gentoo resync : 12.03.2021

21 files changed, 145 insertions, 172 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index c1559b90f1f0..75d14acf6d14 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/embassy-mse/Manifest b/sci-biology/embassy-mse/Manifest
index 9bdb3269980d..2ed7653d9601 100644
--- a/sci-biology/embassy-mse/Manifest
+++ b/sci-biology/embassy-mse/Manifest
@@ -1,4 +1,4 @@
 AUX embassy-mse-3.0.0.650_fix-build-system.patch 4274 BLAKE2B 20674fb79ff55fe7e73f0dc5c62bbe6acec81cb314260a6b879b0881b9f0848204d82301675c5829ef236050af3e4f5d2c31e6cd3a0c2f9554da1408951deb4c SHA512 bfb4663a4b38928f765813cc9b5e773ca712c2333c1650d9c78f457307aa450684f77a20c0a087d3795d5b51f059c6f8113e74da35aa78753c1cc666ba583f4b
 DIST embassy-mse-3.0.0.660.tar.gz 491747 BLAKE2B 7d072458577a90fc367c5b6ed72d1d36592e42b83b3a4e31126b925ddc76f1946fba14e22b7410f66eb837f686f848bdb1033f3b62084f1423543d7605c4f6b9 SHA512 4ae34de71566464e4352ff7b3bbd19b8bf0571013f34253495cf5cc57240bac9c75192c302eb0231763db1745a7e3e79ebcdcb006e36ea4621a886b213eb96d3
-EBUILD embassy-mse-3.0.0.660.ebuild 563 BLAKE2B beadaceac77c0402dd51af2658269a89c80924dbea394b6fa5c3717f655eef6ee2c9a6e28fd10342c0cd1e59e1d08cef54f16dbacc769106084bf1afbc199db8 SHA512 80cc7b8c36d5675f8f4caf9fb244ce1b2740bef6813c4f62e4084a07f31d173abc0fbc4b486e7fda12b701ffe9d99efb023e76fdceaf29c87c2b5182ea1609f9
+EBUILD embassy-mse-3.0.0.660.ebuild 560 BLAKE2B 9eab17caab14b9c89b455239cbf5006ccb4454be3d54c9233cbda6bf107e44f0b8e88e514d60eae529892d80afd59e53e2d0dadaa113d4de50eecd6a693d7bd7 SHA512 a6b0a375dc3fe6035df488732848ac6dde8209a641c7f201ab2d6b6e463be87b505d486d207c64f2b690fe437772f78196ba223678788b879d2b21b2e3e1cedc
 MISC metadata.xml 347 BLAKE2B 2368d452e759747738601ae0e5e5e7181167badeaa28ed89aa8e07b55ebc9d2f1dbcd351cd5569a4548c307cfaa23b26756d88778c078685848db72dd9b094e7 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e
diff --git a/sci-biology/embassy-mse/embassy-mse-3.0.0.660.ebuild b/sci-biology/embassy-mse/embassy-mse-3.0.0.660.ebuild
index c22970155918..f3b553cd1d62 100644
--- a/sci-biology/embassy-mse/embassy-mse-3.0.0.660.ebuild
+++ b/sci-biology/embassy-mse/embassy-mse-3.0.0.660.ebuild
@@ -1,10 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 EBO_DESCRIPTION="MSE - Multiple Sequence Screen Editor"
-
 EBO_EAUTORECONF=1
 
 inherit emboss-r2
@@ -15,6 +14,7 @@ IUSE="ncurses"
 RDEPEND="ncurses? ( sys-libs/ncurses:0= )"
 
 S="${WORKDIR}/MSE-3.0.0.650"
+
 PATCHES=( "${FILESDIR}"/${PN}-3.0.0.650_fix-build-system.patch )
 
 src_configure() {
diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest
index acc4eca43239..d3d3d46bb05a 100644
--- a/sci-biology/emboss/Manifest
+++ b/sci-biology/emboss/Manifest
@@ -4,5 +4,5 @@ AUX emboss-6.6.0_fix-build-system.patch 12599 BLAKE2B dbe6a94a801b0f46df0e7490c7
 AUX emboss-6.6.0_plplot-declarations.patch 1562 BLAKE2B f6c19e6cb7c2eb8110a3841ed566d81411e75a6898cdfbb8ce4754a69291f78a069a44fbc5027430611ee83ca5a7abe1e536a59bedd01e30227c5762622614bd SHA512 fc27b7c1d518b5cdacf1964d56219c6574f43d18dc324e41b9dcdfd1afef17a784f2b209b62c366fb902ba57a50f438a1b328eb2118ee9463ce82b36039bc0bb
 AUX emboss-6.6.0_qa-implicit-declarations.patch 1324 BLAKE2B 42da02b30fa201e24091df762386a88ad76709d192dab95c82cf578126ef9973ba1e927711ac5dd3eee1cfac22a2d29fc75045ce72322cbd7faaa6d50564319e SHA512 15c303fe48a438f50f1c9a0efd7e8fcbcb4102151fc182feb8e0d74c47c3435385a1e44436cebd3c2017c97dd89b82832258748f28f3740e511a92b088f539fb
 DIST EMBOSS-6.6.0.tar.gz 117962028 BLAKE2B 91bf3c680290bd975d2ddb5251089d7f75f8a44a26e1247e93d2c9cf2f23e6b89c4218022ba1af0c940136ff56782f40d2c4604dc756b400ae23f223da7f3cca SHA512 2d28a03381f7dc98d205aa50202fbbac02ad218fc775d86579d310296be124403623484b1907154d915f15cd32a9f8cf16ecfaa6c4a28b362e24dc8e6380b75a
-EBUILD emboss-6.6.0-r1.ebuild 1648 BLAKE2B 0cc2a8c446fbdb13cf5426e1a12b2585d6cd779059a1237e8aa2936e395b608c88eb02d0a591cf708344691a8d83f70e19c046c4f979897913c5abb40b7dba26 SHA512 3ff85cc699f9ccfaf68d8335b8631a7f976ad69e82a8bd0be70123fb61ab90c50250691c1e507b2ba891a07b5e6693612209d44780afe35ceef4e2c431f9d265
+EBUILD emboss-6.6.0-r1.ebuild 1631 BLAKE2B 561dcc9b1dcf2cfe71e6c42e1770d8dfee2a25df7bb86da22d9fe934a118f974f2294f444c0047cd28794d9f94356a201a050c878c2185df20e0a7bea59d819c SHA512 27c4c445c27c3915fac4b35e997ae549c86669b8998c5086af7b533fc69366e118dbb4a8f833e79bd4b8f783af7e2424e398f4b898b002725c42780e24b66bf8
 MISC metadata.xml 1096 BLAKE2B 704b6e7e0e9cb07a4cb184813ede8d7410d6612b2c8626838383a383dbd44f85b7f1dbcc988634f22d06ad76fbac927b4fd8a8836191be702c4f99a26343c6ac SHA512 4964b7e46d9fc16fcc44aaf83d0bb21a5ae860300764ca50e25f51ee0affc55fd863027747eb8e0eeca3578eefecbe23cba5ce68d518960e1721047cbefa9a3d
diff --git a/sci-biology/emboss/emboss-6.6.0-r1.ebuild b/sci-biology/emboss/emboss-6.6.0-r1.ebuild
index 2aa5aa9bc5c9..1c74ded5e22f 100644
--- a/sci-biology/emboss/emboss-6.6.0-r1.ebuild
+++ b/sci-biology/emboss/emboss-6.6.0-r1.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 EBO_EAUTORECONF=1
 
@@ -9,10 +9,11 @@ inherit emboss-r2 readme.gentoo-r1
 
 DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
 SRC_URI="ftp://emboss.open-bio.org/pub/${PN^^}/${P^^}.tar.gz"
+S="${WORKDIR}/${P^^}"
 
+LICENSE+=" Apache-2.0 GPL-3+ CC-BY-3.0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="minimal"
-LICENSE+=" Apache-2.0 GPL-3+ CC-BY-3.0"
 
 RDEPEND="
 	!games-action/xbomber
@@ -27,8 +28,6 @@ PDEPEND="
 		sci-biology/rebase
 	)"
 
-S="${WORKDIR}/${P^^}"
-
 PATCHES=(
 	"${FILESDIR}"/${P}_fix-build-system.patch
 	"${FILESDIR}"/${P}_FORTIFY_SOURCE-fix.patch
@@ -42,20 +41,20 @@ src_install() {
 	readme.gentoo_create_doc
 
 	# Install env file for setting libplplot and acd files path.
-	cat > 22emboss <<- EOF || die
+	newenvd - 22emboss <<- EOF || die
 		# ACD files location
 		EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd"
 		EMBOSS_DATA="${EPREFIX}/usr/share/EMBOSS/data"
 	EOF
-	doenvd 22emboss
 
 	# Remove useless dummy files
-	find "${ED%/}"/usr/share/EMBOSS -name dummyfile -delete || die "Failed to remove dummy files"
+	find "${ED}"/usr/share/EMBOSS -name dummyfile -delete \
+		|| die "Failed to remove dummy files"
 
 	# Move the provided codon files to a different directory. This will avoid
 	# user confusion and file collisions on case-insensitive file systems (see
 	# bug #115446). This change is documented in "README.gentoo".
-	mv "${ED%/}"/usr/share/EMBOSS/data/CODONS{,.orig} \
+	mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} \
 		|| die "Failed to move CODON directory"
 }
 
diff --git a/sci-biology/express/Manifest b/sci-biology/express/Manifest
index 4919e7df05e4..5c4f2edd0ec3 100644
--- a/sci-biology/express/Manifest
+++ b/sci-biology/express/Manifest
@@ -1,5 +1,5 @@
 AUX express-1.5.1-buildsystem.patch 1956 BLAKE2B 3cc9bc2a3fb8bc55444ed17984645bf900f253fed8b611395f7de3e744cd1c448af00bb8a83244f344801b9cc9d68c731e8338689bf29463cf2aacb35765d741 SHA512 246788b75a7f40c825cc7bf811de2bd44607b7ccf139d7302480ed7faae441ec95d5a37aec7f04effb1e3e47ed774b08291321cd227b0fa79306969b39e93d54
 AUX express-1.5.1-gcc6.patch 722 BLAKE2B d4c5972d7f3714e33ca85258a32101cd8975527aaf52846b116b75d0cfba94af9173d338d3de0e9051e844f23d6cf2e578340e0986afa9e5ee1ccc29b0781db3 SHA512 bbc7d7980bc88e241a76ad2b8a661ac8232f2cbc1a8cbf526b43905f9cdc52b57aadf8fb6bb03181b51893ac4e9d384ababb6d34582f7e24e6ef2ecc8fbfd73f
 DIST express-1.5.1-src.tgz 931166 BLAKE2B 5eb185e4b001f26f0dd32885b256b9fa48c89f546d67d7f8472cade69dde25375a5fc8efed5f01b615d63b641b674f7034a13f9483eb7967a6fd784a55c8878e SHA512 59cf6511a879311247c65334285ea056d571d4fd950aa6243041fa10075ff0d1ddd2afbcfe12e5f7f3e7cdd22fe37fd7f6b43ed4a8eb28d7a33d72366dc549ee
-EBUILD express-1.5.1.ebuild 735 BLAKE2B 581596936624a18170d1421adc64abf379a3a34587344fe6360dfffdf242fa9fae9b4030c37707634a0ae3451ae2eefb37f6145eaf133d8d40eecf0d4f3ed801 SHA512 b2d1d4550dedde0e6242a86a72134ef77fe4c016e725dca902e70cbc78c9e78e06aa484fd1ff5b05b7e574bbf28ed7aec42878eb06d7adde881e8ab5c4743783
+EBUILD express-1.5.1.ebuild 723 BLAKE2B 2a8a1963c9604badcca713f60c14e4567f63852271bd0e3dc6eadfdf03fb33b3c4b0697d0b4d2954801a4ed589baca38308256b4ad010d575cfff3c0590d4598 SHA512 2a237c62c543634d73b8e4f9468f510635da3db8705aeb5988daeee4d2208a303787763d6691773268a95cd82a7ebce0fe625b335d789b62b9feb7077ec06177
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/express/express-1.5.1.ebuild b/sci-biology/express/express-1.5.1.ebuild
index 148df8a8ce14..0f8fdce7bbb0 100644
--- a/sci-biology/express/express-1.5.1.ebuild
+++ b/sci-biology/express/express-1.5.1.ebuild
@@ -1,13 +1,13 @@
-# Copyright 1999-2018 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-inherit cmake-utils
+inherit cmake
 
 DESCRIPTION="Streaming RNA-Seq Analysis"
-HOMEPAGE="http://bio.math.berkeley.edu/eXpress/"
-SRC_URI="http://bio.math.berkeley.edu/eXpress/downloads/${P}/${P}-src.tgz"
+HOMEPAGE="https://pachterlab.github.io/eXpress/"
+SRC_URI="https://pachterlab.github.io/eXpress/downloads/${P}/${P}-src.tgz"
 
 LICENSE="Artistic"
 SLOT="0"
@@ -34,5 +34,5 @@ src_configure() {
 	local mycmakeargs=(
 		-DBAMTOOLS_INCLUDE="${EPREFIX}/usr/include/bamtools"
 	)
-	cmake-utils_src_configure
+	cmake_src_configure
 }
diff --git a/sci-biology/fasttree/Manifest b/sci-biology/fasttree/Manifest
index 31f22a31dfc1..ebc955155315 100644
--- a/sci-biology/fasttree/Manifest
+++ b/sci-biology/fasttree/Manifest
@@ -1,7 +1,7 @@
-AUX CMakeLists.txt 948 BLAKE2B b2a5908a2d24533f474d399b97b8941fbbe392e2b078890bc2e62dbd232912e6bbaec25fbb31592b1015c8c4234178a34ffd9bd4815935d64ea6da3dd21cd474 SHA512 9858800bfce8d256ccb834a06bad5a5230f90f025a9c9b3c9aafe7244d219d66810530f6688e02889cdb67d6a9459d8e26cd1a9fcf2e8825278b31d0e8d51ff3
-AUX fasttree-2.1.8-format-security.patch 783 BLAKE2B c400b89a17287817f82a8747082b3bf35d8097941c591923fcff073618fae0423b97fb5bc9a12a199acea0de61d451378beaf0070beb9b20274da81b936f2296 SHA512 9bbf66cddca2b6c202fdeeab4092036852cb1ebe132ebf4d96cba1bea75bb5668dd6ee97d4d020a4b7cf7111bee6d0c3004b0bd74ee4685ef98eeeb5e9a23eb3
-DIST FastTree-2.1.8.c 385231 BLAKE2B 6f42025ef69b990e051263ccfa23f95d0cde326798c54d8f702c50127338711898c380d1dbd82ab775667eada047048ba8d68288b030af4984019a5f2c23729f SHA512 39a7d284412a602208c2a5df3d0a9a30fe3a584f7f7788d741fb1463b698692017f47bb23f70046d0873e9c8fd27c84ec23f6ca48adb0594193765ac732e6559
-DIST FastTreeUPGMA-2.1.8.c 95271 BLAKE2B 1de328881f6452b9c7423c9ed381ab2eb31c4f3ee6426481a6b1089c1359627d4cbbfbea868ebeab9538f82e17f45f1bff8ec07c7370e6432bef6bae449798a8 SHA512 4d6a8e2cb28b8ee201091172a3baa59d432420839c6d2244b5fb8230ed9daa626b6bed22cb692393ca3d78b8f2d071fe18fbb4f9bdcdc47ef149c31e3f45546c
-DIST MOTreeComparison-2.1.8.tar.gz 13523 BLAKE2B 97638edd945412ff00e3dfcfc89ec6ea52ae8c43531d5cb680d97e9c62fcad80e861f58ec987abcd2282166dd7886101edba4875531bd9d6ac23df242e0dbd5b SHA512 24d2247650d7728942bd1d987b548cefd65a16b433a3810876613e9fd1cff223d4349ee720b3d8d10a73af220c2c9f59a24d77ad34ff009325fe9f22aa35c72b
-EBUILD fasttree-2.1.8.ebuild 1170 BLAKE2B afc7e5b975fea59bc720d59732dac792662717aee591f9dc532d532a43ff7a7563f401fce51d0bb9e2d31315b24fe45d098825bdbcbc5264fcfb461cba68ba03 SHA512 798b161e7c9c70e5fd0de3a8018f1e3f95c59b354517ca9539845ec1462d506ab20b4fe629b9666614969a7d05101bf01121c2df34ad9e8a86ff63e136b6f51b
+AUX CMakeLists.txt 985 BLAKE2B b812e5133464f10d25c59155bd49b933a94e6c2480996a114b91dd03e3475b755280c7b58c1195ef6faceb009d9c70220aa41a4501fa44f1c53da571845dfb7b SHA512 9f83060b59c4da4a5ad16789c285bb2c7c25b2906a0bc06614d95086753057c5cfbddcd07cc3514f11604073c8fb6c688107efdb3329e75bf8261f9304a840d3
+AUX fasttree-2.1.11-format-security.patch 788 BLAKE2B 63adc80af602d7d6582201c3184ee18d33bf744041e503d776e542e309a3c285270567b0ef7661746fb8c8bfcaf2517537276aff57e10b5989e49625404ebc50 SHA512 b46fa4f47c2b668df7c776b848583f3438a1bf792c93c57611b84ca84a9725fae2cab138fa3e6fd7080132663347ae35f027730c8845edd35d7e2ee39c900393
+DIST FastTree-2.1.11.c 395543 BLAKE2B 5bea3fba66ddf077ce42c3e1791505a9fa909bb619e30e0c0370631996d932c63ca172fffc1721ac9f081a16bed3b1c99a9c7f6e4a3bb269b82545e2978904d3 SHA512 2bbb1cc078b04125a55b8c02f65c9fbfb6db894c2fbfdaac8f86cc0084f2579723cdc4f6aa63bf4338b767d0fdaffa8dd503e4126c3f5f700d4f3da9fc085ee5
+DIST FastTreeUPGMA-2.1.11.c 95271 BLAKE2B 1de328881f6452b9c7423c9ed381ab2eb31c4f3ee6426481a6b1089c1359627d4cbbfbea868ebeab9538f82e17f45f1bff8ec07c7370e6432bef6bae449798a8 SHA512 4d6a8e2cb28b8ee201091172a3baa59d432420839c6d2244b5fb8230ed9daa626b6bed22cb692393ca3d78b8f2d071fe18fbb4f9bdcdc47ef149c31e3f45546c
+DIST MOTreeComparison-2.1.11.tar.gz 13523 BLAKE2B 97638edd945412ff00e3dfcfc89ec6ea52ae8c43531d5cb680d97e9c62fcad80e861f58ec987abcd2282166dd7886101edba4875531bd9d6ac23df242e0dbd5b SHA512 24d2247650d7728942bd1d987b548cefd65a16b433a3810876613e9fd1cff223d4349ee720b3d8d10a73af220c2c9f59a24d77ad34ff009325fe9f22aa35c72b
+EBUILD fasttree-2.1.11.ebuild 1114 BLAKE2B 72e5dd6d6165167cb7df943d31790cfc3a2742db788665efadeb00e55a71fd2ed2367088ef520875f4aab1cae81fde9614e8f7dda405598d1016cb27666438d9 SHA512 8003b7317d8d25ff703e2cb172e49bf3d8c50228d57417813f7917225ac655845c42c4edcd6b5fb15a354992590abdbb471ef10013dd56dc40e1a04e18f41518
 MISC metadata.xml 410 BLAKE2B 92ee74c67cebb5ac4db5217355e6f01f893387d7fe0da1dd5048207149e385927f05c324d8299682b42bc7ba895e1f42a0ee5d7e9442d03d33ea3511dc704ffd SHA512 6f380e2353b1a0ff33c75cd593d2cf3e12d56c99478e7a5bdb37459b10449ae88065d265820f2a9c6d61d53a295ed1a4e18b8595e23c137c9788c658080caff0
diff --git a/sci-biology/fasttree/fasttree-2.1.8.ebuild b/sci-biology/fasttree/fasttree-2.1.11.ebuild
index 3f9e4ad5f759..cb2d16791ee3 100644
--- a/sci-biology/fasttree/fasttree-2.1.8.ebuild
+++ b/sci-biology/fasttree/fasttree-2.1.11.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2018 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-inherit cmake-utils
+inherit cmake
 
 DESCRIPTION="Fast inference of approximately-maximum-likelihood phylogenetic trees"
 HOMEPAGE="http://www.microbesonline.org/fasttree/"
@@ -29,11 +29,7 @@ src_unpack() {
 	cd "${S}" || die
 	unpack ${A}
 	cp "${DISTDIR}"/{FastTreeUPGMA-${PV}.c,FastTree-${PV}.c} . || die
-}
-
-src_prepare() {
 	cp "${FILESDIR}"/CMakeLists.txt . || die
-	cmake-utils_src_prepare
 }
 
 src_configure() {
@@ -43,5 +39,5 @@ src_configure() {
 		-DUSE_OPENMP=$(usex openmp)
 		-DUSE_DOUBLE=$(usex double-precision)
 	)
-	cmake-utils_src_configure
+	cmake_src_configure
 }
diff --git a/sci-biology/fasttree/files/CMakeLists.txt b/sci-biology/fasttree/files/CMakeLists.txt
index e7c53afdaf36..c52b90cc7be2 100644
--- a/sci-biology/fasttree/files/CMakeLists.txt
+++ b/sci-biology/fasttree/files/CMakeLists.txt
@@ -1,23 +1,24 @@
-cmake_minimum_required (VERSION 2.6)
+cmake_minimum_required (VERSION 2.8.12)
 project(fasttree C)
 
+include(GNUInstallDirs)
+
 option(USE_OPENMP "Use OpenMP to parallelize many of the steps in computing a tree" ON)
-option(USE_DOUBLE "Use double precission" OFF)
+option(USE_DOUBLE "Use double precision" OFF)
 option(HAS_SSE3 "Use SSE2/SSE3 instructions to speed up some inner loops" ON)
 
 if(USE_OPENMP)
-	SET( CMAKE_C_FLAGS  "${CMAKE_C_FLAGS} -DOPENMP -fopenmp" )
-	SET( CMAKE_EXE_LINKER_FLAGS  "${CMAKE_EXE_LINKER_FLAGS} -DOPENMP -fopenmp" )
-endif(USE_OPENMP)
+	set( CMAKE_C_FLAGS  "${CMAKE_C_FLAGS} -DOPENMP -fopenmp" )
+	set( CMAKE_EXE_LINKER_FLAGS  "${CMAKE_EXE_LINKER_FLAGS} -DOPENMP -fopenmp" )
+endif()
 
 if(USE_DOUBLE)
-	SET( CMAKE_C_FLAGS  "${CMAKE_C_FLAGS} -DUSE_DOUBLE" )
-endif(USE_DOUBLE)
+	set( CMAKE_C_FLAGS  "${CMAKE_C_FLAGS} -DUSE_DOUBLE" )
+endif()
 
 if(NOT HAS_SSE3)
-	SET( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DNO_SSE" )
-endif(NOT HAS_SSE3)
-
+	set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DNO_SSE" )
+endif()
 
 add_executable(FastTree FastTree-${VERSION}.c)
 add_executable(FastTreeUPGMA FastTreeUPGMA-${VERSION}.c)
@@ -25,6 +26,6 @@ add_executable(FastTreeUPGMA FastTreeUPGMA-${VERSION}.c)
 target_link_libraries(FastTree m)
 target_link_libraries(FastTreeUPGMA m)
 
-install (TARGETS FastTree FastTreeUPGMA DESTINATION bin)
+install (TARGETS FastTree FastTreeUPGMA DESTINATION ${CMAKE_INSTALL_BINDIR})
 
-install(FILES MOTree.pm CompareTree.pl CompareToBootstrap.pl DESTINATION share/fasttree)
+install(FILES MOTree.pm CompareTree.pl CompareToBootstrap.pl DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/fasttree)
diff --git a/sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch b/sci-biology/fasttree/files/fasttree-2.1.11-format-security.patch
index 15f5c174ec40..45023e4215f6 100644
--- a/sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch
+++ b/sci-biology/fasttree/files/fasttree-2.1.11-format-security.patch
@@ -1,10 +1,10 @@
- FastTreeUPGMA-2.1.8.c | 4 ++--
+ FastTreeUPGMA-2.1.11.c | 4 ++--
  1 file changed, 2 insertions(+), 2 deletions(-)
 
-diff --git a/FastTreeUPGMA-2.1.8.c b/FastTreeUPGMA-2.1.8.c
+diff --git a/FastTreeUPGMA-2.1.11.c b/FastTreeUPGMA-2.1.11.c
 index af76cb1..4065f42 100644
---- a/FastTreeUPGMA-2.1.8.c
-+++ b/FastTreeUPGMA-2.1.8.c
+--- a/FastTreeUPGMA-2.1.11.c
++++ b/FastTreeUPGMA-2.1.11.c
 @@ -535,7 +535,7 @@ int main(int argc, char **argv) {
        break;
    }
diff --git a/sci-biology/phylip/Manifest b/sci-biology/phylip/Manifest
index c88142631f51..e32039f426a1 100644
--- a/sci-biology/phylip/Manifest
+++ b/sci-biology/phylip/Manifest
@@ -2,5 +2,5 @@ AUX README.Gentoo 643 BLAKE2B 95193d4c9c8fc8fb5796bb0a8ca470f440ac66eb1da9b9ed47
 AUX phylip-3.698-fno-common.patch 1934 BLAKE2B 613149dd930aa3efc921d5844e97c76475bffaedfe701d46ae980a4fabd0896d6d81fde4722599217508689d41ec70e110cbf0638abad13b2c0dbbf1c6c2f159 SHA512 4e89f330338da601ac7311995a341cab235288d82b9a63ba632b830eb99052191a920f51f43236c1a71f07ce3e427dd58ff5bc0004d1ed4ebbea8bf223390aa1
 AUX phylip-3.698-makefile.patch 9481 BLAKE2B fc8b863c05953333588f174251e40a86138a5cf2b08206861bef594ebea1d7d63b53895517bb6916e1c06c700b379cd93e76a673af4ec225502ac886dbe702d5 SHA512 6713644543f676dd6b21408675ac65c38f6a2fed4bd04619c19de881e5269e4c0bb89e440cf59dd0f1f13ad72cbbf420baccdaeb6a0c7a2a807895f87376d76f
 DIST phylip-3.698.zip 9675991 BLAKE2B 8d020cf17b3245b9827af4bdd1d17167c3e1a41ae805766c4b72f09de107775314a2a296c00f84f928487403cc02741fd46ae73585d0dba143f4b926777e9add SHA512 7f822dabd1ffdb6a689e0c308f5a3ae129bd86e305086a18c0c755ac3c6ca28a4337d52ced76b280706926370e23f19f304851ef82e32833d1945ed277f7d70d
-EBUILD phylip-3.698.ebuild 1193 BLAKE2B c196d7cdfe79a17691c2fe5567a30c0b937015ef3f8f1ce11a317dd1c86913487e6ac9a80f6ec21b80be804e7fcc1193522d3c4879d32e7510e7a9b89f1ce3b3 SHA512 da567382dfd57d40fca30845346f6ae8a5ce1bf16475bb1bdd5a220eb47d629b9904d4e0e76797971fcb2cfa795cc69a1480292a262350eb891b407e44f00509
+EBUILD phylip-3.698.ebuild 1192 BLAKE2B a91ddcba5b9ab2edfe4a3a201c640c72f0b6b51f79ddcdf81c133807cf0f12c17e4c591dd470391fa494e1d0ce1e115cc3c4b09a0165235278a8f8ec0840524b SHA512 652292c5969d9fffa6b99c3db183a58d09b1f24eef1be4269492f5bf97d6e2cb795103a8791355cea18bf4cdcf60f91c5a96cef364865aadd7b53a3a8de94494
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/phylip/phylip-3.698.ebuild b/sci-biology/phylip/phylip-3.698.ebuild
index 0a8ef8f815ec..34bfd5699b03 100644
--- a/sci-biology/phylip/phylip-3.698.ebuild
+++ b/sci-biology/phylip/phylip-3.698.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
 inherit flag-o-matic toolchain-funcs
 
-DESCRIPTION=" The PHYLogeny Inference Package"
+DESCRIPTION="The PHYLogeny Inference Package"
 HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html"
 SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.zip"
 
diff --git a/sci-biology/seqan/Manifest b/sci-biology/seqan/Manifest
index 97b76d002547..8d7f1285b2e6 100644
--- a/sci-biology/seqan/Manifest
+++ b/sci-biology/seqan/Manifest
@@ -1,5 +1,6 @@
+AUX seqan-2.4.0-cmake-add_library-static.patch 1542 BLAKE2B 08f006302c4b284bbbfc2967a34d94a20ebb65faefce293adac326eb46adb18a2442206a0cd3e98820af2372f0201627c3de259fb2df8fa9575e9568f26337f7 SHA512 e17058da311266e75bbef3d331b7a516490c8f8b63144e1466072a08b165ec88130e93336d164c58269920ad9ef9d34ced58e928c14a7b3a5352af6e7c3b255c
 AUX seqan-2.4.0-fix-pthread.patch 541 BLAKE2B 16d42c72d6ea0654ba6727ce1007b89d3fc76141320f5a71cfd0fe102b8e511ccb36d48e021baf0928ac8857e97f6addde3f15f4f0577c531285027f23f5eea8 SHA512 f8a3df0892a81a65562dbd85f0945e5722df524e07b9949f860df4e0f07c285df3a48a112c8e1e5dca28a97c219dc9feed677e803ec5d3964216f7052b6f431b
+AUX seqan-2.4.0-installpaths.patch 1661 BLAKE2B 6548f5b7cd0e26d187ff61a8e8e3db008700b5131a57228f0cd567642fae12778ff2a77960fa318f6244a80f94e771ebeb218fee8eaf6ec1a4c827e972d1ac90 SHA512 9b2100cd2a4069fd9022723ca6972251d2307f4886b3dcdf68816e78d38359d8767e20e19b4170213abb905bc3b570ed257e025e063a475ff3406d8f1e8d3313
 DIST seqan-v2.4.0.tar.gz 109626901 BLAKE2B a10b5ee9a95667f560a8c2aec3808131f5f838f3c07d56584f4b29e9622912bf3d00b958b02db7c9d62dd52d9d08a171abcccef7f50cddf0407538168cf2c592 SHA512 f92cfc97304581920850c5d49fe4336f7c3855e99c3bcb035b6172fa7307e08e6f06fb06d1cd8f5b447c3220fc7f669684fbfe25641b43e9f6953999cf9ddd4b
-EBUILD seqan-2.4.0.ebuild 1624 BLAKE2B e2b8d8c2e7f87abc063255e0c6c826a57e4da29b063eb3fc82d143593e06d8cbbf5744cd6e39e9cc1b2623c010d181e4361665946a8489ad454f3e1fb9a33c88 SHA512 1d39216baa3877df91b19f36519103114a6858b4600d5bfe3ba01e5619bcfb2543d208e7d5af2806a5c964ebcb8399a8244ca65f4e7ecf169e02827e055545d3
-EBUILD seqan-9999.ebuild 1567 BLAKE2B b171570acf62243121541b771c26fd7ef86e4be86878c060050af2cd665973182e2498f9ba9c336e8a382768b71aa3547edde927682dcdd844c6fd0ed9e2cd99 SHA512 b91b532d3655de47c0cfb9f243e46c120d5259f9166be4e41d7b0dd02a6f681e714fd5941aadb54b6ee89a0f5a4aa10628157c9b25bfd8074178dc36b70e5944
+EBUILD seqan-2.4.0-r1.ebuild 1592 BLAKE2B 98ca9dce72bca2d2069eb94a9f998c5f7d25d303c053930264a51231dc3972243ef7433d9a750f9b0d4b26950a7adc7ccf7f863a8a87f3393821f72f285591bd SHA512 e63405b1c8ab04bf2e635601b27effa62b116e4d5c14f4244f2a5cbd1047e22c2b4c8793602535225ad426ccf8f69b0f68967d47db81b65ae3c0abeee6b5d057
 MISC metadata.xml 372 BLAKE2B d620401f1aab9be80ddb6dc7abe737fd3e6322c560136e2c3b33d9246beca2986b4d91225b506e8c3035550994c3f714a11c0d8b17efd30c29278002d4eb7a12 SHA512 ae6c49e7e45c0ce4dd4fe27d21c5376c6fb8d7bfd2f98b7775f4689811680fa92c0b71ac0db70f6969660c4aee344f710ef752a467d6d46dd83aa47386d2ec17
diff --git a/sci-biology/seqan/files/seqan-2.4.0-cmake-add_library-static.patch b/sci-biology/seqan/files/seqan-2.4.0-cmake-add_library-static.patch
new file mode 100644
index 000000000000..7617d9f9a665
--- /dev/null
+++ b/sci-biology/seqan/files/seqan-2.4.0-cmake-add_library-static.patch
@@ -0,0 +1,38 @@
+From 1877d143ad9f42d80692073538e3f32b37e15967 Mon Sep 17 00:00:00 2001
+From: Andreas Sturmlechner <asturm@gentoo.org>
+Date: Sun, 7 Mar 2021 19:35:44 +0100
+Subject: [PATCH] Fix linking with BUILD_SHARED_LIBS=ON default in EAPI-7
+
+Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
+---
+ apps/mason2/CMakeLists.txt         | 2 +-
+ apps/pair_align/lib/CMakeLists.txt | 2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/apps/mason2/CMakeLists.txt b/apps/mason2/CMakeLists.txt
+index 2218187..c042ea7 100644
+--- a/apps/mason2/CMakeLists.txt
++++ b/apps/mason2/CMakeLists.txt
+@@ -52,7 +52,7 @@ add_definitions (-DSEQAN_REVISION="${SEQAN_REVISION}")
+ add_definitions (-DSEQAN_DATE="${SEQAN_DATE}")
+ 
+ # We define a library for the reusable parts of Mason.
+-add_library (mason_sim
++add_library (mason_sim STATIC
+              external_split_merge.h
+              external_split_merge.cpp
+              fragment_generation.h
+diff --git a/apps/pair_align/lib/CMakeLists.txt b/apps/pair_align/lib/CMakeLists.txt
+index 75faef7..3b9576e 100644
+--- a/apps/pair_align/lib/CMakeLists.txt
++++ b/apps/pair_align/lib/CMakeLists.txt
+@@ -53,5 +53,5 @@ endforeach(GAPS_T)
+ 
+ # This part can be used instead for cmake version greater or equal to 2.8.8. 
+ # This requires to update the script above as well.
+-add_library(pair_align_lib pair_align_lib.cpp pair_align_lib.h ${LIB_TARGETS})
++add_library(pair_align_lib STATIC pair_align_lib.cpp pair_align_lib.h ${LIB_TARGETS})
+ target_link_libraries(pair_align_lib ${SEQAN_LIBRARIES})
+-- 
+2.30.1
+
diff --git a/sci-biology/seqan/files/seqan-2.4.0-installpaths.patch b/sci-biology/seqan/files/seqan-2.4.0-installpaths.patch
new file mode 100644
index 000000000000..35f0718f9d8d
--- /dev/null
+++ b/sci-biology/seqan/files/seqan-2.4.0-installpaths.patch
@@ -0,0 +1,24 @@
+--- a/util/cmake/SeqAnBuildSystem.cmake	2018-01-11 12:32:45.591134000 +0100
++++ b/util/cmake/SeqAnBuildSystem.cmake	2018-01-11 12:51:55.193282581 +0100
+@@ -399,10 +399,10 @@
+         # Install pkg-config file, except on Windows.
+         if (NOT CMAKE_SYSTEM_NAME MATCHES Windows)
+             configure_file("util/pkgconfig/seqan.pc.in" "${CMAKE_BINARY_DIR}/util/pkgconfig/seqan-${SEQAN_VERSION_MAJOR}.pc" @ONLY)
+-            install(FILES "${CMAKE_BINARY_DIR}/util/pkgconfig/seqan-${SEQAN_VERSION_MAJOR}.pc" DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/pkgconfig)
++            install(FILES "${CMAKE_BINARY_DIR}/util/pkgconfig/seqan-${SEQAN_VERSION_MAJOR}.pc" DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
+         endif (NOT CMAKE_SYSTEM_NAME MATCHES Windows)
+         # Install FindSeqAn TODO(h-2) rename seqan-config.cmake to seqan-config${SEQAN_VERSION_MAJOR}.cmake after 2.x cycle
+-        install(FILES "${CMAKE_CURRENT_SOURCE_DIR}/util/cmake/seqan-config.cmake" DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/cmake/seqan/)
++        install(FILES "${CMAKE_CURRENT_SOURCE_DIR}/util/cmake/seqan-config.cmake" DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/seqan2/)
+ 
+         # Install headers
+         file (GLOB HEADERS
+@@ -473,7 +473,7 @@
+             set (CMAKE_INSTALL_DOCDIR "${CMAKE_INSTALL_DATAROOTDIR}/doc" CACHE STRING "Documentation root (DATAROOTDIR/doc)" FORCE)
+         endif ()
+         set (SEQAN_PREFIX_SHARE "${CMAKE_INSTALL_DATADIR}/${APP_NAME}")
+-        set (SEQAN_PREFIX_SHARE_DOC "${CMAKE_INSTALL_DOCDIR}/${APP_NAME}")
++        set (SEQAN_PREFIX_SHARE_DOC "${CMAKE_INSTALL_DOCDIR}/examples/")
+     endif ()
+ endmacro (seqan_setup_install_vars)
+ 
diff --git a/sci-biology/seqan/seqan-9999.ebuild b/sci-biology/seqan/seqan-2.4.0-r1.ebuild
index b344b39cbc46..76a73d759bef 100644
--- a/sci-biology/seqan/seqan-9999.ebuild
+++ b/sci-biology/seqan/seqan-2.4.0-r1.ebuild
@@ -1,14 +1,12 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-: ${CMAKE_MAKEFILE_GENERATOR:=ninja}
-
-inherit cmake-utils multibuild toolchain-funcs
+inherit cmake multibuild toolchain-funcs
 
 DESCRIPTION="C++ Sequence Analysis Library"
-HOMEPAGE="http://www.seqan.de/"
+HOMEPAGE="https://www.seqan.de/"
 
 if [[ ${PV} == *9999 ]]; then
 	inherit git-r3
@@ -17,8 +15,7 @@ if [[ ${PV} == *9999 ]]; then
 else
 	SRC_URI="https://github.com/seqan/seqan/archive/seqan-v${PV}.tar.gz"
 	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-	S=${WORKDIR}/seqan-seqan-v${PV}
+	S="${WORKDIR}"/seqan-seqan-v${PV}
 fi
 
 LICENSE="BSD GPL-3"
@@ -28,28 +25,29 @@ REQUIRED_USE="cpu_flags_x86_sse4_1"
 
 RDEPEND="
 	app-arch/bzip2:=
-	sys-libs/zlib:=
+	sys-libs/zlib
 	!!sci-biology/seqan:2.0
 	!!sci-biology/seqan:2.1
 	!!sci-biology/seqan:2.2"
-DEPEND="
-	${RDEPEND}"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-fix-pthread.patch
+	"${FILESDIR}"/${P}-installpaths.patch
+	"${FILESDIR}"/${P}-cmake-add_library-static.patch
+)
 
 pkg_setup() {
 	if [[ ${MERGE_TYPE} != binary ]]; then
 		use tools && tc-check-openmp
 
-		MULTIBUILD_VARIANTS=(
-			$(usev tools)
-			library
-		)
+		MULTIBUILD_VARIANTS=( $(usev tools) library )
 	fi
 }
 
 src_configure() {
 	my_configure() {
 		local mycmakeargs=(
-			-DCMAKE_INSTALL_DOCDIR="share/doc/${PF}"
 			-DSEQAN_NO_DOX=ON
 		)
 		case "${MULTIBUILD_ID}" in
@@ -67,15 +65,15 @@ src_configure() {
 				die "${MULTIBUILD_ID} is not recognized"
 				;;
 		esac
-		cmake-utils_src_configure
+		cmake_src_configure
 	}
 	multibuild_foreach_variant my_configure
 }
 
 src_compile() {
-	multibuild_foreach_variant cmake-utils_src_compile
+	multibuild_foreach_variant cmake_src_compile
 }
 
 src_install() {
-	multibuild_foreach_variant cmake-utils_src_install
+	multibuild_foreach_variant cmake_src_install
 }
diff --git a/sci-biology/seqan/seqan-2.4.0.ebuild b/sci-biology/seqan/seqan-2.4.0.ebuild
deleted file mode 100644
index 5653a1ec94e4..000000000000
--- a/sci-biology/seqan/seqan-2.4.0.ebuild
+++ /dev/null
@@ -1,83 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-: ${CMAKE_MAKEFILE_GENERATOR:=ninja}
-
-inherit cmake-utils multibuild toolchain-funcs
-
-DESCRIPTION="C++ Sequence Analysis Library"
-HOMEPAGE="http://www.seqan.de/"
-
-if [[ ${PV} == *9999 ]]; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/seqan/seqan.git"
-	EGIT_BRANCH="develop"
-else
-	SRC_URI="https://github.com/seqan/seqan/archive/seqan-v${PV}.tar.gz"
-	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-	S=${WORKDIR}/seqan-seqan-v${PV}
-fi
-
-LICENSE="BSD GPL-3"
-SLOT="0"
-IUSE="cpu_flags_x86_sse4_1 tools"
-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="
-	${RDEPEND}"
-
-PATCHES=( "${FILESDIR}"/${PN}-2.4.0-fix-pthread.patch )
-
-pkg_setup() {
-	if [[ ${MERGE_TYPE} != binary ]]; then
-		use tools && tc-check-openmp
-
-		MULTIBUILD_VARIANTS=(
-			$(usev tools)
-			library
-		)
-	fi
-}
-
-src_configure() {
-	my_configure() {
-		local mycmakeargs=(
-			-DCMAKE_INSTALL_DOCDIR="share/doc/${PF}"
-			-DSEQAN_NO_DOX=ON
-		)
-		case "${MULTIBUILD_ID}" in
-			tools)
-				mycmakeargs+=(
-					-DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_APPS
-				)
-				;;
-			library)
-				mycmakeargs+=(
-					-DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY
-				)
-				;;
-			*)
-				die "${MULTIBUILD_ID} is not recognized"
-				;;
-		esac
-		cmake-utils_src_configure
-	}
-	multibuild_foreach_variant my_configure
-}
-
-src_compile() {
-	multibuild_foreach_variant cmake-utils_src_compile
-}
-
-src_install() {
-	multibuild_foreach_variant cmake-utils_src_install
-}
diff --git a/sci-biology/uchime/Manifest b/sci-biology/uchime/Manifest
index 7aaf4944f6af..b64b2369ba21 100644
--- a/sci-biology/uchime/Manifest
+++ b/sci-biology/uchime/Manifest
@@ -1,4 +1,4 @@
-AUX CMakeLists.txt 549 BLAKE2B 7c71a80c53bfa1e1c6a1726668866baf4e2b53b29abee4ef3f3c825cadaf8ceac0499c6a702054e9e9698a463ad04668b2a043b17d9cf587c61d8abf5c04076d SHA512 02b43fbfa0a8fd9e5389033e5a8b97d356dfc2d29d076539eea5830b30526745014bc1eab302ccb8fd27b65a1afd92537b94c3c266a4b285de1b7a287fa8a867
+AUX CMakeLists.txt 589 BLAKE2B 183caf5f107482c410296eee8136271e261696a3c11255960b840bd4db16cf461c386fa7374b3a2afb3fd38e97593ad98f9efc621104106cfe4463939c6d0d31 SHA512 06e9f9c8806c27b268968b28fb6059fc6d52295a5d38635612728ac577656fcfae5eb6b15c63e3e9de57e1c8cac832cd4dff70d8a6f3182358a5eb06eb354642
 DIST uchime4.2.40_src.tar.gz 66772 BLAKE2B 9133853d616ab6e1e6a397da78fc846ba00fc70c2c375eb16a98fbdec25ba6034bd1c876b7ec4a99305e76e47cf7984c1aa30b64bdc96e125f661a0150bae060 SHA512 c3afecb23d164d9c3db6229f54faa13120ac4d88132d9aef707f8d043091099db4205ac80f60242920af6efc23813b3e7e4966d562bdb75ff53244fd525e656b
-EBUILD uchime-4.2.40.ebuild 500 BLAKE2B b971e082e7e03cacdc9f178ead195d4b2ae340eafd856cff2081faa0e6879522f1d1058f46bd330ea144394c4552860568d6cb7833c2b1c525b5b457b292fc40 SHA512 5e5757f0fb4de458662828805fc8b2d63573a450c7b6f5249f05103061f6f577ea91d7ec1fdea6889c3690647c536f79b35894e9d99040e12e111c2436b4c258
+EBUILD uchime-4.2.40.ebuild 513 BLAKE2B 85980c9a60fbfd3d155e371b9638606bc4a0e54ca670a12e5f0f8bfa647c6d27b27879aaa1d5c7f724c2f0135d384b54fa61ab334c9a6382140004261334b7e1 SHA512 0c1a1f0f78d1b8da99153a601f5012ae7b74d05a672dc649cdcdfe62b4231474801165bdb70b4be17182ff8da0c77395638e465997715d94fbdd7b745a942210
 MISC metadata.xml 896 BLAKE2B 1041ed416b2ba4670f85856ed2bfe1508d3bea0a310a29a9265b04372df51ee39090d76fa6a282c908e26541986bd10dd47ea73260d5180fe382fc97de556509 SHA512 641d91bff3651a49a3b7e15260cf2a758199ae49ece16643d3104f0f4e202938935edeb3bef18f7afc40a4eb1b1b3e469b07fec95d30a5e686e4b66535ff3e7e
diff --git a/sci-biology/uchime/files/CMakeLists.txt b/sci-biology/uchime/files/CMakeLists.txt
index 54b0a3ba0d30..a9319293e10b 100644
--- a/sci-biology/uchime/files/CMakeLists.txt
+++ b/sci-biology/uchime/files/CMakeLists.txt
@@ -1,11 +1,12 @@
-cmake_minimum_required(VERSION 2.6)
+cmake_minimum_required(VERSION 2.8.12)
 project(UCHIME)
 
+include(GNUInstallDirs)
+
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D_FILE_OFFSET_BITS=64 -DUCHIMES=1")
 
 # Simply copy the source files from the mk script
 add_executable(uchime 
 				addtargets2.cpp alignchime.cpp alignchimel.cpp alnparams.cpp alpha.cpp alpha2.cpp fractid.cpp getparents.cpp globalalign2.cpp make3way.cpp mx.cpp myutils.cpp path.cpp searchchime.cpp seqdb.cpp setnucmx.cpp sfasta.cpp tracebackbit.cpp uchime_main.cpp usort.cpp viterbifast.cpp writechhit.cpp)
 
-INSTALL(TARGETS uchime
-        DESTINATION bin)
+INSTALL(TARGETS uchime DESTINATION ${CMAKE_INSTALL_BINDIR})
diff --git a/sci-biology/uchime/uchime-4.2.40.ebuild b/sci-biology/uchime/uchime-4.2.40.ebuild
index dd2201547ae0..75827ab3a304 100644
--- a/sci-biology/uchime/uchime-4.2.40.ebuild
+++ b/sci-biology/uchime/uchime-4.2.40.ebuild
@@ -1,18 +1,17 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
-
-inherit cmake-utils
+EAPI=7
 
 MY_P="${PN}${PV}_src"
+inherit cmake
 
 DESCRIPTION="Fast, accurate chimera detection"
-HOMEPAGE="http://www.drive5.com/uchime/"
-SRC_URI="http://drive5.com/${PN}/${MY_P}.tar.gz"
+HOMEPAGE="https://www.drive5.com/usearch/manual/uchime_algo.html"
+SRC_URI="https://www.drive5.com/${PN}/${MY_P}.tar.gz"
 
-SLOT="0"
 LICENSE="public-domain"
+SLOT="0"
 KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
 IUSE="debug"
 
@@ -20,6 +19,5 @@ S="${WORKDIR}"/${MY_P}
 
 src_prepare() {
 	cp "${FILESDIR}"/CMakeLists.txt . || die
-
-	cmake-utils_src_prepare
+	cmake_src_prepare
 }