gentoo resync : 29.12.2022

author: V3n3RiX <venerix@koprulu.sector> 2022-06-29 12:04:12 +0100
committer: V3n3RiX <venerix@koprulu.sector> 2022-06-29 12:04:12 +0100
commit: 0f558761aa2dee1017b4751e4017205e015a9560 (patch)
tree: 037df795519468a25d9362b4e95cdaeb84eb1cf9 /sci-biology
parent: 752d6256e5204b958b0ef7905675a940b5e9172f (diff)
37 files changed, 152 insertions, 233 deletions
diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 52b23c3b700c..abaa252910a4 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/aaindex/Manifest b/sci-biology/aaindex/Manifest
index 472521c5a2e6..b5ff9e70e11f 100644
--- a/sci-biology/aaindex/Manifest
+++ b/sci-biology/aaindex/Manifest
@@ -1,3 +1,3 @@
 DIST aaindex-9.1.tar.bz2 133780 BLAKE2B 2e0a3c9f6f9e9a6d18f7812196595776a03e688b83799a24b63f659fe4c08b50de396d6aa07e80e3beea776d29210c1c71194deecea19faa8bf36204d8544f42 SHA512 d35760712a3f9d8c0d64e32ff450802eab20294851e569cbb9614610704f687c9ec56c440e6009b5c75c45ae12bd7968e28afcc414309318e94b092507df16d8
-EBUILD aaindex-9.1-r1.ebuild 968 BLAKE2B 557da1f01228bb57d9248dec2c50675b9825e1f2739412a6d585972e3f0182fdc1cd52b2c10b605dc615891e4fa14583fc7c9b11f1b716b87983a206be4a0e1f SHA512 a23cac16ea0ceb6368a2e7f68c35514a8be1b9b6eba416347a713c7877bd7da25e2ce1b64367e33263c80ad5bfcab50a3446b11d7568eeda9530641a7e72f70c
+EBUILD aaindex-9.1-r2.ebuild 966 BLAKE2B 846c4b60872c2f0f0e288ffb7f8887350da42dc30b87a8dae91d0923b0c3ea46756e9ab00301805a592470673b8ecd556d7b18f3c535456dc609e344f0b9f04f SHA512 829b6836599994bc2cf39b9b9e5a0c97ca18eaa6a5d239a48629054e28c93e7c0201d879b55753bdd5c7b6faa4c8bb7f06134636e2defbfe0913b8389123f144
 MISC metadata.xml 1318 BLAKE2B 2a5b66b8e2ad719be1daf46ee237dffccab7b3472677deb918a35cd714035e5b57c8da64b5d7e4fb0fbe069c4812a4118f3d013a36f01009399bc4b2653110ed SHA512 a79444974fbd48c567293eebdde27066b67cd55afa668e9360dadfac63da200a25a9692ba6134557d94a0dcd110db92fe14974bc2392196e3162cef446d9d481
diff --git a/sci-biology/aaindex/aaindex-9.1-r1.ebuild b/sci-biology/aaindex/aaindex-9.1-r2.ebuild
index b51f64beaefc..76b95ddb1bcf 100644
--- a/sci-biology/aaindex/aaindex-9.1-r1.ebuild
+++ b/sci-biology/aaindex/aaindex-9.1-r2.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=8
 
 DESCRIPTION="Amino acid indices and similarity matrices"
 HOMEPAGE="https://www.genome.jp/aaindex/"
@@ -14,14 +14,14 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="emboss minimal"
 
-DEPEND="emboss? ( sci-biology/emboss )"
-RDEPEND="${DEPEND}"
+BDEPEND="emboss? ( sci-biology/emboss )"
+RDEPEND="${BDEPEND}"
 
 src_compile() {
 	if use emboss; then
 		mkdir AAINDEX || die
 		einfo
-		einfo "Indexing AAindex for usage with EMBOSS."
+		einfo "Indexing AAindex for usage with EMBOSS"
 		EMBOSS_DATA="." aaindexextract -auto -infile ${PN}1 || die "Indexing AAindex failed"
 		einfo
 	fi
diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index 4b221bb1a0f8..71dc6fb7d0a0 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1,5 +1,3 @@
-DIST bcftools-1.13.tar.bz2 6906796 BLAKE2B 4c02d65733d28684f9a976e082913d79dbac4463c9471fc26d8ee0cbe7ad25af429cf7d01b9771bc34309386ccd2d77ebd54fbf64ed4183d1c2ebfbc0e727afb SHA512 aa533233dd2fec2279859204be39430c4fc630137a91d57fe917fd7a220044d5202ddc3d44bcffc3bd5bd5bb64f6ea4c8ec3c31e5e1ec72399998f1e6f23a55a
-DIST bcftools-1.15.tar.bz2 6899394 BLAKE2B 44d11f5d594c547c0e3dfdcc9b2d8b55d837d17cf98465c4ce153ad0a8dce3db172276bdd24ad3dcecb3c9a064c649f3cbcc13e09194c2f655796e9a478cb27f SHA512 43fd7414c93175c6a8d69c8f8ba681a8c1f6b934ce0834dc130ff367825e60aa57736e36d379e5bdee84a01d018ee36eeeedebdbce85161745a5a063abdbca44
-EBUILD bcftools-1.13.ebuild 896 BLAKE2B 74b1387b81ec75926bd76d62033d7cf0708ac3b9a0b0b0573fec1c70efb47b84bd3fa626f3ff3144e380f07822bd3d9e56f4ddb1e09a4a09082cb1d6d3229b39 SHA512 bb0f18c2102fbfa8d5ee636c81308ea8a0ef6de80943423377846ebd2180881ca745e7eddd94be7ad7b34a2313acc43553d8a31ee474542de5d29d4874e935e4
-EBUILD bcftools-1.15.ebuild 896 BLAKE2B bbeeefad535f45694b8bce683c356e26543b63338e52ccd163ec5edbd54eb3847e5998b9f5a49012d011e9b4567b09eaa61e2a9be8f2d6a9424b543056825601 SHA512 727ffc3f6288117af87c2dfaf5597995743ad326f986777c0507d134b41895bb5039f932090a5d9962a1fcb10604c343c98c1c7b60bf0325d67bcee040820052
+DIST bcftools-1.15.1.tar.bz2 6917252 BLAKE2B d2389df8d2a1bbc48fcaccad47d77ff99d700e82e04330189e7d93acdac97a13506c2b799fbba31bdc0988977c7df7c699e7b156f3530dd35e5f052c6f977731 SHA512 60fedacc41051675d372e68146ac8fa0dc019a7fb694fda487d89e62f34edaf5ac11cca38779e9bcfcf8b3148802fadabed12f7e46ad534ad5087b8d6383f97b
+EBUILD bcftools-1.15.1.ebuild 891 BLAKE2B 532c584a7620b40136572ac4d8e73b09d9c80bd96cb39992dddc0366323cf96dd30d86bf968129f4bdd49f9f25cc6ad631327a3d4bc325e8f22242461af13806 SHA512 d585cbda0b571576139f1e4edf8c51e64665b06fd73e2ea81f5e9a94d765ff4c4438dfdc3e11ced9e6e05ccefce13997b5faa70905f43b8f27ca07f2db976af7
 MISC metadata.xml 344 BLAKE2B 37f8e82e8a5a9ad572580a7e5ae6daa6911d672f17b8526f81b236cbc2e50a32c4cd2566aaed9f5feee016d7e2de7db2a40b60616e86c3e8cae307d60cebc70e SHA512 0160c9606089d610613d71dc0aa9c9c5e5266483fdc9c407b6e0ed911eac8f8b32ffaf5a49bbb427393c8240e9868df51f0fc68b2f45467f65d9b3d54b0ddde1
diff --git a/sci-biology/bcftools/bcftools-1.13.ebuild b/sci-biology/bcftools/bcftools-1.13.ebuild
deleted file mode 100644
index b0ddd23857c2..000000000000
--- a/sci-biology/bcftools/bcftools-1.13.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{8..10} )
-
-inherit python-single-r1
-
-DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
-HOMEPAGE="http://www.htslib.org"
-SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	dev-lang/perl
-	$(python_gen_cond_dep '
-		dev-python/matplotlib[${PYTHON_USEDEP}]
-	')
-	=sci-libs/htslib-${PV}*:=
-	sys-libs/zlib
-	${PYTHON_DEPS}"
-DEPEND="${RDEPEND}"
-BDEPEND="${PYTHON_DEPS}"
-
-src_prepare() {
-	default
-
-	python_fix_shebang misc/{gff2gff,guess-ploidy,plot-roh}.py
-
-	# remove bundled htslib
-	rm -r htslib-* || die
-}
-
-src_configure() {
-	econf \
-		--disable-bcftools-plugins \
-		--disable-libgsl \
-		--with-htslib=system
-}
diff --git a/sci-biology/bcftools/bcftools-1.15.ebuild b/sci-biology/bcftools/bcftools-1.15.1.ebuild
index 4ec6b0a7e097..7de00114bfa6 100644
--- a/sci-biology/bcftools/bcftools-1.15.ebuild
+++ b/sci-biology/bcftools/bcftools-1.15.1.ebuild
@@ -18,9 +18,7 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 RDEPEND="
 	dev-lang/perl
-	$(python_gen_cond_dep '
-		dev-python/matplotlib[${PYTHON_USEDEP}]
-	')
+	$(python_gen_cond_dep 'dev-python/matplotlib[${PYTHON_USEDEP}]')
 	=sci-libs/htslib-${PV}*:=
 	sys-libs/zlib
 	${PYTHON_DEPS}"
diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
index 9739c4cfdbfd..51328d1d80c0 100644
--- a/sci-biology/biopython/Manifest
+++ b/sci-biology/biopython/Manifest
@@ -1,3 +1,3 @@
 DIST biopython-1.79.tar.gz 16738730 BLAKE2B 8c97fc23e458f7bc98b0ed0226bd6fb42f6c6f3ce03d562b13fac66c5061451595cd5bd01cad07bbe1fc6b20f4de21b0f03766b5a20e602545da888047a57185 SHA512 81e2718f4015bb038637b4d1181e6bea48018fec1e769c5f0ab75442a769336899191f1222e82e1b9569c1fac470500d7582420e5cbe9bce0056b41751adeaaa
-EBUILD biopython-1.79.ebuild 1887 BLAKE2B b3f3f50434e77dae22a744a0eeb795690a8e828167aeb0755081286de38ca4f61e661536547405cc9026ba52466c678ee1f0af291c26658eba9afec36322bb9e SHA512 74feee0feff9df45fc16f512bc48ec6c0934608783def71fd5f1373a2ad57379e77c8dd6bdd94fbe755033e5a5f9881a64e106cb1f8be738137a77584d2c83fe
+EBUILD biopython-1.79.ebuild 1889 BLAKE2B 9ffcae7f95b1c8a66cdea172842ace6a9e3d8e524dfe3b588059d509728074f7b2c8a0974513309dd517d52a68909db0a51de1ddd35e6c56818158b5e4b4e81d SHA512 a9a0a08f35b4d448655fb391c45eb428131205e6af433cea5d3c8f77763b002b2c3a35466fb30307b22927aee052960019a41f80c6106726e18a5f9516165229
 MISC metadata.xml 334 BLAKE2B 4d97c23444fdddcca57631fa2ddf4a11cfcef0accf91db65071d520f6601c0626e290e67cbf162abdefe7a74f4b410f8366a23186fc417e1fab7e9ce157d7610 SHA512 a870bd044d0e0d4e2a0c48b50f710845c6269e038790243f1d1de65b1252fd653f0f403fc55b98946df8eb27f24dfae5c84f52fcc38c969afcbdb548ccbb7a59
diff --git a/sci-biology/biopython/biopython-1.79.ebuild b/sci-biology/biopython/biopython-1.79.ebuild
index cef9a670130a..a2939330806e 100644
--- a/sci-biology/biopython/biopython-1.79.ebuild
+++ b/sci-biology/biopython/biopython-1.79.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
@@ -55,7 +55,7 @@ python_install_all() {
 pkg_postinst() {
 	optfeature_header "For database support you need to install:"
 	optfeature "MySQL database support" dev-python/mysqlclient
-	optfeature "PostgreSQL database support" dev-python/psycopg
+	optfeature "PostgreSQL database support" dev-python/psycopg:2
 
 	optfeature_header "Some applications need extra packages:"
 	optfeature "EMBOSS (The European Molecular Biology Open Software Suite)" sci-biology/emboss
diff --git a/sci-biology/cutg/Manifest b/sci-biology/cutg/Manifest
index 3a9c7ef277ba..3206e130a7c5 100644
--- a/sci-biology/cutg/Manifest
+++ b/sci-biology/cutg/Manifest
@@ -1,3 +1,3 @@
 DIST cutg-160.tar.xz 178015420 BLAKE2B acfc65f4f152b7293cb8ec8e2bfa3c2c33c5da7bcdcae5349d13122e36c4061931195034548963cb78f6350bce88f72e4fc764f119e181f1f6278ee837b65b6e SHA512 9b72283f311fb805b7b22f59f3ca8fed2ab0af72b82247900922999792c1b112dcaca9b29b265a1e0e7b9eaf9ff846a1dc4c196fb95ddbfb3ee5175755ffb8e7
-EBUILD cutg-160-r1.ebuild 1013 BLAKE2B b60896afcc643f6c0d79361839b004e641f648fdbd48ee1e697a4f6a2b4197f7dd3e752561c7e050bbfc4bd0e7577b1af04c1518bf70015e25a4b502845f602f SHA512 38fc329c36da76f23593ab61bb5a0d09d7018044d398cc014462a63e333b8437e447988acbc091afedea50386f70c9b6948deff1090855c7be74bd97c8956dff
+EBUILD cutg-160-r1.ebuild 1016 BLAKE2B 106fc8f97b36a2af8da78fd43485518c62c7756d3e4705838f848bb22b5d9a1b10d766fd175d5c668a48c5f75dedc945d29058145e619211d52d3ffd3ec62370 SHA512 752fbd3be449f714dda8f57e5fd5b1f9ca4bc32fcb08c20aad1a6a2ef8166f88f77221ff6638b40b13bf991020a8526d47fbba62659ec5ee43de0d18eb05f8da
 MISC metadata.xml 602 BLAKE2B fa4e2a4934efb0b72ffa489d8bd39b55b9fb4aa69b518a5cb8234dbaefb6ca9d5131645a508e23f97457564044e3a63d3a418f510e4dc2a3bd72bc623315d7f0 SHA512 baa307664c0b34158d243b6387ab1d2f377dca143ec5a87b6c074e5c40588c7e8f76779dde3deeb4fa920426c8754e60b23a04f3952690fa34fe3a402c6c69dd
diff --git a/sci-biology/cutg/cutg-160-r1.ebuild b/sci-biology/cutg/cutg-160-r1.ebuild
index 97abacaab1e4..417248e5890c 100644
--- a/sci-biology/cutg/cutg-160-r1.ebuild
+++ b/sci-biology/cutg/cutg-160-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -22,8 +22,8 @@ src_compile() {
 	if use emboss; then
 		mkdir CODONS || die
 		ebegin "Indexing CUTG for usage with EMBOSS."
-		EMBOSS_DATA="." cutgextract -auto -directory "${S}" || die "Indexing CUTG failed"
-		eend
+		EMBOSS_DATA="." cutgextract -auto -directory "${S}"
+		eend $? "Indexing CUTG failed" || die
 	fi
 }
 
diff --git a/sci-biology/fastx_toolkit/Manifest b/sci-biology/fastx_toolkit/Manifest
index 7d285c45f56e..8c90a18c5941 100644
--- a/sci-biology/fastx_toolkit/Manifest
+++ b/sci-biology/fastx_toolkit/Manifest
@@ -1,5 +1,5 @@
 AUX fastx_toolkit-0.0.14-fix-build-system.patch 1885 BLAKE2B f97c5e847be5e746df5b5b37d69a3b5f410e97136ed8a294b846efddb4d3ee599835b393abb5251b7230c56f109f3a7ee6f3b5092e0f37cd849e3deda3cf9229 SHA512 72fd5048a9cda4a0afb9af7ee040ed2efa5941f6f4103d0fd83465f89f636c5282381122690dd581138318ab2d2327837e4412ab9e06cd2aeeabd6db82cbf83e
 AUX fastx_toolkit-0.0.14-gcc7.patch 225 BLAKE2B 72f7b80d0cdd3ade66ae3a83340e8b31d6f8f3b71901953ae8f56e856787b546700036c1331aad884175e2a4d659588ab80097244970b764092f87ffb08d1f44 SHA512 b0e679d367f50b8f29aa759c55e2d31e859b84e53da32ef92263b258bd6163d19c44b1ed68085b1a3600e8fb19cddee9cbb5019d6050da6c028cfc291ade504c
 DIST fastx_toolkit-0.0.14.tar.bz2 543018 BLAKE2B d61456252ada507efd4cc45ff2f0d54f7a6c55b185d41eb5f5accd7e73184b8b80b2c415b38f8e4ccd687ae715191785a89e64f790fe598ba477901c12d514a1 SHA512 e1df1486e853b3ecee71e677cd6e86246a3993174016111eb84910625dc7ec11d37aff75de7ccefad1e019e75fe72050d6529add2116b759d5056b8096286c05
-EBUILD fastx_toolkit-0.0.14.ebuild 687 BLAKE2B db00581b41017886ce6c560788cb6efb3f0a45663f3cb215dfba85267c276354d418a2d036ca757f1d675af7503430b0c39fa39f9593524c7120495f432c2c38 SHA512 0254e55a40f055eb18a31a0bd0bae97e1e6c190bf73094f591cdaea15ba413d00f2f9589369eaeaa60f93f135889a1da79ae81ae32fdb765ed162bbbce152f86
+EBUILD fastx_toolkit-0.0.14-r1.ebuild 667 BLAKE2B 782a8e1f9934d73a34557f7745ed8c234eaf4a9030c39dea49301d86a13d12a8b568f8dc4433f633e71788a95e6ebddee12943ac586a6c5e0ca45d2deb735830 SHA512 106b437007c160c27e7cd22ed406ee10f0d4180734187e68c9aef871367266301196eae525037edc08dcc1d0e7f977ba142734d00a5fef49706d51f874f10c30
 MISC metadata.xml 340 BLAKE2B 96ca4df8a89f9f978a7e0babedc427c3374f336eb145f6f89bab8469488b3b5955898eb881b311aefe640fd8148c6136e723259963a62c4eb0ad0f445c3c8650 SHA512 dacca026042185296c0069b5e249b277e21843a5d5c32bfb1c5cefcdc5aa4aa5ddd7cd4f0fdf3e65230d7c76d405bfee5831fc24df2684849424bf93ec3f16f0
diff --git a/sci-biology/fastx_toolkit/fastx_toolkit-0.0.14.ebuild b/sci-biology/fastx_toolkit/fastx_toolkit-0.0.14-r1.ebuild
index d9012a54e166..24c67f24c536 100644
--- a/sci-biology/fastx_toolkit/fastx_toolkit-0.0.14.ebuild
+++ b/sci-biology/fastx_toolkit/fastx_toolkit-0.0.14-r1.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=8
 
 inherit autotools
 
@@ -12,16 +12,14 @@ SRC_URI="https://github.com/agordon/fastx_toolkit/releases/download/${PV}/${P}.t
 LICENSE="AGPL-3"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 
-DEPEND="
-	sci-biology/libgtextutils
-	virtual/pkgconfig"
+DEPEND="sci-biology/libgtextutils:="
 RDEPEND="
+	${DEPEND}
 	dev-perl/PerlIO-gzip
 	dev-perl/GDGraph
-	sci-biology/libgtextutils:=
 	sci-visualization/gnuplot"
+BDEPEND="virtual/pkgconfig"
 
 PATCHES=(
 	"${FILESDIR}"/${P}-fix-build-system.patch
diff --git a/sci-biology/libgtextutils/Manifest b/sci-biology/libgtextutils/Manifest
index 9f30234d87ca..28fd096088cc 100644
--- a/sci-biology/libgtextutils/Manifest
+++ b/sci-biology/libgtextutils/Manifest
@@ -1,5 +1,5 @@
 AUX libgtextutils-0.6.1-fix-build-system.patch 1719 BLAKE2B 993f1e68f960853a264d5e9b9cd1352df123424f4cfbf79f2cbb4451ff6ec0fed985a1b184bfe200e036ef65a07f7e4e258f731cc12d708ed68f278b2934904c SHA512 9889fe99addb820f049800fa8aec414c28d87bbaae209af0e45614d4592d578a7309376aa69f58e7c9879ad64a20be417e9d05ebf45ec4af2729c591517e610e
 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
+EBUILD libgtextutils-0.6.1-r1.ebuild 538 BLAKE2B b21cf5c1ac3c9f5587ac3618546a9db22ad9be70c45aa78e72958e0d0c58e29d4d40b5862fe43cce533a731fc54107f07d1a8c394a1795d4092002687696a6f8 SHA512 a1638effaeb0db9d67413b516ea21bf19aa366c7629cb8733c946a30ea15c52dd1f1cbf3cafe205a795cc4143e4a3ca8046c19956018f6c5f32df92e332a63f9
 MISC metadata.xml 385 BLAKE2B 9ea1955bdfe1dfba6a10590f53882a0db769438fd2a9e258e9f30df8a9f4eed827b671b3e8ba51428de37e88e2423d78f82d4e9223605be9de79291f5ea6df7b SHA512 05c7969622e9535b1ec2b791dd4dd8496ea96d51f9ccbd6ba98ca807124e5eb4ddc3fb6104817aaccd50446d990c06e13517a76b1e5192ae5b992f138ecaaa44
diff --git a/sci-biology/libgtextutils/libgtextutils-0.6.1.ebuild b/sci-biology/libgtextutils/libgtextutils-0.6.1-r1.ebuild
index 8f0455e5322c..2ffb1c3338b8 100644
--- a/sci-biology/libgtextutils/libgtextutils-0.6.1.ebuild
+++ b/sci-biology/libgtextutils/libgtextutils-0.6.1-r1.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=8
 
 inherit autotools
 
@@ -12,7 +12,6 @@ SRC_URI="http://hannonlab.cshl.edu/fastx_toolkit/${P}.tar.bz2"
 LICENSE="AGPL-3"
 SLOT="0/0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 
 PATCHES=(
 	"${FILESDIR}"/${P}-fix-build-system.patch
@@ -24,13 +23,8 @@ src_prepare() {
 	eautoreconf
 }
 
-src_configure() {
-	econf --disable-static
-}
-
 src_install() {
 	default
 
-	# package installs .pc files
-	find "${D}" -name '*.la' -delete || die
+	find "${ED}" -name '*.la' -delete || die
 }
diff --git a/sci-biology/mafft/Manifest b/sci-biology/mafft/Manifest
index 4525adca70e4..623b6345d4f9 100644
--- a/sci-biology/mafft/Manifest
+++ b/sci-biology/mafft/Manifest
@@ -1,4 +1,3 @@
-AUX mafft-7.305-fno-common.patch 185 BLAKE2B 1230b838fa93b560fe0b0d9dd124cec2daf92d1dbcd75e371af92cc070bf62cea23c7c9ee3d87798de70911e4c316e444c875e79b3cf93f757b7a6fdfe2e279b SHA512 fe9de41eaea3bf799065fac88b336ec45af3c5b4d7d5272a477d99165b88c27f7e7765908e7955eaa0a74bb59df10a0ab77b822fd29bebca601d124938f3489d
-DIST mafft-7.305-without-extensions-src.tgz 458448 BLAKE2B 5d5fa86e6faa472182c5c48f42056d81bbf545db56426969ff44a24146d4189a7650e85ea6e9fa8b40bb613392bf53bc5dea26012a86eb873c18bee91e6fdc41 SHA512 2aa351dd9b329024f183642cd98287239d12a00a2a65937e072560cba54925bed1fab19fafc734d9a5048ff85151560193ddb0796e0d7510d921fafc4553ebb9
-EBUILD mafft-7.305.ebuild 2056 BLAKE2B 4d6599082401880abfa483f5fc23b9379dfca2fd410d948138b0005fcd43737b0dd92777d19b606a9c9ef77a03fdb667122eb8d56d053753d3e83452d0a24a6d SHA512 a6fc3af370b4e677d49372aa7c3908e33574cf7eeaf7cb02025c89b8654152a8cb622850d0f28f880f27cbb3e4743933798c9d843060383339c56ddb6b7792c5
+DIST mafft-7.490-without-extensions-src.tgz 605510 BLAKE2B f432ea3001f1d9c18cecea50d19f48570ffe7edf56e64088f8854acc1ee17fd7c1696244133f90ae0bf916f4499becfbfa8a770ca51a370219191f2a29f73db4 SHA512 dd87b731fdee48828da93c715ef480de474870de2fa42727e8d34b62bc136fb486dd9079ca2acdf1745f0a621fe4f413e25c05f7534f1673b6f9c1199ce70b8e
+EBUILD mafft-7.490.ebuild 1864 BLAKE2B 1590550e268ebd45f9a5ea166369c2874e8782c135f38311ac1fc3c10548da7c0630ec13bd0d2062344642b6876734c1a68858d6c545f127cf8e23f7e7eb85a7 SHA512 324e752905d927cd5dc9823e6d40a0c91d9002e4dedc95bf9c7d0463c14d85022f239764400e409416cba8eab7b2c921362f1292ea9327fb175449d304f12a0f
 MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de
diff --git a/sci-biology/mafft/files/mafft-7.305-fno-common.patch b/sci-biology/mafft/files/mafft-7.305-fno-common.patch
deleted file mode 100644
index 0287b6367f8b..000000000000
--- a/sci-biology/mafft/files/mafft-7.305-fno-common.patch
+++ /dev/null
@@ -1,8 +0,0 @@
---- a/core/mltaln.h
-+++ b/core/mltaln.h
-@@ -336,4 +336,4 @@
- 
- extern double sueff_global;
- extern double lenfaca, lenfacb, lenfacc, lenfacd;
--int maxl, tsize;
-+extern int maxl, tsize;
diff --git a/sci-biology/mafft/mafft-7.305.ebuild b/sci-biology/mafft/mafft-7.490.ebuild
index 105b5ce9883e..a5ff0a5764d6 100644
--- a/sci-biology/mafft/mafft-7.305.ebuild
+++ b/sci-biology/mafft/mafft-7.490.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=8
 
 inherit flag-o-matic toolchain-funcs
 
@@ -10,21 +10,15 @@ EXTENSIONS="-without-extensions"
 DESCRIPTION="Multiple sequence alignments using a variety of algorithms"
 HOMEPAGE="https://mafft.cbrc.jp/alignment/software/index.html"
 SRC_URI="https://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz"
+S="${WORKDIR}/${P}${EXTENSIONS}"
 
 LICENSE="BSD"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-IUSE="threads"
-
-S="${WORKDIR}/${P}${EXTENSIONS}"
-PATCHES=( "${FILESDIR}"/${PN}-7.305-fno-common.patch )
 
 src_prepare() {
 	default
 
-	append-cflags -Wno-unused-result
-	use threads && append-cppflags -Denablemultithread
-
 	sed \
 		-e 's/(PREFIX)\/man/(PREFIX)\/share\/man/' \
 		-e 's:$(LDFLAGS)::g' \
@@ -34,10 +28,12 @@ src_prepare() {
 		-i core/Makefile || die
 }
 
+src_configure() {
+	append-cflags -Wno-unused-result
+}
+
 src_compile() {
-	cd core || die
-	emake \
-		$(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \
+	emake -C core \
 		PREFIX="${EPREFIX}"/usr \
 		CC="$(tc-getCC)" \
 		CFLAGS="${CFLAGS}"
@@ -61,9 +57,6 @@ src_test() {
 }
 
 src_install() {
-	DOCS=( readme )
-	einstalldocs
-
-	cd core || die
-	emake PREFIX="${ED%/}/usr" install
+	emake -C core DESTDIR="${D}" STRIP=":" PREFIX="${EPREFIX}"/usr install
+	dodoc readme
 }
diff --git a/sci-biology/mosaik/Manifest b/sci-biology/mosaik/Manifest
index 3ce1cb1c5223..e4124e1c6468 100644
--- a/sci-biology/mosaik/Manifest
+++ b/sci-biology/mosaik/Manifest
@@ -1,8 +1,9 @@
 AUX mosaik-2.2.30-Wformat-security.patch 3296 BLAKE2B f75a4dde6fb88e0175989ff9ddfd6dfd2450eb0df24e4e5f60943fbd9fcc40b798d7d7bca2d57e25c4201f6a7cbf8eb66b2f3573f54fc05b5b3a46e3e01a1ddb SHA512 e72fa7cac8798425ac1dd4d3358bfdff640cc831a01531749ee2fad99f8b53bd64e8c7fcdddce205e9f6dd312cc74376afcba395ab8d508d92416190b7eed1df
 AUX mosaik-2.2.30-fix-build-system.patch 8056 BLAKE2B 4c795e790718dca2a46e25fd67499612ad1226c6e6ad73d7543cd1c1aa1dacabc0ed77ade798b2602d8f661eeb9cd7b033bd8945d4384d01e2d279762f40fa14 SHA512 ed4a6efd9fb2fabd6c24adaa5894fde80024d8ee930450711c07388b62969a41e801f052ee88d7890355f1ddfc5ef9fbb40bfdabfbfae364c64c673ce08958c6
 AUX mosaik-2.2.30-gcc11.patch 1189 BLAKE2B 29b54205cf90bdf0815d16876db32a2109493f659cc06d4f0f3a9dffb3dcc6ef119a0b567197541226cd77ab8a33e8fab5f7d53ee107ff5ec987493e93ac8db8 SHA512 57aed21aca8b1c5c512bd77d7f5bf1a9846b9f30cb72890f614670930139c5ac8817d2b88b5e39c943c604c736a1a27ee91a01c3f0cdd9a534d8b4185cbdfcf6
+AUX mosaik-2.2.30-gcc12-time.patch 277 BLAKE2B e2fbd8f573238f78b9730c1e349a30b48ca8b38955a31a311ebc6e19ce69126afce95fb1fde197f8354304f684fe6ce2f64e0b34b6ffd0004f59faa20a692c2a SHA512 ee640a56833866feaa75917c223409541d98ff2aeaa016d3568409d1692f9d254e35ac85da7dfd56f062f8c94877197755c665be011bf5bb532f70c7ef6b41e6
 AUX mosaik-2.2.30-gcc7.patch 1252 BLAKE2B 896d662807c223cc69eacfa2e1fcb457c696e0d198dfa718f0f7eb9060d9c0491a18017901385227c2c0906e02c61a8fb9a9deb71f228d4c6195cdf0b5696515 SHA512 fc7dd31d2fcce7a4e624e759ee08b8997757bf4ce3ae3f98080e6e6252dfc647de4848f6a736b35090e8c8da37618baaf08e19be9ddfc408bbc5f7200f44cbba
 AUX mosaik-2.2.30-remove-platform-code.patch 399 BLAKE2B ec711a9b112efa87b2811e4545bfc58716393576915f71167ff700ccd809be4fad5e07bac7a5cb7df911615f4c996284cd711c1d1cb62c5a18695e719e6574c6 SHA512 4aec709660b41fb61bb9219a587255a5f416992a4478c2a7eb67374d1425f0a4e0b4d356827a9214e2f2718b635169c95d3288bf10388a74e50d498c39c2f259
 DIST mosaik-2.2.30.tar.gz 4387062 BLAKE2B 6f373aeae4f68be2455556e7f79a5850e25d804bd482d85a846b44f8adaabb2513ffc7ced774f5ead6dbc8fc9dca9d64f76f83bc5b55b1be4073a8cf309e121b SHA512 1acf534e6defc927fc22937a7bae6786e85ab7aa234b4209169f1267f1a9bd68415b441c6aed2e7cd667f694a562017ebc9457251958f77386259ffce9812b10
-EBUILD mosaik-2.2.30.ebuild 1137 BLAKE2B 74fd6384486e9cf6c92dd5b8aa96f9c1398ed80431eff23d748db70c9627450845164b1f3b4d496bdffdfeb79a36bac610558a0516057a771e1681dfa6f1eda6 SHA512 d59fbcc3b31cb8b94aba101e9743b522b7ef853ddf198608d022a3a0a091d55aeeeb2ca44a2bb7266fdd2980153a863cb0ae3bc21cd4ba9f2b2ab4a190b14513
+EBUILD mosaik-2.2.30.ebuild 1174 BLAKE2B 4ea2485f378fef5b2b0d67f42693b5c1ae3544df23ca97b1d0412bea7a06cbad083503a75a96b57208c23d270870d8d6404c638928e687fc422267cbb0551d30 SHA512 efcf58bbbec183a7b634e4f00b8abcd8cc33b5c4312a258e6d3376d790a11f696a91987f34b035c61d751fc04ea901f95911660c25c021d7425cd8287018f4fe
 MISC metadata.xml 415 BLAKE2B a1ecb68c52443bc41061019f246474a105586328dec03e3c26ec9f2ad9688a69b1bb7b2de1c9cd4bae1039927e2285c50dc7a0165e2464cfdef86b66e278becb SHA512 117976f4cd570fc0e481aa7419fecc7ddcbf3ac4484efc05bd293db239798e1591e6d775e9290f492b003860d135aa8a0bd08f93e7088410ebaac73b2fa8a37c
diff --git a/sci-biology/mosaik/files/mosaik-2.2.30-gcc12-time.patch b/sci-biology/mosaik/files/mosaik-2.2.30-gcc12-time.patch
new file mode 100644
index 000000000000..1bc63bfd4776
--- /dev/null
+++ b/sci-biology/mosaik/files/mosaik-2.2.30-gcc12-time.patch
@@ -0,0 +1,11 @@
+https://bugs.gentoo.org/851669
+--- a/CommonSource/Utilities/SafeFunctions.h
++++ b/CommonSource/Utilities/SafeFunctions.h
+@@ -17,6 +17,7 @@
+ #include <cstdio>
+ #include <cstdarg>
+ #include <cstring>
++#include <ctime>
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <errno.h>
diff --git a/sci-biology/mosaik/mosaik-2.2.30.ebuild b/sci-biology/mosaik/mosaik-2.2.30.ebuild
index 0aee0a2cfbd9..a929f1160f67 100644
--- a/sci-biology/mosaik/mosaik-2.2.30.ebuild
+++ b/sci-biology/mosaik/mosaik-2.2.30.ebuild
@@ -20,6 +20,7 @@ PATCHES=(
 	"${FILESDIR}"/${P}-Wformat-security.patch
 	"${FILESDIR}"/${P}-gcc7.patch
 	"${FILESDIR}"/${P}-gcc11.patch
+	"${FILESDIR}"/${P}-gcc12-time.patch
 )
 
 src_configure() {
diff --git a/sci-biology/primer3/Manifest b/sci-biology/primer3/Manifest
index a8ab456f2e41..f6611ee55622 100644
--- a/sci-biology/primer3/Manifest
+++ b/sci-biology/primer3/Manifest
@@ -1,5 +1,5 @@
-AUX primer3-2.3.4-buildsystem.patch 5460 BLAKE2B 1e7680501e9c4a74c599f52caa787751f74f6a4fd028d8273d00364c7d2e59c0a641d343386e6ff7598d7d0bbfa66ce80412d300646cd54d0112ce118ff8422d SHA512 52f539f52c92e5e21c3166da62813c6fa9f90fd9e0ca87d9ab67658496e13f4b5ce5c53770802cb1cdd21044244e21f09b0de2ce3c6d3db0182b3d9cbf64a037
+AUX primer3-2.3.7-buildsystem.patch 5855 BLAKE2B 74395e3ecaf16e10bce493337681f2ab7b2b6016bb784854777c2a00cb09f9ab1275d9955d622bdd2d887bb7763a5d2addd7064fafb00b4d2102463491a112d1 SHA512 4cc3492b1c93e2d736493fe04e18b544dc9487ded5e6ebb4bc64e19b38ca125aafa4732e80cfab83d6467ba4d8e11ca7c59342188c7e4464e9a674e7ac26c59f
 AUX primer3-2.3.7-gcc7.patch 421 BLAKE2B 3f861ecb493ce9673cdebac9ea224a0588bd3b758d72a7ef4e41d4efb929db444a8c2808a55ead42dcb174265a926c021a89dd83dc8a1e5ba4eb5ed26280be43 SHA512 c818cd80e4762ef46e4e52acd27f4eb966d676995154b3503c98d8defb545c3dd7ea307c8946b5b5c462dd7f5dee6abc254cea59e21e2229cb779a7178dec04d
 DIST primer3-2.3.7.tar.gz 1658090 BLAKE2B 0bc9a0faa19c4ac3b48680d65b0d91a13d8bdd651ad3a0d344b4f50ce8dc510fe7a22665192751fb2c8ff6282b560daf4540a02cc70482dba0fcc344f7727e37 SHA512 f227f80d395cb682a9d65e0ac3afdcacb8385d66e721b9163fda939a9c788a7c6907273f6223782702b48d7df66ea2331114f6303fcd29e3b3c50a2717da2fa7
-EBUILD primer3-2.3.7.ebuild 1116 BLAKE2B 1aff6985a9ad3ad0ee523f18061c7f31bd26d3cc6c72f440a15c0ae2bc21f84ad360f51b021079efde09ef386f1c92f4dec7d155b970247e9ee87c376e0b36ee SHA512 56b127a7282b1c9dcc514758899d46e23ad79178f402beee270a03959eb01ae28e03720fba1c4dfbfc050e2932a15f5e2254705a048acf8ef8f7db0998327e61
+EBUILD primer3-2.3.7-r1.ebuild 1080 BLAKE2B 89a48de004236190b5708cf8e1ce256af3b6f6a5cbd1ed03b2f54bba5ff162cb88dd81117cce9737714b53ea2ad247f3d07da02b2d912006f903aabdb4d3d6af SHA512 a879dc2c2cc5b8799e05334226f1aa612c2534bb94404d3ce4d4649e6b7322890a549c56f961c869cfe3cdd2d0e613345dd70dbc11ee3e42af34fb8955c936b6
 MISC metadata.xml 798 BLAKE2B b57850f7ea949d9e026fba81ffb483b542f725aa96477b013ac635ef058c42fa925cc104ccac89e07cb655939364effc5193c9665264145b6d892593c133856a SHA512 1f1541c1a632b9ad37359bb60cb7e4fa4e583d9eafa10f9ec43450c30ade6ae88289ca62c793ec63da376306ab383b399ff4ab89483bcc43588aab78249100f8
diff --git a/sci-biology/primer3/files/primer3-2.3.4-buildsystem.patch b/sci-biology/primer3/files/primer3-2.3.7-buildsystem.patch
index cf47b35af502..8f9bf4042758 100644
--- a/sci-biology/primer3/files/primer3-2.3.4-buildsystem.patch
+++ b/sci-biology/primer3/files/primer3-2.3.7-buildsystem.patch
@@ -1,11 +1,6 @@
- src/Makefile | 61 ++++++++++++++++++++++++++++++------------------------------
- 1 file changed, 31 insertions(+), 30 deletions(-)
-
-diff --git a/src/Makefile b/src/Makefile
-index 607ab45..a88adf4 100644
 --- a/src/Makefile
 +++ b/src/Makefile
-@@ -52,15 +52,16 @@ TESTOPTS=
+@@ -52,15 +52,13 @@
  WINMAKE=mingw32-make
  
  LDLIBS     = -lm
@@ -15,56 +10,66 @@ index 607ab45..a88adf4 100644
 -O_OPTS     = -O2
 -CC_OPTS    = -g -Wall -D__USE_FIXED_PROTOTYPES__
 -P_DEFINES  =
-+AR         ?= ar
-+CC         ?= gcc
-+CXX        ?= g++
+-
+-CFLAGS  = $(CC_OPTS) $(O_OPTS)
+-LDFLAGS = -g
 +O_OPTS     ?= 
 +CC_OPTS    ?= -Wall -D__USE_FIXED_PROTOTYPES__
 +P_DEFINES  ?=
- 
--CFLAGS  = $(CC_OPTS) $(O_OPTS)
--LDFLAGS = -g
++
 +CFLAGS    += $(CC_OPTS) $(O_OPTS)
 +CXXFLAGS  += $(CC_OPTS) $(O_OPTS)
 +LDFLAGS   +=
  # Note, for profiling, use
  # make O_OPTS='-pg -O0' LDFLAGS='-g -pg'
  
-@@ -92,7 +93,7 @@ LIBPRIMER3      = libprimer3.a
+@@ -92,7 +90,6 @@
  LIBPRIMER3_DYN  = libprimer3.so.1.0.0
  LIBRARIES       = $(LIBPRIMER3) $(LIBDPAL) $(LIBTHAL) $(LIBOLIGOTM) 
  DYNLIBS         = $(LIBPRIMER3_DYN) $(LIBDPAL_DYN) $(LIBTHAL_DYN) $(LIBOLIGOTM_DYN)
 -RANLIB          = ranlib
-+RANLIB          ?= ranlib
  
  PRIMER_OBJECTS1=primer3_boulder_main.o\
                  format_output.o\
-@@ -127,85 +128,85 @@ $(LIBOLIGOTM): oligotm.o
- 	$(RANLIB) $@
+@@ -119,93 +116,89 @@
+ ifeq ($(TESTOPTS),--windows)
+ 	cd ..\test & $(WINMAKE) clean TESTOPTS=$(TESTOPTS)
+ else
+-	cd ../test/; make clean
++	cd ../test/ && $(MAKE) clean
+ endif
+ 
+ $(LIBOLIGOTM): oligotm.o
+-	$(AR) rv $@ oligotm.o
+-	$(RANLIB) $@
++	$(AR) rcs $@ oligotm.o
  
  $(LIBOLIGOTM_LIB): oligotm.o
 -	$(CC) -shared -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o
 +	$(CC) $(LDFLAGS) -shared -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o
  
  $(LIBDPAL): dpal_primer.o
- 	$(AR) rv $@ dpal_primer.o
- 	$(RANLIB) $@
+-	$(AR) rv $@ dpal_primer.o
+-	$(RANLIB) $@
++	$(AR) rcs $@ dpal_primer.o
  
  $(LIBDPAL_DYN): dpal_primer.o
 -	$(CC) -shared -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o
 +	$(CC) $(LDFLAGS) -shared -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o
  
  $(LIBTHAL): thal_primer.o
- 	$(AR) rv $@ thal_primer.o
- 	$(RANLIB) $@
+-	$(AR) rv $@ thal_primer.o
+-	$(RANLIB) $@
++	$(AR) rcs $@ thal_primer.o
  
  $(LIBTHAL_DYN): thal_primer.o
 -	$(CC) -shared -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o
 +	$(CC) $(LDFLAGS) -shared -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o
  
  $(LIBPRIMER3): libprimer3.o p3_seq_lib.o
- 	$(AR) rv $@ libprimer3.o p3_seq_lib.o
- 	$(RANLIB) $@
+-	$(AR) rv $@ libprimer3.o p3_seq_lib.o
+-	$(RANLIB) $@
++	$(AR) rcs $@ libprimer3.o p3_seq_lib.o
  
  $(LIBPRIMER3_DYN): libprimer3.o p3_seq_lib.o
 -	$(CC) -shared -W1,-soname,liprimer3.so.1 -o $(LIBPRIMER3_DYN) libprimer3.o p3_seq_lib.o
@@ -146,3 +151,23 @@ index 607ab45..a88adf4 100644
  
  primer_test: test
  
+@@ -213,7 +206,7 @@
+ ifeq ($(TESTOPTS),--windows)
+ 	cd ..\test & $(WINMAKE) TESTOPTS=$(TESTOPTS)
+ else
+-	cd ../test; make test
++	cd ../test && $(MAKE) test
+ endif
+ 
+ # ======================================================================
+--- a/test/Makefile
++++ b/test/Makefile
+@@ -86,7 +86,7 @@
+ ifeq ($(TESTOPTS),--windows)
+ 	cd ..\src & $(WINMAKE)
+ else
+-	cd ../src; make
++	cd ../src && $(MAKE)
+ endif
+ 
+ clean:
diff --git a/sci-biology/primer3/primer3-2.3.7.ebuild b/sci-biology/primer3/primer3-2.3.7-r1.ebuild
index 4c6c9ce7bf44..b36e9291db94 100644
--- a/sci-biology/primer3/primer3-2.3.7.ebuild
+++ b/sci-biology/primer3/primer3-2.3.7-r1.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=8
 
 inherit toolchain-funcs
 
@@ -13,12 +13,11 @@ LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
 
-DEPEND="dev-lang/perl"
-RDEPEND=""
+BDEPEND="dev-lang/perl"
 
 PATCHES=(
-	"${FILESDIR}"/${PN}-2.3.4-buildsystem.patch
-	"${FILESDIR}"/${PN}-2.3.7-gcc7.patch
+	"${FILESDIR}"/${P}-buildsystem.patch
+	"${FILESDIR}"/${P}-gcc7.patch
 )
 
 src_prepare() {
@@ -29,7 +28,7 @@ src_prepare() {
 }
 
 src_configure() {
-	tc-export CC CXX AR RANLIB
+	tc-export AR CC CXX
 }
 
 src_compile() {
@@ -38,7 +37,7 @@ src_compile() {
 
 src_test() {
 	emake -C test | tee "${T}"/test.log
-	grep -q "\[FAILED\]" && die "test failed. See "${T}"/test.log"
+	grep -q "\[FAILED\]" && die "test failed. See ${T}/test.log"
 }
 
 src_install() {
diff --git a/sci-biology/prints/Manifest b/sci-biology/prints/Manifest
index aff9f9a9349a..eee2b82ee3af 100644
--- a/sci-biology/prints/Manifest
+++ b/sci-biology/prints/Manifest
@@ -1,3 +1,3 @@
 DIST prints-39.0.tar.bz2 26277011 BLAKE2B a815e93f41694c76d62c6809f05457b286333ad103852eb493b0e723c54a088825f262a64ff8db0e47ff8a97c37fbf670c6c7967aabb303fd7d454982e4dff5e SHA512 4ea48a2a0892739ac4e32a6309922b7b4ad01f9d2f847f7c42c7e6a00e8f56bab0771d272adcaed1f85516ea93245fb8c7864762c4699023a8d85d61c012bdc7
-EBUILD prints-39.0-r1.ebuild 1044 BLAKE2B 607892ae4ae91c40570da9f3d8cf2f422f404a05b2bac7afbde751c011c88545092464e0661e80fd4f2852d4f0fccb9565483f6bd1cd3e828290c5595c7c14dd SHA512 056458b00dbcee0f8720e1a74512ab513836d3ec762cd0b764c4fe3c2a8f450b76af21bff93e75fd37d0b00317bac7087c24032683125b26bbf9699b62f9cf9d
+EBUILD prints-39.0-r2.ebuild 1043 BLAKE2B ce22669244961c26b533922140280ce3e6561f2318086f1302e51d79383984f8f48fe001e63098883f8008e45d557f3bec710114ef55a526c38469f8d2aa4ec9 SHA512 e0e25d1a5611530ab9eb8a21443a66e8847f61c37051ae3a7a895c661fbf325c1743c7a059421c9d35f9c2577d1096c3f5acb76dfe4ddfd50e06038f005c4fc8
 MISC metadata.xml 884 BLAKE2B 2f44013f0925749670db4c405034f7aaa4bf2ffc4cab4cde22595489eeba2ebb03eb4a4c79a87d1b33d7bd89742c232940c313fd693c8551b2e670902ae1c336 SHA512 ce4a4c14cd10efdd051fa1089b8ef1692d56ee73f8755bf03dc8d28e88b4d8ee5c64064dac1bcc7f60a19eabd0494c0903708d898a59cdc99c725b8575c0d4cc
diff --git a/sci-biology/prints/prints-39.0-r1.ebuild b/sci-biology/prints/prints-39.0-r2.ebuild
index f9833579e71f..9fb721842798 100644
--- a/sci-biology/prints/prints-39.0-r1.ebuild
+++ b/sci-biology/prints/prints-39.0-r2.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=8
 
 MY_PV="${PV/./_}"
 
@@ -16,8 +16,8 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="emboss minimal"
 
-DEPEND="emboss? ( sci-biology/emboss )"
-RDEPEND="${DEPEND}"
+BDEPEND="emboss? ( sci-biology/emboss )"
+RDEPEND="${BDEPEND}"
 
 src_compile() {
 	if use emboss; then
diff --git a/sci-biology/prosite/Manifest b/sci-biology/prosite/Manifest
index 9e438a2cf3f1..a591785fae7d 100644
--- a/sci-biology/prosite/Manifest
+++ b/sci-biology/prosite/Manifest
@@ -1,3 +1,3 @@
 DIST prosite2017_02.tar.bz2 9234253 BLAKE2B e818ba766a0761336b3f06b173fe98133e3c6fd9ee21198234fdfaf711ac2bf6ee68513c073a09765b050ffdcfe8c8d83a2ae91b89558db18ac6039798201c68 SHA512 2b8a26a44d62d17108afc43a3ab65d024f76e41ea9c9f477024700621323d2606fcaec54411e1d3f4ddad40717ad9ce3a1989ffd92220e0d3c2acf70400d2e43
-EBUILD prosite-2017.02.ebuild 981 BLAKE2B 6ec1b47ed30ef51891901ea2f67ec0e0729903672437824d0b06f05a8fed9083a750336190b5d396c91c7f5bcfb2fcec849889475a12dfd186351ac711122df9 SHA512 0f0c805052daa587cd8699965230fc36dd118b53855fe13ad8127b7556192778dfd05e21145b0ac13922cc84c3cab88c758f0f8fb874d90a3221e41e1169568b
+EBUILD prosite-2017.02-r1.ebuild 981 BLAKE2B fa82b2f47b8f03b9c9d3d612b0133f653e8dff44c80fec30bb868b46cc44a477e14717b15b1bf5647f004bb2dfa746fd2b9e49a6dbd1be601adfd3c95727b8ff SHA512 ffc9ad456bc2da48562b422857a3bab21119cac5eba788549378328eb5d7574d248d16408aeb93de5a6087f8bc7e3ef93d3a33fe7962cdf3f88584c0f1a83fa3
 MISC metadata.xml 818 BLAKE2B 586074d5bd8c663a273350e8c6daaabb8a3e0b5db1c4b32e891612b20c03c354c3bacf8fe5469d80bac19580c9dbf7c78ffb23ce8acbeef7b3378e33ad488c2a SHA512 672884e4a9c279c2bef33494c8692ea475ca05010505c10c22564206575302dc3dd2beae96fdc588e1a539cceb5673b4ed49abdb8fccb5e1d82b9b6a805e22be
diff --git a/sci-biology/prosite/prosite-2017.02.ebuild b/sci-biology/prosite/prosite-2017.02-r1.ebuild
index 6003b17cff85..a5efbed1626b 100644
--- a/sci-biology/prosite/prosite-2017.02.ebuild
+++ b/sci-biology/prosite/prosite-2017.02-r1.ebuild
@@ -1,11 +1,12 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=8
 
 DESCRIPTION="A protein families and domains database"
 HOMEPAGE="https://prosite.expasy.org/"
 SRC_URI="ftp://ftp.expasy.org/databases/prosite/old_releases/prosite${PV//./_}.tar.bz2"
+S="${WORKDIR}"
 
 LICENSE="swiss-prot"
 SLOT="0"
@@ -14,10 +15,8 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="emboss minimal"
 
-DEPEND="emboss? ( sci-biology/emboss )"
-RDEPEND="${DEPEND}"
-
-S=${WORKDIR}
+BDEPEND="emboss? ( sci-biology/emboss )"
+RDEPEND="${BDEPEND}"
 
 src_compile() {
 	if use emboss; then
diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index c990614486e8..01d3cd352fa6 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1,3 +1,3 @@
-DIST pysam-0.17.0.tar.gz 3579324 BLAKE2B 6b88fe771350f20fa7c90a4c02c60fefd6a34d979c687fce1e34a17e1ff203c7d2d07e36b64f7a73f99676b805334df7f049932ce15e26362a5214da03435d64 SHA512 16740f08fb68a1f24656454b834dd9ac52ad9f864f307564566fc244bbd2efb7cb17107b2e85ca5c56af817918a138d1c071533de1b80e5bba42b01bbad7f552
-EBUILD pysam-0.17.0.ebuild 1586 BLAKE2B 38351a74c0a57348fdc1999f35b10cd8645160175386b94885e49bbd99bc64f577c326d04e09ba56abce0c0c01331276ebef080fbf519dbfbae41960b6ccc61a SHA512 bd0e336603727c67cd363c628daa9aa9b95e6fe2dbcc06425fcbcf03bd8bd4bd79e651b637434cdbbecd85ebc2841647863910e31f94dd9641694fb4c68de8d4
+DIST pysam-0.19.1.gh.tar.gz 3649711 BLAKE2B dac3ab5a86ef95048e966fc007a0aa1c96ca8498f7c2672c2ed024f34b508bac42048e58b8ae0b538cea137a51e1874bb5c2c4976c7f3dc657a4c2cf5f9a27fb SHA512 719f3a15e7dd277a90cce7f938b674ff86ef6b8f2d3440c3a0bf2ea22c4fbc2b3c9e0cf297d958c99e09dcd6e9905f32e8c632158aa8d5af8210e79705e1c479
+EBUILD pysam-0.19.1.ebuild 1597 BLAKE2B 37065e16bd756380808b1eb48c78296e2652e7aaa59dbb63ed66ea81049c9c4daa6516c4cd20fd572213e3d43c34a5e118ae11a6eb42c7da61f7b67c8b5b651b SHA512 27ef49bddd395ca67db60a2b34bcc9dc184c035b42c66410274f47d47cf03e6f712231b89cbd18657157b5d8a511b82fdc4272a599f71eca5f879f895fb8d93e
 MISC metadata.xml 442 BLAKE2B e3d339868a09d8930ff6d83f414f8166ed283a66d83d5b0fed0031024db151b17b1347f5e015f2b9c2152a041e2beb70696362be9b4e3fc225078bc5c520ad58 SHA512 4b1d08c5524e1bb04129e0d38f0584654b34979024afd2cf15bd482654ca8fac9c82e6db0661f7370f9fefa6949f1291ba3c18a9dca5d5041bd6f76554fa33c7
diff --git a/sci-biology/pysam/pysam-0.17.0.ebuild b/sci-biology/pysam/pysam-0.19.1.ebuild
index afdc4777e20e..41afb5307775 100644
--- a/sci-biology/pysam/pysam-0.17.0.ebuild
+++ b/sci-biology/pysam/pysam-0.19.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_{8..11} )
 
 inherit distutils-r1
 
@@ -11,20 +11,20 @@ DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping for
 HOMEPAGE="
 	https://github.com/pysam-developers/pysam
 	https://pypi.org/project/pysam/"
-SRC_URI="https://github.com/pysam-developers/pysam/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/pysam-developers/pysam/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
 
 LICENSE="MIT"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 
-RDEPEND="=sci-libs/htslib-1.13*:="
+RDEPEND="=sci-libs/htslib-1.15.1*:="
 DEPEND="${RDEPEND}
 	dev-python/cython[${PYTHON_USEDEP}]
 	dev-python/setuptools[${PYTHON_USEDEP}]"
 BDEPEND="
 	test? (
-		=sci-biology/bcftools-1.13*
-		=sci-biology/samtools-1.13*
+		=sci-biology/bcftools-1.15.1*
+		=sci-biology/samtools-1.15.1*
 	)"
 
 distutils_enable_tests pytest
@@ -40,8 +40,8 @@ EPYTEST_DESELECT=(
 python_prepare_all() {
 	# unbundle htslib
 	export HTSLIB_MODE="external"
-	export HTSLIB_INCLUDE_DIR="${EPREFIX}"/usr/include
-	export HTSLIB_LIBRARY_DIR="${EPREFIX}"/usr/$(get_libdir)
+	export HTSLIB_INCLUDE_DIR="${ESYSROOT}"/usr/include
+	export HTSLIB_LIBRARY_DIR="${ESYSROOT}"/usr/$(get_libdir)
 	rm -r htslib || die
 
 	# prevent setup.py from adding RPATHs (except $ORIGIN)
diff --git a/sci-biology/rebase/Manifest b/sci-biology/rebase/Manifest
index 04e08f78ab4e..f7450ce0bedb 100644
--- a/sci-biology/rebase/Manifest
+++ b/sci-biology/rebase/Manifest
@@ -1,3 +1,3 @@
 DIST rebase-1901.tar.xz 182532548 BLAKE2B 5ac8d26ab057bcd21dc9c57abeb226ac70cfabb156b48a51f820789626257be55bb21c9eb2099e6e55b1cfe3691480df0ec9b3f4b18b50ba2712b986c6d057b4 SHA512 1e3553e59c3520190754cb40bb0900e466d9ffd206e6460d3262a7d7d2af8aab0e28f3e60187665362824fa3730211c0e2119016ce5fed49095f9de46c7f25d4
-EBUILD rebase-1901.ebuild 1088 BLAKE2B 9364896661246fc5d46a524874f95e395d3648239e89d2de265356e4b949ecd275c4d3e808e7bd60af27aa95257c1a92deac21eb1258e87bb318ba25896c1ada SHA512 d0e971497259f6989f4bd73ee9a5719276e200372d943dbc6c9f9eec4de7e8d71ffa413b19b162c7b028332a82b516e572515bc9e9e0e638a39933b6fdd0a831
+EBUILD rebase-1901-r1.ebuild 1082 BLAKE2B 664fe7c05d97d493ed451965467fbcf3a644cca64229c96a8f186e66382de36433c4dbd77430e94ec6a65e3dd411bd5e53562ced6aa386f3b6b2e6b4b6129e67 SHA512 b801b2b467b8107a6e37bc2356ea9f1ef9b8216dd5d10b7f9fe5630eff2aaa900507aaf3a14111c44786d7d4a84bbe7a2d4028c15c378b9a8d600d31c2b46b98
 MISC metadata.xml 908 BLAKE2B c5b8a6f961e426788c9a6b84d01c468fa7613b52da52bf4ba4d057f0c1966ac1092acd219160e96bc2778673ebe82398471044a34e775ded0a5d72221adf363b SHA512 0c9bc87df88e5485350071b4b219dbf90958de0394444fda093fdef18ede4378c0463b6e81bd48c5c162ae0c581d186c693d3474f895a4e4de59d36c3f5a0588
diff --git a/sci-biology/rebase/rebase-1901.ebuild b/sci-biology/rebase/rebase-1901-r1.ebuild
index f85a4b1698bb..a993a8c2c44a 100644
--- a/sci-biology/rebase/rebase-1901.ebuild
+++ b/sci-biology/rebase/rebase-1901-r1.ebuild
@@ -1,32 +1,32 @@
-# Copyright 1999-2018 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=8
 
-MY_PV=${PV#1}
+MY_PV="${PV#1}"
 
 DESCRIPTION="A restriction enzyme database"
 HOMEPAGE="http://rebase.neb.com"
 SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
 
-SLOT="0"
 LICENSE="public-domain"
+SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris"
 IUSE="emboss minimal"
-
-RDEPEND="emboss? ( >=sci-biology/emboss-5.0.0 )"
-DEPEND="${RDEPEND}"
-
 RESTRICT="binchecks strip"
 
+BDEPEND="emboss? ( sci-biology/emboss )"
+REPEND="${BDEPEND}"
+
 src_compile() {
 	if use emboss; then
-		echo; einfo "Indexing Rebase for usage with EMBOSS."
+		einfo
+		einfo "Indexing Rebase for usage with EMBOSS"
 		mkdir REBASE || die
 		EMBOSS_DATA="." rebaseextract -auto -infile withrefm.${MY_PV} \
 				-protofile proto.${MY_PV} -equivalences \
-				|| die "Indexing Rebase failed."
-		echo
+				|| die "Indexing Rebase failed"
+		einfo
 	fi
 }
 
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 2f378c0428d2..1c8c07cfbbda 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,8 +1,6 @@
 AUX samtools-0.1.20-buildsystem.patch 6737 BLAKE2B 71445f57735903bccc2720a32f42b27093f670e383d2d194b5692b1ba536e3df44204711cf4574b3933e5ce00605b661b1a36d79ca7f193ce36816271a3f8214 SHA512 ecb05971fbea4570ec161a165cb581b38ed727bb7e5b769862984bf035414cd564ab809882dc3272f8b192feeb86e29247d7327afa73ff668b01c03c58bb177d
 DIST samtools-0.1.20.tar.gz 566387 BLAKE2B a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2 SHA512 15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
-DIST samtools-1.13.tar.bz2 7984998 BLAKE2B e46161c43d4ea51c3ef1d9ed74c40c21b70aef80aa903a49b94b3d468f9211e9147281204eb61b9843c071f09ead08c924e3d624d4df76a1d02ba9ceb318399a SHA512 647fbad2935dfc3e4f85da257a6ee59af40078024a3b77f117dada5f55846e381a096db3cf62a63c04ae95dfc9fadb1d515b8d618e6388bc93f0b2ac85eaf6ea
-DIST samtools-1.15.tar.bz2 7832423 BLAKE2B 5bdfaec750faaa8d84eb601e75f513d726724d3f2f882d9e16edfe4802bd1ad8fee5f1208c93f450fff37125998cb50ff2247fce514d94e580d5d292555da930 SHA512 21ce4aff90514a393e685cbb6fa7833c88010b18846be0190d49e8da70995252c2e17b5108113d2313a752706618041c74680efc9ed5539b97ebc0589cb6c6e7
+DIST samtools-1.15.1.tar.bz2 7831692 BLAKE2B 0fe94ff05075b219c77d0da8500c64bdffd53927950b5a67f8708c5c326ebc90a40c193b3bcf0baf3d09baed6fa596d9d024cb529340c6887de88614c9ff4bd6 SHA512 54a8a394b6b5231bd942236ec353027caaf48b4552a00b35573a1e71d680320d8140a73409bb76066c82e86fe62cf74f2f8f2f1a1e4aec96e4e8b9aff0d44a46
 EBUILD samtools-0.1.20-r4.ebuild 2049 BLAKE2B d377712eaca931258b37645e6a6b3cc379fdb550ef83a0c272a3eb564d7753185fea53416973e4fdf2c25b79475a81ae72b646ce22c570c934e4eabce8a9ded6 SHA512 c0d387f715ebf1f746ea4e4a7eab85a86ef0bff646c9a69639b17ef02e93c39982941d7eb811a6d67b0e635c9c4e05924d2b89a6809c3bd0592db91894dab4aa
-EBUILD samtools-1.13.ebuild 886 BLAKE2B e96ccbff6d7310e4691118bc191a020525a92aa49dd24478be11185e1767788849bae9d575d59dc139f77b0c977222684c82a45487b4d10d77da20347f5170b5 SHA512 3eb07532ae9d7995279663d8e09602e30a5055b13388ceb83aa369e52bb2291f21014f60dccc5569825f6e7683801b737557539270007bc16a12015d86c17fec
-EBUILD samtools-1.15.ebuild 886 BLAKE2B 8d87c954c2f16dc2ad093d41c6b123a7b46473afe662dae9a69c8bb5200b805ce8abba43b8b6ce47caf4647bc2b566d53b613bc786190ad77feca26be538cce3 SHA512 0a6db9a7e3d943043fad935a41451ee58d28feb66eb9263a12d4e5adeae187e4aba8d4e3529eabeaf3b8fb9705172a32d65fa77a5b866a805721fb87d6b253c8
+EBUILD samtools-1.15.1.ebuild 917 BLAKE2B ce0e56d9fd4d45f32d53e014648ea154b55363f9b48f1293f1687c2f2c668d7f498bb346bc291bf30c0be23499326cc38eb93065114c932269808825ece939e6 SHA512 dee59486e4942a45450b41aa1df296264dcc6396463a8e2e3ce93f4d7fb14acae252d4798492a19912999ca621c2188ef25ee6063fee7c9bc673ba57169a99c6
 MISC metadata.xml 409 BLAKE2B c94eab9ebda4844beb471694106e353ccbbaca53e69de680301c6cfab3f3b6224ec94fcd631c9de2811d309463e5ee6decf2e443bfc68921f3362c6a312cd3af SHA512 fb2d3686e1ee70e4e80266a26603b3e52b680b1537a4569493a3a0511b93e2acdb2be3136df7ae54905a9f86fb7e53fa054607262751ebd8f54903f1905dad24
diff --git a/sci-biology/samtools/samtools-1.13.ebuild b/sci-biology/samtools/samtools-1.13.ebuild
deleted file mode 100644
index 3165c7b7381c..000000000000
--- a/sci-biology/samtools/samtools-1.13.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
-HOMEPAGE="http://www.htslib.org/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-
-RDEPEND="
-	dev-lang/perl
-	=sci-libs/htslib-${PV}*:=
-	sys-libs/ncurses:=[unicode(+)]
-	sys-libs/zlib"
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-src_prepare() {
-	default
-
-	# remove bundled htslib
-	rm -r htslib-* || die
-}
-
-src_configure() {
-	econf \
-		--with-ncurses \
-		--with-htslib=system \
-		CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)"
-}
-
-src_compile() {
-	emake AR="$(tc-getAR)"
-}
-
-src_install() {
-	default
-
-	dodoc -r examples
-	docompress -x /usr/share/doc/${PF}/examples
-}
diff --git a/sci-biology/samtools/samtools-1.15.ebuild b/sci-biology/samtools/samtools-1.15.1.ebuild
index 74aee5acaaa2..21d2b8a5077d 100644
--- a/sci-biology/samtools/samtools-1.15.ebuild
+++ b/sci-biology/samtools/samtools-1.15.1.ebuild
@@ -7,7 +7,7 @@ inherit toolchain-funcs
 
 DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
 HOMEPAGE="http://www.htslib.org/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
+SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"
 
 LICENSE="MIT"
 SLOT="0"
diff --git a/sci-biology/seqan/Manifest b/sci-biology/seqan/Manifest
index 161725918529..e2f7fa97b28e 100644
--- a/sci-biology/seqan/Manifest
+++ b/sci-biology/seqan/Manifest
@@ -3,6 +3,6 @@ AUX seqan-2.4.0-fix-pthread.patch 541 BLAKE2B 16d42c72d6ea0654ba6727ce1007b89d3f
 AUX seqan-2.4.0-installpaths.patch 1661 BLAKE2B 6548f5b7cd0e26d187ff61a8e8e3db008700b5131a57228f0cd567642fae12778ff2a77960fa318f6244a80f94e771ebeb218fee8eaf6ec1a4c827e972d1ac90 SHA512 9b2100cd2a4069fd9022723ca6972251d2307f4886b3dcdf68816e78d38359d8767e20e19b4170213abb905bc3b570ed257e025e063a475ff3406d8f1e8d3313
 DIST seqan-v2.4.0.tar.gz 109626901 BLAKE2B a10b5ee9a95667f560a8c2aec3808131f5f838f3c07d56584f4b29e9622912bf3d00b958b02db7c9d62dd52d9d08a171abcccef7f50cddf0407538168cf2c592 SHA512 f92cfc97304581920850c5d49fe4336f7c3855e99c3bcb035b6172fa7307e08e6f06fb06d1cd8f5b447c3220fc7f669684fbfe25641b43e9f6953999cf9ddd4b
 DIST seqan3-3.1.0-Source.tar.xz 2656120 BLAKE2B 6a18844f62d935fdbd7008822f83ffeefd596e93b704a8c7b0f478dec87b2265ff532be107ebfd1adc248e2b1db65e4b86cdce2e989c7ac097054d43633a24bd SHA512 686d0ffbe32951e7f831e399a3eab35b7249f45408b7de27ee9cfd6a012215603f033afa6082c8a81783de1cc7c93d3ffbae42cabc122d3b77988c236a049ffd
-EBUILD seqan-2.4.0-r1.ebuild 1592 BLAKE2B 98ca9dce72bca2d2069eb94a9f998c5f7d25d303c053930264a51231dc3972243ef7433d9a750f9b0d4b26950a7adc7ccf7f863a8a87f3393821f72f285591bd SHA512 e63405b1c8ab04bf2e635601b27effa62b116e4d5c14f4244f2a5cbd1047e22c2b4c8793602535225ad426ccf8f69b0f68967d47db81b65ae3c0abeee6b5d057
-EBUILD seqan-3.1.0.ebuild 631 BLAKE2B e06d561fa203a74aad25ccc47bcf158ec84e8576c6e0d95cd34f9042607bc3f78c4aa81d5453d4d92ba8af4d0744051f4c8fc1a0c17c87025c18984e9be0b8c3 SHA512 32ba2e7f44d5e6269dda19475b7c75d5ec2b8b97657472d046013129c358aee94b1c49154f2a3a308df8ea66c848f93e76978e70563e8f4f0657792822a8f524
+EBUILD seqan-2.4.0-r1.ebuild 1674 BLAKE2B 706295eac1c0a74f33823afc6968b5ac971f578a7f2bf99a690d4e351ee2a82a52fe125095b0bb3982f1c39d500ca83b5e367f6ad30a0e38373f2647a2c40022 SHA512 42ee3ad643cb535fa8e0831debff9e8c33a71c510f722f83140de0a9177e8d33b677af3b7569ee59242ec5e26189a73a84ec8eae83a8ae5d89d7071c8c3610e9
+EBUILD seqan-3.1.0.ebuild 636 BLAKE2B b8bc983979a79cded722d13d4b8206472a5542ef917896b8a08592ff5e1f1e481b9f526258a0ae30b1e090374599cba744160b2fdc3709579d5d22018b7bc544 SHA512 4446b71a6ca1d5d9d7212f9916c8750b01d98ffd426c2f441234635b41b6431c7497aa3601814366a42e93317b864baddd9e14990474ecea3194a74de887e907
 MISC metadata.xml 373 BLAKE2B 1fd7eb9978c4b1e8fee1edb30bef8e18de04fdbc6677f8442e0cb706512b7a49c0681737ade6b9c96f67e234907890694bafe8edfb6c35ef25cd570920ea07f7 SHA512 b273e12542b160e215945d85504a3e9ba9973b68e6870f9d27104024fb09b8e293d8f6f71f8a005ad35690a530cec608e5e01a5158b747e1003ce9c87add8486
diff --git a/sci-biology/seqan/seqan-2.4.0-r1.ebuild b/sci-biology/seqan/seqan-2.4.0-r1.ebuild
index 76a73d759bef..933b55e04eab 100644
--- a/sci-biology/seqan/seqan-2.4.0-r1.ebuild
+++ b/sci-biology/seqan/seqan-2.4.0-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -37,6 +37,10 @@ PATCHES=(
 	"${FILESDIR}"/${P}-cmake-add_library-static.patch
 )
 
+pkg_pretend() {
+	[[ ${MERGE_TYPE} != binary ]] && use tools && tc-check-openmp
+}
+
 pkg_setup() {
 	if [[ ${MERGE_TYPE} != binary ]]; then
 		use tools && tc-check-openmp
diff --git a/sci-biology/seqan/seqan-3.1.0.ebuild b/sci-biology/seqan/seqan-3.1.0.ebuild
index fc9dd78e4233..976430bec641 100644
--- a/sci-biology/seqan/seqan-3.1.0.ebuild
+++ b/sci-biology/seqan/seqan-3.1.0.ebuild
@@ -12,7 +12,7 @@ S="${WORKDIR}/seqan3-${PV}-Source"
 
 LICENSE="BSD GPL-3"
 SLOT="0"
-KEYWORDS="~amd64 ~amd64-linux"
+KEYWORDS="~amd64 ~x86 ~amd64-linux"
 IUSE="cpu_flags_x86_sse4_2"
 REQUIRED_USE="cpu_flags_x86_sse4_2"
author	V3n3RiX <venerix@koprulu.sector>	2022-06-29 12:04:12 +0100
committer	V3n3RiX <venerix@koprulu.sector>	2022-06-29 12:04:12 +0100
commit	0f558761aa2dee1017b4751e4017205e015a9560 (patch)
tree	037df795519468a25d9362b4e95cdaeb84eb1cf9 /sci-biology
parent	752d6256e5204b958b0ef7905675a940b5e9172f (diff)