fb8d7bfd2f98b7775f4689811680fa92c0b71ac0db70f6969660c4aee344f710ef752a467d6d46dd83aa47386d2ec17
diff --git a/sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch b/sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch
deleted file mode 100644
index 4c7893e90c05..000000000000
--- a/sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-Add default disabled flag to enable generation of documentation.
-For SeqAn 1.4.2 we generally do not want docs, as 1.4.2 is only a
-support library for legacy tools.
-
---- seqan-1.4.2/CMakeLists.txt
-+++ seqan-1.4.2/CMakeLists.txt
-@@ -123,10 +123,12 @@
- add_subdirectory (core)
- message (STATUS "Configuring extras")
- add_subdirectory (extras)
-+if (NOT SEQAN_NO_DOX)
- message (STATUS "Configuring docs")
- add_subdirectory (docs)
- message (STATUS "Configuring manual")
- add_subdirectory (manual)
-+endif ()
- message (STATUS "Configuring sandbox")
- add_subdirectory (sandbox)
- message (STATUS "Configuring util/py_lib")
---- seqan-1.4.2/docs/main.py
-+++ seqan-1.4.2/docs/main.py
-@@ -123,7 +123,7 @@
- 
-         # Done, print end message.
-         print 'Documentation created/updated.'
--        return dddoc_html.WARNING_COUNT > 0
-+        return 0
-     
-     
- def main(argv):
diff --git a/sci-biology/seqan/files/seqan-1.4.2-include.patch b/sci-biology/seqan/files/seqan-1.4.2-include.patch
deleted file mode 100644
index 5baee4d8ebc0..000000000000
--- a/sci-biology/seqan/files/seqan-1.4.2-include.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- core/include/seqan/index/index_qgram_openaddressing.h | 2 ++
- 1 file changed, 2 insertions(+)
-
-diff --git a/core/include/seqan/index/index_qgram_openaddressing.h b/core/include/seqan/index/index_qgram_openaddressing.h
-index 4a6c2e6..8cc9a42 100644
---- a/core/include/seqan/index/index_qgram_openaddressing.h
-+++ b/core/include/seqan/index/index_qgram_openaddressing.h
-@@ -35,6 +35,8 @@
- #ifndef SEQAN_HEADER_INDEX_QGRAM_OPENADRESSING_H
- #define SEQAN_HEADER_INDEX_QGRAM_OPENADRESSING_H
- 
-+#include <smmintrin.h>
-+
- namespace SEQAN_NAMESPACE_MAIN
- {
- 
diff --git a/sci-biology/seqan/files/seqan-1.4.2-shared.patch b/sci-biology/seqan/files/seqan-1.4.2-shared.patch
deleted file mode 100644
index 0f438ff07bce..000000000000
--- a/sci-biology/seqan/files/seqan-1.4.2-shared.patch
+++ /dev/null
@@ -1,22 +0,0 @@
- util/cmake/SeqAnBuildSystem.cmake | 8 ++++----
- 1 file changed, 4 insertions(+), 4 deletions(-)
-
-diff --git a/util/cmake/SeqAnBuildSystem.cmake b/util/cmake/SeqAnBuildSystem.cmake
-index bcba2c0..d53cd01 100644
---- a/util/cmake/SeqAnBuildSystem.cmake
-+++ b/util/cmake/SeqAnBuildSystem.cmake
-@@ -144,10 +144,10 @@ macro (seqan_register_apps)
-     set (CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -DSEQAN_ENABLE_DEBUG=1")
- 
-     # enable static linkage for seqan apps
--    if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW)
--      set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
--      set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
--    endif ()
-+#    if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW)
-+#      set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
-+#      set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
-+#    endif ()
- 
-     # Get all direct entries of the current source directory into ENTRIES.
-     file (GLOB ENTRIES
diff --git a/sci-biology/seqan/seqan-1.4.2-r1.ebuild b/sci-biology/seqan/seqan-1.4.2-r1.ebuild
deleted file mode 100644
index 3a7f55c710c3..000000000000
--- a/sci-biology/seqan/seqan-1.4.2-r1.ebuild
+++ /dev/null
@@ -1,79 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils python-any-r1 versionator
-
-DESCRIPTION="C++ Sequence Analysis Library"
-HOMEPAGE="http://www.seqan.de/"
-SRC_URI="http://packages.${PN}.de/${PN}-src/${PN}-src-${PV}.tar.gz"
-
-SLOT="$(get_version_component_range 1-2)"
-LICENSE="BSD GPL-3"
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
-IUSE="cpu_flags_x86_sse4_1 test"
-RESTRICT="!test? ( test )"
-REQUIRED_USE="cpu_flags_x86_sse4_1"
-
-RDEPEND="
-	app-arch/bzip2
-	sys-libs/zlib"
-DEPEND="
-	${RDEPEND}
-	test? (
-		$(python_gen_any_dep 'dev-python/nose[${PYTHON_USEDEP}]')
-		${PYTHON_DEPS}
-	)"
-
-PATCHES=(
-	"${FILESDIR}/${P}-shared.patch"
-	"${FILESDIR}/${P}-include.patch"
-	"${FILESDIR}/${P}-buildsystem.patch"
-)
-
-pkg_setup() {
-	use test && python-any-r1_pkg_setup
-}
-
-src_prepare() {
-	# pkg-config file, taken from seqan 2.1
-	cp "${FILESDIR}"/${PN}.pc.in ${PN}-${SLOT}.pc || die
-	sed -e "s#@CMAKE_INSTALL_PREFIX@#${EPREFIX}/usr#" \
-		-e "s#includedir=\${prefix}/include#includedir=\${prefix}/include/${PN}-${SLOT}#" \
-		-e "s#@CMAKE_PROJECT_NAME@#${PN}#" \
-		-e "s#@SEQAN_VERSION_STRING@#${PV}#" \
-		-i ${PN}-${SLOT}.pc || die
-
-	rm -f util/cmake/FindZLIB.cmake || die
-	cmake-utils_src_prepare
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DBoost_NO_BOOST_CMAKE=ON
-		-DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY
-		-DSEQAN_NO_DOX=ON
-	)
-	cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-
-	# SLOT header such that different seqan versions can be used in parallel
-	mkdir "${ED}"/usr/include/${PN}-${SLOT} || die
-	mv "${ED}"/usr/include/{${PN},${PN}-${SLOT}/} || die
-
-	# pkg-config file
-	insinto /usr/share/pkgconfig/
-	doins ${PN}-${SLOT}.pc
-}
-
-pkg_postinst() {
-	einfo "${CATEGORY}/${PF} is only intended as support library for older"
-	einfo "bioinformatics tools relying on the SeqAn 1.* API. Please develop"
-	einfo "any new software against the latest SeqAn release and not this one."
-}
diff --git a/sci-biology/seqan/seqan-2.2.0-r1.ebuild b/sci-biology/seqan/seqan-2.2.0-r1.ebuild
deleted file mode 100644
index 5e139cd7e601..000000000000
--- a/sci-biology/seqan/seqan-2.2.0-r1.ebuild
+++ /dev/null
@@ -1,94 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils python-any-r1 versionator
-
-DESCRIPTION="C++ Sequence Analysis Library"
-HOMEPAGE="http://www.seqan.de/"
-SRC_URI="http://packages.${PN}.de/${PN}-src/${PN}-src-${PV}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD GPL-3"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="cpu_flags_x86_sse4_1 doc test"
-RESTRICT="!test? ( test )"
-REQUIRED_USE="cpu_flags_x86_sse4_1"
-
-RDEPEND="
-	app-arch/bzip2
-	sys-libs/zlib
-	!!sci-biology/seqan:2.0
-	!!sci-biology/seqan:2.1
-	!!sci-biology/seqan:2.2"
-DEPEND="
-	${RDEPEND}
-	doc? (
-		$(python_gen_any_dep 'dev-python/sphinx[${PYTHON_USEDEP}]')
-		${PYTHON_DEPS}
-	)
-	test? (
-		$(python_gen_any_dep 'dev-python/nose[${PYTHON_USEDEP}]')
-		${PYTHON_DEPS}
-	)"
-
-S="${WORKDIR}"/${PN}-${PN}-v${PV}
-
-pkg_setup() {
-	if use test || use doc; then
-		python-any-r1_pkg_setup
-	fi
-}
-
-src_prepare() {
-	seqan_major_ver=$(get_version_component_range 1)
-	seqan_majorminor_ver=$(get_version_component_range 1-2)
-
-	# install docs in proper Gentoo structure
-	sed -e "s#share/doc/seqan#share/doc/${PF}#" \
-		-e "s#\"share/doc/\${APP_NAME}\"#\"share/doc/${PF}/\${APP_NAME}\"#" \
-		-i util/cmake/SeqAnBuildSystem.cmake dox/CMakeLists.txt || die
-
-	# cmake module
-	sed -e "s#find_path(_SEQAN_BASEDIR \"seqan\"#find_path(_SEQAN_BASEDIR \"seqan-${seqan_majorminor_ver}\"#" \
-		-e 's#NO_DEFAULT_PATH)#PATHS /usr)#' \
-		-e "s#set(SEQAN_INCLUDE_DIRS_MAIN \${SEQAN_INCLUDE_DIRS_MAIN} \${_SEQAN_BASEDIR})#set(SEQAN_INCLUDE_DIRS_MAIN \${SEQAN_INCLUDE_DIRS_MAIN} \${_SEQAN_BASEDIR}/seqan-${seqan_majorminor_ver})#" \
-		-i util/cmake/FindSeqAn.cmake || die
-
-	# pkg-config file
-	sed -e "s#includedir=\${prefix}/include#includedir=\${prefix}/include/${PN}-${seqan_majorminor_ver}#" \
-		-i util/pkgconfig/${PN}.pc.in || die
-
-	rm -f util/cmake/FindZLIB.cmake || die
-	cmake-utils_src_prepare
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY
-		-DSEQAN_NO_DOX=$(usex !doc)
-	)
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	cmake-utils_src_compile
-	use doc && cmake-utils_src_compile -C "${BUILD_DIR}" dox
-}
-
-src_install() {
-	cmake-utils_src_install
-
-	# multi-version header such that different seqan versions can be installed in parallel
-	mkdir "${ED%/}"/usr/include/${PN}-${seqan_majorminor_ver} || die
-	mv "${ED%/}"/usr/include/${PN}{,-${seqan_majorminor_ver}/} || die
-
-	# pkg-config file
-	mv "${ED%/}"/usr/share/pkgconfig/${PN}-{${seqan_major_ver},${seqan_majorminor_ver}}.pc || die
-
-	# create pkg-config symlink to restore default behaviour
-	dosym ${PN}-${seqan_majorminor_ver}.pc /usr/share/pkgconfig/${PN}-${seqan_major_ver}.pc
-}
diff --git a/sci-biology/seqan/seqan-2.4.0.ebuild b/sci-biology/seqan/seqan-2.4.0.ebuild
index 8b337e77e6be..5653a1ec94e4 100644
--- a/sci-biology/seqan/seqan-2.4.0.ebuild
+++ b/sci-biology/seqan/seqan-2.4.0.ebuild
@@ -1,12 +1,11 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
 
 : ${CMAKE_MAKEFILE_GENERATOR:=ninja}
-PYTHON_COMPAT=( python2_7 )
 
-inherit cmake-utils multibuild python-any-r1 toolchain-funcs
+inherit cmake-utils multibuild toolchain-funcs
 
 DESCRIPTION="C++ Sequence Analysis Library"
 HOMEPAGE="http://www.seqan.de/"
@@ -24,7 +23,7 @@ fi
 
 LICENSE="BSD GPL-3"
 SLOT="0"
-IUSE="cpu_flags_x86_sse4_1 doc tools"
+IUSE="cpu_flags_x86_sse4_1 tools"
 REQUIRED_USE="cpu_flags_x86_sse4_1"
 
 RDEPEND="
@@ -34,21 +33,12 @@ RDEPEND="
 	!!sci-biology/seqan:2.1
 	!!sci-biology/seqan:2.2"
 DEPEND="
-	${RDEPEND}
-	doc? (
-		$(python_gen_any_dep 'dev-python/sphinx[${PYTHON_USEDEP}]')
-		${PYTHON_DEPS}
-	)"
+	${RDEPEND}"
 
 PATCHES=( "${FILESDIR}"/${PN}-2.4.0-fix-pthread.patch )
 
-python_check_deps() {
-	use doc && has_version "dev-python/sphinx[${PYTHON_USEDEP}]"
-}
-
 pkg_setup() {
 	if [[ ${MERGE_TYPE} != binary ]]; then
-		use doc && python-any-r1_pkg_setup
 		use tools && tc-check-openmp
 
 		MULTIBUILD_VARIANTS=(
@@ -60,18 +50,19 @@ pkg_setup() {
 
 src_configure() {
 	my_configure() {
-		local mycmakeargs=( -DCMAKE_INSTALL_DOCDIR="share/doc/${PF}" )
+		local mycmakeargs=(
+			-DCMAKE_INSTALL_DOCDIR="share/doc/${PF}"
+			-DSEQAN_NO_DOX=ON
+		)
 		case "${MULTIBUILD_ID}" in
 			tools)
 				mycmakeargs+=(
 					-DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_APPS
-					-DSEQAN_NO_DOX=ON
 				)
 				;;
 			library)
 				mycmakeargs+=(
 					-DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY
-					-DSEQAN_NO_DOX=$(usex !doc)
 				)
 				;;
 			*)
diff --git a/sci-biology/seqan/seqan-9999.ebuild b/sci-biology/seqan/seqan-9999.ebuild
index 0005819ff4d3..b344b39cbc46 100644
--- a/sci-biology/seqan/seqan-9999.ebuild
+++ b/sci-biology/seqan/seqan-9999.ebuild
@@ -1,12 +1,11 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
 
 : ${CMAKE_MAKEFILE_GENERATOR:=ninja}
-PYTHON_COMPAT=( python2_7 )
 
-inherit cmake-utils multibuild python-any-r1 toolchain-funcs
+inherit cmake-utils multibuild toolchain-funcs
 
 DESCRIPTION="C++ Sequence Analysis Library"
 HOMEPAGE="http://www.seqan.de/"
@@ -24,7 +23,7 @@ fi
 
 LICENSE="BSD GPL-3"
 SLOT="0"
-IUSE="cpu_flags_x86_sse4_1 doc tools"
+IUSE="cpu_flags_x86_sse4_1 tools"
 REQUIRED_USE="cpu_flags_x86_sse4_1"
 
 RDEPEND="
@@ -34,19 +33,10 @@ RDEPEND="
 	!!sci-biology/seqan:2.1
 	!!sci-biology/seqan:2.2"
 DEPEND="
-	${RDEPEND}
-	doc? (
-		$(python_gen_any_dep 'dev-python/sphinx[${PYTHON_USEDEP}]')
-		${PYTHON_DEPS}
-	)"
-
-python_check_deps() {
-	use doc && has_version "dev-python/sphinx[${PYTHON_USEDEP}]"
-}
+	${RDEPEND}"
 
 pkg_setup() {
 	if [[ ${MERGE_TYPE} != binary ]]; then
-		use doc && python-any-r1_pkg_setup
 		use tools && tc-check-openmp
 
 		MULTIBUILD_VARIANTS=(
@@ -58,18 +48,19 @@ pkg_setup() {
 
 src_configure() {
 	my_configure() {
-		local mycmakeargs=( -DCMAKE_INSTALL_DOCDIR="share/doc/${PF}" )
+		local mycmakeargs=(
+			-DCMAKE_INSTALL_DOCDIR="share/doc/${PF}"
+			-DSEQAN_NO_DOX=ON
+		)
 		case "${MULTIBUILD_ID}" in
 			tools)
 				mycmakeargs+=(
 					-DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_APPS
-					-DSEQAN_NO_DOX=ON
 				)
 				;;
 			library)
 				mycmakeargs+=(
 					-DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY
-					-DSEQAN_NO_DOX=$(usex !doc)
 				)
 				;;
 			*)