gentoo resync : 20.03.2022

author: V3n3RiX <venerix@koprulu.sector> 2022-03-20 00:40:44 +0000
committer: V3n3RiX <venerix@koprulu.sector> 2022-03-20 00:40:44 +0000
commit: 4cbcc855382a06088e2f016f62cafdbcb7e40665 (patch)
tree: 356496503d52354aa6d9f2d36126302fed5f3a73 /sci-biology
parent: fcc5224904648a8e6eb528d7603154160a20022f (diff)
84 files changed, 854 insertions, 511 deletions
diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 04f9efb648be..75ba74eeea3d 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/STAR/Manifest b/sci-biology/STAR/Manifest
index 3fb4a0879865..8f7c05fc8c7f 100644
--- a/sci-biology/STAR/Manifest
+++ b/sci-biology/STAR/Manifest
@@ -1,4 +1,7 @@
 AUX STAR-2.5.3a-fix-build-system.patch 5318 BLAKE2B 28a839eb61a5b1adef804249328c7917dca2ec765f00a48b90aa42d7da3ca393f7726b7aafdb6d0429a55fe696bd51b0e06d85ef6e50a3a4f5874c731b194f1e SHA512 412bdf74c50869f470f3d7452d3799e92a45da198e50ecad63688e4c24444a25f044d464e462e19ba41c5abf590865e43542cd1b60a1f3948bf357be468e8441
+AUX STAR-2.7.10a-fix-build-system.patch 7176 BLAKE2B 24a14d2d8af26565a3a7f754e9633c54c2cdaf72bf4e3b4fe3390a3790be16620117f576abf82d91e8816478fc1a012e7424ab6d93bb6161b975acd08627d3f0 SHA512 4d854336b2e0c61ca1ac604cded7f08e484974e1ec6d78928e5eb21eb7adb0ae3f6ec9deb3dc050dcffe1732f9076f2b4cddad7aa18ccad20f9232c9e11d1856
 DIST STAR-2.5.3a.tar.gz 9857460 BLAKE2B 32cc633862e6e81f5a5bdfc59986dca74e8adc4970a11a06c501065c5ad9cb37fc788f8e67ab2353292e683c8c385778cd0ffee69c0b15803796dbc445013a43 SHA512 8bd86ad384f2c0331fd701873b02641301f4205a5ff0fceeb800d425da42c53b6c61a74500d37fee7fc13a5bff10e1fb44b9142811883b8f5cd012f51f1f9fdf
+DIST STAR-2.7.10a.tar.gz 12270915 BLAKE2B 51a9cf2c838cfeb313df9e5024b53cd5a89088f08ac88c8dc57a9e08cd3ba394e46ffe86a8ff3b9484b25b681ecd960098c06d879e772d21afe8cc2d0d35175d SHA512 19a5f3c25d147bcd96cf68249d275dad7fd11425031a40c97c7ae15846f55839ced897d541ed60b426a6bf089d968ac86625af774db3950dc459035ac2b659c9
 EBUILD STAR-2.5.3a.ebuild 881 BLAKE2B 692466b512aaa3da2e2323f90576d47c2f5e694a4ac8ee8ce2d887435a1ef964dcab9adbdb3c3f88b43cc5463b258635be0f2b542485ee16bc9ec32b655fcf65 SHA512 9b8a80c19b0da8e697c913a8401c08a71a07511477c71b1dd20748e5487e8bb5ab870c37058d49abc27a5ac56722e98b2d784431c19f7173275b82f41f9a2663
+EBUILD STAR-2.7.10a.ebuild 970 BLAKE2B 63bc2b4656d4e672faf819f83bd2a930851e0b5c2d1ff422c5a72b655d5c68515a317675c59df2ff9256e4653351f1f180d9c94dbd256c89810d31ca3940b9ad SHA512 76841ebb6bb3a7c15da15c2124287959938beeb1c6e1a5fa362c476283b51dca49bcca83be9e10d5f39702f23b01ee131f8ab2f568b986e529fc006e65a25ffb
 MISC metadata.xml 341 BLAKE2B 5cf54dcbc5013bbebd80edd8d03456553ec6f7f52527d076f921916ebe9b862c97aae6f641741b81ac44cfc84356ca13e19dd3be2b63c075923a701c22e695c1 SHA512 888d00d5873390206f21aa9daaf78fc8c3f9b88e528c38ca7696779b221fd21acc6beadf543c14e16f74cb600cab479bc3f9bba8625214480583f369e6ea67a8
diff --git a/sci-biology/STAR/STAR-2.7.10a.ebuild b/sci-biology/STAR/STAR-2.7.10a.ebuild
new file mode 100644
index 000000000000..7239efcfe45c
--- /dev/null
+++ b/sci-biology/STAR/STAR-2.7.10a.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays"
+HOMEPAGE="https://github.com/alexdobin/STAR"
+SRC_URI="https://github.com/alexdobin/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="sci-libs/htslib:="
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+PATCHES=( "${FILESDIR}"/${PN}-2.7.10a-fix-build-system.patch )
+DOCS=( README.md CHANGES.md RELEASEnotes.md doc/STARmanual.pdf )
+
+pkg_pretend() {
+	[[ ${MERGE_TYPE} != binary ]] && tc-check-openmp
+}
+
+pkg_setup() {
+	[[ ${MERGE_TYPE} != binary ]] && tc-check-openmp
+}
+
+src_prepare() {
+	default
+
+	# remove bundled htslib
+	rm -r source/htslib || die
+}
+
+src_configure() {
+	tc-export CC CXX PKG_CONFIG
+}
+
+src_compile() {
+	emake -C source STAR
+}
+
+src_install() {
+	dobin source/STAR
+	einstalldocs
+}
diff --git a/sci-biology/STAR/files/STAR-2.7.10a-fix-build-system.patch b/sci-biology/STAR/files/STAR-2.7.10a-fix-build-system.patch
new file mode 100644
index 000000000000..0f06c94fb109
--- /dev/null
+++ b/sci-biology/STAR/files/STAR-2.7.10a-fix-build-system.patch
@@ -0,0 +1,195 @@
+--- a/source/bam_cat.c
++++ b/source/bam_cat.c
+@@ -52,8 +52,8 @@
+ #include <stdlib.h>
+ #include <unistd.h>
+ 
+-#include "htslib/htslib/bgzf.h"
+-#include "htslib/htslib/sam.h"
++#include <htslib/bgzf.h>
++#include <htslib/sam.h>
+ #include <cstring>
+ 
+ #define BUF_SIZE 0x10000
+--- a/source/bam_cat.h
++++ b/source/bam_cat.h
+@@ -1,7 +1,7 @@
+ #ifndef CODE_bam_cat
+ #define CODE_bam_cat
+ 
+-#include "htslib/htslib/sam.h"
++#include <htslib/sam.h>
+ 
+ int bam_cat(int nfn, char * const *fn, const bam_hdr_t *h, const char* outbam);
+ 
+--- a/source/BAMfunctions.cpp
++++ b/source/BAMfunctions.cpp
+@@ -1,5 +1,5 @@
+ #include "BAMfunctions.h"
+-#include "htslib/htslib/kstring.h"
++#include <htslib/kstring.h>
+ 
+ 
+ string bam_cigarString (bam1_t *b) {//output CIGAR string
+--- a/source/bamRemoveDuplicates.cpp
++++ b/source/bamRemoveDuplicates.cpp
+@@ -1,7 +1,7 @@
+ #include <unordered_map>
+ #include "bamRemoveDuplicates.h"
+ #include <iostream>
+-#include "htslib/htslib/sam.h"
++#include <htslib/sam.h>
+ #include "IncludeDefine.h"
+ #include SAMTOOLS_BGZF_H
+ #include "ErrorWarning.h"
+--- a/source/IncludeDefine.h
++++ b/source/IncludeDefine.h
+@@ -30,8 +30,8 @@
+ #define ERROR_OUT string ( __FILE__ ) +":"+ to_string ( (uint) __LINE__ ) +":"+ string ( __FUNCTION__ )
+ 
+ //external libs
+-#define SAMTOOLS_BGZF_H "htslib/htslib/bgzf.h"
+-#define SAMTOOLS_SAM_H  "htslib/htslib/sam.h"
++#define SAMTOOLS_BGZF_H <htslib/bgzf.h>
++#define SAMTOOLS_SAM_H  <htslib/sam.h>
+ 
+ using namespace std;
+ 
+--- a/source/Makefile
++++ b/source/Makefile
+@@ -12,11 +12,7 @@
+ CXX ?= g++
+ 
+ # pre-defined flags
+-LDFLAGS_shared := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz
+-LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz
+-LDFLAGS_Mac :=-pthread -lz htslib/libhts.a
+-LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a
+-LDFLAGS_gdb := $(LDFLAGS_shared)
++LIBS := -pthread -lhts -lz
+ 
+ DATE_FMT = --iso-8601=seconds
+ ifdef SOURCE_DATE_EPOCH
+@@ -27,7 +23,7 @@
+ 
+ BUILD_PLACE ?= $(HOSTNAME):$(shell pwd)
+ 
+-COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(BUILD_DATE) $(BUILD_PLACE)"'
++COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE=""'
+ 
+ 
+ GIT_CHECK := $(shell git status 1> /dev/null 2> /dev/null && echo 0)
+@@ -41,13 +37,13 @@
+ 
+ # Defaults, can be overridden by make arguments or environment
+ CXXFLAGS ?= -pipe -Wall -Wextra
+-CFLAGS ?= -pipe -Wall -Wextra -O3
++CFLAGS ?= -pipe -Wall -Wextra
+ CXXFLAGS_SIMD ?= -mavx2
+ 
+ # Unconditionally set essential flags and optimization options
+ CXXFLAGS_common := -std=c++11 -fopenmp $(COMPTIMEPLACE) $(GIT_BRANCH_COMMIT_DIFF)
+-CXXFLAGS_main := -O3 $(CXXFLAGS_common)
+-CXXFLAGS_gdb := -O0 -g3 $(CXXFLAGS_common)
++CXXFLAGS_main := $(CXXFLAGS_common)
++CXXFLAGS_gdb := $(CXXFLAGS_common)
+ 
+ ##########################################################################################################
+ OBJECTS = SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall_multiMappers.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o \
+@@ -130,7 +126,7 @@
+ ifneq ($(MAKECMDGOALS),clean_solo)
+ ifneq ($(MAKECMDGOALS),STARforMac)
+ ifneq ($(MAKECMDGOALS),STARforMacGDB)
+-Depend.list: $(SOURCES) parametersDefault.xxd htslib
++Depend.list: $(SOURCES) parametersDefault.xxd
+ 	echo $(SOURCES)
+ 	'rm' -f ./Depend.list
+ 	$(CXX) $(CXXFLAGS_common) -MM $^ >> Depend.list
+@@ -142,57 +138,43 @@
+ endif
+ endif
+ 
+-htslib : htslib/libhts.a
+-
+-htslib/libhts.a :
+-	$(MAKE) -C htslib lib-static
+-
+ parametersDefault.xxd: parametersDefault
+ 	xxd -i parametersDefault > parametersDefault.xxd
+ 
+ STAR$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS)
+-STAR$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
+ STAR$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS)
+-	$(CXX) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
++	$(CXX) $(LDFLAGS) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS)
+ 
+ STARstatic$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS)
+-STARstatic$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS)
+ STARstatic$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS)
+-	$(CXX) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
++	$(CXX) $(LDFLAGS) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS)
+ 
+ STARlong$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)
+-STARlong$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
+ STARlong$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS)
+-	$(CXX) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
++	$(CXX) $(LDFLAGS) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS)
+ 
+ STARlongStatic$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)
+-STARlongStatic$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS)
+ STARlongStatic$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS)
+-	$(CXX) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
++	$(CXX) $(LDFLAGS) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS)
+ 
+ 
+ 
+ POSIXSHARED : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -DPOSIX_SHARED_MEM $(CXXFLAGS)
+-POSIXSHARED : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
+ POSIXSHARED : Depend.list parametersDefault.xxd $(OBJECTS)
+-	$(CXX) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
++	$(CXX) $(LDFLAGS) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS)
+ 
+ gdb : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_gdb) $(CXXFLAGS)
+-gdb : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_gdb) $(LDFLAGS)
+ gdb : Depend.list parametersDefault.xxd $(OBJECTS)
+-	$(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
++	$(CXX) $(LDFLAGS) -o STAR $(CXXFLAGS) $(OBJECTS) $(LIBS)
+ 
+ gdb-long : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_gdb) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)
+-gdb-long : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_gdb) $(LDFLAGS)
+ gdb-long : Depend.list parametersDefault.xxd $(OBJECTS)
+-	$(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
++	$(CXX) $(LDFLAGS) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LIBS)
+ 
+ STARforMacStatic : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_MAC' $(CXXFLAGS)
+-STARforMacStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_Mac_static) $(LDFLAGS)
+ STARforMacStatic : Depend.list parametersDefault.xxd $(OBJECTS)
+-	$(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
++	$(CXX) $(LDFLAGS) -o STAR $(CXXFLAGS) $(OBJECTS) $(LIBS)
+ 
+ STARlongForMacStatic : CXXFLAGS := -D'COMPILE_FOR_LONG_READS' $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_MAC' $(CXXFLAGS)
+-STARlongForMacStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_Mac_static) $(LDFLAGS)
+ STARlongForMacStatic : Depend.list parametersDefault.xxd $(OBJECTS)
+-	$(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
++	$(CXX) $(LDFLAGS) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LIBS)
+--- a/source/signalFromBAM.h
++++ b/source/signalFromBAM.h
+@@ -1,6 +1,6 @@
+ #ifndef CODE_signalFromBAM
+ #define CODE_signalFromBAM
+-#include "htslib/htslib/sam.h"
++#include <htslib/sam.h>
+ #include  <fstream>
+ #include <string>
+ #include "Stats.h"
+--- a/source/STAR.cpp
++++ b/source/STAR.cpp
+@@ -29,7 +29,7 @@
+ 
+ #include "twoPassRunPass1.h"
+ 
+-#include "htslib/htslib/sam.h"
++#include <htslib/sam.h>
+ #include "parametersDefault.xxd"
+ 
+ void usage(int usageType) {
diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index 572ee9298e8a..4b221bb1a0f8 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1,3 +1,5 @@
 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
 MISC metadata.xml 344 BLAKE2B 37f8e82e8a5a9ad572580a7e5ae6daa6911d672f17b8526f81b236cbc2e50a32c4cd2566aaed9f5feee016d7e2de7db2a40b60616e86c3e8cae307d60cebc70e SHA512 0160c9606089d610613d71dc0aa9c9c5e5266483fdc9c407b6e0ed911eac8f8b32ffaf5a49bbb427393c8240e9868df51f0fc68b2f45467f65d9b3d54b0ddde1
diff --git a/sci-biology/bcftools/bcftools-1.15.ebuild b/sci-biology/bcftools/bcftools-1.15.ebuild
new file mode 100644
index 000000000000..4ec6b0a7e097
--- /dev/null
+++ b/sci-biology/bcftools/bcftools-1.15.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2022 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/bedtools/Manifest b/sci-biology/bedtools/Manifest
index 31952fc3668b..c806da84e07a 100644
--- a/sci-biology/bedtools/Manifest
+++ b/sci-biology/bedtools/Manifest
@@ -1,8 +1,5 @@
 AUX bedtools-2.29.2-buildsystem.patch 2002 BLAKE2B 7925c788858515ec4454ece3823680e99053790aeb30b2dcab06a52f6827c3cca85543c899fbabcc75ac5872cdfe632c9c5bf8b5dc24146c50a00dbd4ea56a1d SHA512 a76ec350aedfce4926f8fbaed742a992f81b2280727383f7aefd7f3629f7e04f300f9d3d9cce2a98c6fe2767cb6d2261074bd6242d6d5ae26a5095730c054a85
 AUX bedtools-2.29.2-python.patch 1235 BLAKE2B 34381a33be915f983b2c93f04954486e7611f56b1bc3259887e5ac3aa54107e3392a784980779948136f97424485a31a53959f2f76b573cb44b7d83023c69005 SHA512 8c22230e3bc1eaeb7d85379eab402eb1e95443f88f60a9c04f628cd38a96b91d138149a1a46d941189a8cd6097e075a8bde8d4ad883757ec7b2c129268cdb37f
-AUX bedtools-2.29.2-samtools-1.10.patch 659 BLAKE2B 5ec159e0a9bc9f4b5d661bcf93ba8a0cd08f62e8e6d3f92229b71d5dfb122d89eb6a68637e12394e6082cf9be99014787f9a780f7fb547ec61f5f8b8d405713d SHA512 0160c54ad3781e17df53b2525cbf0e6b5d1ebf5ce07257b16c35eed525623aa46b5ee32f158ab64b2e18a283eba0f8331a521ac8382cc31ca03cd88d1376c057
-DIST bedtools-2.29.2.tar.gz 20646485 BLAKE2B cdfff7a0f5300f31c2487e98bd28dc7e8b7f3575a098947c2c7b3a6e30272a80d35f07997d3a00bd42d91bf60899f32358b25b054b6f40b761cc66e2788508b3 SHA512 138ff029995e9889d2e43f884fa15bb5614d11cf75dfe18e2999aad0915e80f49444e67c9934c92ca8e28caad399394b493db8a1bee9f5304413a8c41c22c6d5
 DIST bedtools-2.30.0.tar.gz 20648577 BLAKE2B 042bc31e846455cb1c20199f7a27a3850851f7c256a45b1e674c7aa48ecedc211b0fdfc5e25f915b588f21447e757ebff2bba16a65905bb10d3c88e4b17b1db1 SHA512 3993243cc3db12d194d6220aeae200e6af843d6d32d4e5a9a82d04c9d119f8ed47e618e87241edfa82cfac081bc9a40ada18f097d21b0cafc5f912ae012701c9
-EBUILD bedtools-2.29.2.ebuild 1232 BLAKE2B 77bf05d3c03b9f38a3ebd4ef4028666a2ae445aa9605f5d1d457bf7a26bdfc362fedfc5906994fddc24b29e18214484e3b464ce3d8644bc4ccb006dfb76051be SHA512 862ee4bbaee73a9274a8f9c9bbadedbd00f3d6d59380abcd48d35c9d922e7e2a849e4c8357f65657e55258afea611dbe34ed77735f1cb79fab5bada5cbfa79af
 EBUILD bedtools-2.30.0.ebuild 1184 BLAKE2B 128c85d2fae5a45068f3c6f0c64b93902dcfaf0eb1464fbc8546ac7b62827d62fbd01cab422e23153cc9e2975f3d43f628305a3986caf6df36923059f45d6a6c SHA512 77c36f5abcf230a4eff2f7215998ed8188d0e6dda8c1c1de94c16e6dd3b7b480bb6abed0d6bcf0baec2ebbb1d678c51a0c1b16aebc34785e49245e5d30b0626a
 MISC metadata.xml 407 BLAKE2B f3c2890ef1648dcfc7ae92c56fec8c111de2cb82ba4c8f7402756fa9db6f2ee43fa3ccb9a75db5d1e2ca7893ed3041efc22452814944e0e56f1a589353b47774 SHA512 925406053fd5c1aecb5ef26c522b3f410c6f9a639dc1ab7790a4124513c870af5b818adc53875c93ab19a36d444b8fb23c5ef10cc11ed50080785bbe60d1eb98
diff --git a/sci-biology/bedtools/bedtools-2.29.2.ebuild b/sci-biology/bedtools/bedtools-2.29.2.ebuild
deleted file mode 100644
index c90bc512fe34..000000000000
--- a/sci-biology/bedtools/bedtools-2.29.2.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit python-any-r1 toolchain-funcs
-
-DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats"
-HOMEPAGE="https://bedtools.readthedocs.io/"
-SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
-	app-arch/bzip2
-	app-arch/xz-utils
-	sys-libs/zlib"
-DEPEND="${RDEPEND}"
-BDEPEND="
-	${PYTHON_DEPS}
-	test? ( >=sci-biology/samtools-1.10:0 )"
-
-S="${WORKDIR}"/${PN}2
-
-# bedtools2 has a *terrible* build system and development practices.
-# Upstream has forked htslib 1.9 and extended it by adding clever callbacks
-# that make unbundling it nigh impossible. There are no signs of upstream porting
-# their fork to 1.10, which means we're stuck with the bundled version.
-PATCHES=(
-	"${FILESDIR}"/${PN}-2.29.2-buildsystem.patch
-	"${FILESDIR}"/${PN}-2.29.2-python.patch
-	"${FILESDIR}"/${PN}-2.29.2-samtools-1.10.patch
-)
-
-src_configure() {
-	tc-export AR CC CXX RANLIB
-}
-
-src_install() {
-	default
-
-	insinto /usr/share/${PN}
-	doins -r genomes
-}
diff --git a/sci-biology/bedtools/files/bedtools-2.29.2-samtools-1.10.patch b/sci-biology/bedtools/files/bedtools-2.29.2-samtools-1.10.patch
deleted file mode 100644
index 7cc0e23de2d4..000000000000
--- a/sci-biology/bedtools/files/bedtools-2.29.2-samtools-1.10.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- a/test/intersect/new_test-intersect.sh
-+++ b/test/intersect/new_test-intersect.sh
-@@ -975,8 +975,8 @@
- #  Test intersect preserve the text header in bam
- ############################################################
- echo -e "    intersect.new.t78...\c"
--echo -e "@HD     VN:1.5  SO:coordinate" > exp
--echo "@HD     VN:1.5  SO:coordinate" | samtools view -b  | $BT intersect -a /dev/stdin -b b.bed | samtools view -H >obs
-+echo -e "@HD	VN:1.5	SO:coordinate" > exp
-+echo "@HD	VN:1.5	SO:coordinate" | samtools view --no-PG -b | $BT intersect -a /dev/stdin -b b.bed | samtools view --no-PG -H >obs
- check exp obs
- rm exp obs
- [[ $FAILURES -eq 0 ]] || exit 1;
diff --git a/sci-biology/bioperl-network/Manifest b/sci-biology/bioperl-network/Manifest
index fbf732ca2134..7559088328af 100644
--- a/sci-biology/bioperl-network/Manifest
+++ b/sci-biology/bioperl-network/Manifest
@@ -1,3 +1,3 @@
 DIST BioPerl-Network-1.006900.tar.gz 2198089 BLAKE2B 67197ed356f642d9e85f779019f6854f4baa3963e059895b89c75ae56f8b5a075ca04b04ce5c7622d46a3a2f55e1c7d80af695085c607ed7fda5517c71c579f3 SHA512 d0a95af17cb024cbc615c784f1dbcddd7bfc5b54524163ab127f1077ded18df222fe067c085f3dd17dd416d6417b8f726526be164e1e33144991393f6b6d5842
-EBUILD bioperl-network-1.6.9.ebuild 634 BLAKE2B 7cb788c94d5017434f0f81dc5adbd3d64c31980d12f4e739862fc5127dea25f40964f11b384d42e73022b3fa4031d69e78bcb9f8933bab867827144d83596a02 SHA512 491c8190c28b7add4c1263038534705a7798afd29fbdfc853267f4b663b1fd92c21acfe47330357b83323e4ac05e39e52f78fa526ae1ae0059701a002f7ce03c
+EBUILD bioperl-network-1.6.9-r1.ebuild 554 BLAKE2B a569458f835cfe5950784aad33b8b3dc5330ef7e81036215354fec4f57c77142c3879c5d9e706ad8278d7651ff50a15f278bba67a58a846408197fbaf225eae1 SHA512 3e8e84fb53f91ff2c752c07af5e739dfc9f68e9142557d3914c17f553a702540d20b6642fdd8a382694f958fb75ca00628426cbe4c0a017b43203ee11ba63d99
 MISC metadata.xml 350 BLAKE2B 3ed0b50a1cba8de14da5b9a7c73e9b4ae75ab71a4065e950115d0fbe29ca948e23597ecd14e921f64a22ccd023a991c1f8eb8e6571c7fa6280116664f9e6f6c1 SHA512 ef397b00868ba21c8718958189efd201deb6316ed7030cc07547cee07c20b98af13c57f778e39835abc9dbbd6898a497e2a371bb3c0803fbf06bfdf44ea2b90f
diff --git a/sci-biology/bioperl-network/bioperl-network-1.6.9-r1.ebuild b/sci-biology/bioperl-network/bioperl-network-1.6.9-r1.ebuild
new file mode 100644
index 000000000000..513429a9e292
--- /dev/null
+++ b/sci-biology/bioperl-network/bioperl-network-1.6.9-r1.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+BIOPERL_RELEASE=1.6.9
+
+DIST_AUTHOR=CJFIELDS
+DIST_NAME=BioPerl-Network
+DIST_VERSION=1.006900
+inherit perl-module
+
+DESCRIPTION="Perl tools for bioinformatics - Analysis of protein-protein interaction networks"
+HOMEPAGE="http://www.bioperl.org/"
+
+SLOT="0"
+KEYWORDS="amd64 x86"
+RESTRICT="test" # bug 298326
+
+RDEPEND="
+	>=sci-biology/bioperl-${PV}
+	>=dev-perl/Graph-0.86"
+DEPEND="${RDEPEND}"
+BDEPEND="dev-perl/Module-Build"
+
+mydoc="AUTHORS BUGS"
diff --git a/sci-biology/bioperl-network/bioperl-network-1.6.9.ebuild b/sci-biology/bioperl-network/bioperl-network-1.6.9.ebuild
deleted file mode 100644
index 65a72e06634f..000000000000
--- a/sci-biology/bioperl-network/bioperl-network-1.6.9.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI="5"
-
-BIOPERL_RELEASE=1.6.9
-
-MY_PN=BioPerl-Network
-MODULE_AUTHOR=CJFIELDS
-MODULE_VERSION=1.006900
-inherit perl-module
-
-DESCRIPTION="Perl tools for bioinformatics - Analysis of protein-protein interaction networks"
-HOMEPAGE="http://www.bioperl.org/"
-
-SLOT="0"
-KEYWORDS="amd64 x86"
-IUSE="test"
-RESTRICT="!test? ( test )"
-SRC_TEST="do"
-
-CDEPEND=">=sci-biology/bioperl-${PV}
-	>=dev-perl/Graph-0.86"
-DEPEND="dev-perl/Module-Build
-	${CDEPEND}"
-RDEPEND="${CDEPEND}"
-
-src_install() {
-	mydoc="AUTHORS BUGS"
-	perl-module_src_install
-}
diff --git a/sci-biology/bioperl-run/Manifest b/sci-biology/bioperl-run/Manifest
index 636cac1d11c0..6ff8fd52a6b7 100644
--- a/sci-biology/bioperl-run/Manifest
+++ b/sci-biology/bioperl-run/Manifest
@@ -1,3 +1,3 @@
 DIST BioPerl-Run-1.006900.tar.gz 14546677 BLAKE2B 9faf58796b9874b19b66e74abc51ed1d1b6e2928bcf9904506b2af6b2b7c1772a90eab24bf0e7c050fd4a2b120ba506ad5edb8a693496b7468fe7c8d05d11f0a SHA512 47f2b853885c604291ac0aba3269b897de59cf7da6f7d54a50ff950cca836338091309df550f32695159c620be23391306d0421d2bbc22eebbb61a9e280ad83c
-EBUILD bioperl-run-1.6.9.ebuild 927 BLAKE2B 035f172e5ee9d617bb5eb0b522d17f07624be54773c58b21b5435835ebc3cde67028ef7cc3254cec5f257b67256d10bd19c2f1d390b26e73cc877971320b3116 SHA512 798dfb678a67013499b317281bbe8b0f6012fa2daabb5f77223e1839f1dc2b926c866e39164de745855577adea46f972a25726b8fcc8bcfe969c44634c38455b
+EBUILD bioperl-run-1.6.9-r1.ebuild 650 BLAKE2B a214f71456de9391214b0a7f34dadf26613c9879e395062b5e48af26692a3d252c07527cd05ced889a6b9a03ba06d61b19362d936e9d984753b898bdc6bdbd70 SHA512 be72eba0015551c616680ecc1f623d3818f48a6bef98532c90f2abca325952c16dd9be8ded66bc9e5ff89c70345d343cb9f7e40c7594995ab286ad5e2b3eb64d
 MISC metadata.xml 346 BLAKE2B 95f61e91a850b29694d458a88cca4d4594bc307c3ff2f3987b8da6d0d1344cb00f9c8d0c2657b35adc167887cc75340808a3637f571bdf4de12d52f92b87bae3 SHA512 2ffa2072f142a304c63e4b2403eaf1f65fcf61aee9798c08c896ccab9569fa90926c83652589190a2ba60170fff20ccc106e0b8397fe7e8d3519cce4064ed000
diff --git a/sci-biology/bioperl-run/bioperl-run-1.6.9-r1.ebuild b/sci-biology/bioperl-run/bioperl-run-1.6.9-r1.ebuild
new file mode 100644
index 000000000000..2541aab82506
--- /dev/null
+++ b/sci-biology/bioperl-run/bioperl-run-1.6.9-r1.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+BIOPERL_RELEASE=1.6.9
+
+DIST_AUTHOR=CJFIELDS
+DIST_NAME=BioPerl-Run
+DIST_VERSION=1.006900
+inherit perl-module
+
+DESCRIPTION="Perl wrapper modules for key bioinformatics applications"
+HOMEPAGE="http://www.bioperl.org/"
+
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE="minimal test"
+RESTRICT="test"
+
+RDEPEND="
+	>=sci-biology/bioperl-${BIOPERL_RELEASE}
+	!minimal? (
+		dev-perl/Algorithm-Diff
+		dev-perl/XML-Twig
+		dev-perl/IO-String
+		dev-perl/IPC-Run
+		dev-perl/File-Sort
+	)"
+DEPEND="${RDEPEND}"
+BDEPEND="dev-perl/Module-Build"
+
+mydoc="AUTHORS BUGS FAQ"
diff --git a/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild b/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild
deleted file mode 100644
index 461c4f51b071..000000000000
--- a/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI="5"
-
-BIOPERL_RELEASE=1.6.9
-
-MY_PN=BioPerl-Run
-MODULE_AUTHOR=CJFIELDS
-MODULE_VERSION=1.006900
-inherit perl-module
-
-DESCRIPTION="Perl wrapper modules for key bioinformatics applications"
-HOMEPAGE="http://www.bioperl.org/"
-
-SLOT="0"
-KEYWORDS="amd64 x86"
-IUSE="minimal test"
-#SRC_TEST="do"
-
-RESTRICT="test"
-
-CDEPEND=">=sci-biology/bioperl-${BIOPERL_RELEASE}
-	!minimal? (
-		dev-perl/Algorithm-Diff
-		dev-perl/XML-Twig
-		dev-perl/IO-String
-		dev-perl/IPC-Run
-		dev-perl/File-Sort
-	)"
-DEPEND="dev-perl/Module-Build
-	${CDEPEND}"
-RDEPEND="${CDEPEND}"
-
-src_install() {
-	mydoc="AUTHORS BUGS FAQ"
-	perl-module_src_install
-	# TODO: File collision in Bio/ConfigData.pm (a Module::Build internal file)
-	# with sci-biology/bioperl. Workaround: the "nuke it from orbit" solution :D
-	#find "${D}" -name '*ConfigData*' -print -delete
-}
diff --git a/sci-biology/bioperl/Manifest b/sci-biology/bioperl/Manifest
index c7533e05fdc8..e08d199b50f6 100644
--- a/sci-biology/bioperl/Manifest
+++ b/sci-biology/bioperl/Manifest
@@ -1,3 +1,3 @@
 DIST BioPerl-1.6.901.tar.gz 12284856 BLAKE2B 004947fde9d02355ac96f71b67a33a27d6d0163892c978ac9059e70e089fb83b473e21252c5217dfba8faaa65bc3d2eebb8826d03f29a13409e2b6d337316b42 SHA512 227387437c940da1435ed83fad6ec2168ca12a729c90dc557e84750c6474213874c23a8f23e50db4027909469627baee581faa11be6208c8e0a5453a01c7eca4
-EBUILD bioperl-1.6.9.ebuild 1542 BLAKE2B 199c44bf5e2b018efa79c387c247adcade5e477199b9ac7c9dcff8fa98db413520d8365c16ebfe2e38afd799cbd3f1f07a49a24272f3afa3bb8a9aa6a326a493 SHA512 f810d4f0290cfffc3efadc3ce597de747e877c02a302de0614b82209b776dc8c631eeabc3331e9ee4cb590255c5aeb75703f48361453f779c477ed7b64ae8c03
+EBUILD bioperl-1.6.9-r1.ebuild 1488 BLAKE2B 7a8ad3ad21b292fed0453d9965694aad7f383539f4ff2a689c26c0ff129e8a3d40a8fced69222423e39344e947fb58489620b34fb6bf904f1d4bc6747aa53d42 SHA512 2c41a0018ec7f11f3f45a9c2b003921a88e7205b22ac82fd4255267e825080e5f0e8bd1adb2b86b3c204eafb8920bad4ac9f34b4a100b71103469fb1dd46a9e3
 MISC metadata.xml 542 BLAKE2B 3ad1ab0c76d1fa604901646d0431a46718a0c01ce90c964e0f3855d3f487ae4a36d1550737cb5f4dc3f800d0a81329e742c9ed9b5fec346a4d53c71cf7543cae SHA512 289ed0f5f8fff5dee11c050dd37b53418ef9278071dc5700288392ae5e3e44b706692eb89ad61a31327218458926017aefa7320c8c51395c5c6400d10eb4b516
diff --git a/sci-biology/bioperl/bioperl-1.6.9.ebuild b/sci-biology/bioperl/bioperl-1.6.9-r1.ebuild
index c39c6244592b..2896271e137a 100644
--- a/sci-biology/bioperl/bioperl-1.6.9.ebuild
+++ b/sci-biology/bioperl/bioperl-1.6.9-r1.ebuild
@@ -1,25 +1,25 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI="5"
+EAPI=8
 
-MY_PN=BioPerl
-MODULE_AUTHOR=CJFIELDS
-MODULE_VERSION=1.6.901
+DIST_AUTHOR=CJFIELDS
+DIST_NAME=BioPerl
+DIST_VERSION=1.6.901
 inherit perl-module
 
 SUBPROJECTS="+db +network +run"
-MIN_PV=${PV}
+MIN_PV="${PV}"
 
 DESCRIPTION="Perl tools for bioinformatics - Core modules"
 HOMEPAGE="http://www.bioperl.org/"
+
 SLOT="0"
 KEYWORDS="amd64 x86"
 IUSE="minimal graphviz sqlite ${SUBPROJECTS}"
-
 REQUIRED_USE="minimal? ( !graphviz )"
 
-CDEPEND="
+RDEPEND="
 	dev-perl/libwww-perl
 	!minimal? (
 		dev-perl/Algorithm-Munkres
@@ -54,14 +54,11 @@ CDEPEND="
 	)
 	graphviz? ( dev-perl/GraphViz )
 	sqlite? ( dev-perl/DBD-SQLite )"
-DEPEND="dev-perl/Module-Build
-	${CDEPEND}"
-RDEPEND="${CDEPEND}"
-PDEPEND="db? ( >=sci-biology/bioperl-db-${MIN_PV} )
+DEPEND="${RDEPEND}"
+PDEPEND="
+	db? ( >=sci-biology/bioperl-db-${MIN_PV} )
 	network? ( >=sci-biology/bioperl-network-${MIN_PV} )
 	run? ( >=sci-biology/bioperl-run-${MIN_PV} )"
+BDEPEND="dev-perl/Module-Build"
 
-src_install() {
-	mydoc="AUTHORS BUGS FAQ"
-	perl-module_src_install
-}
+mydoc="AUTHORS BUGS FAQ"
diff --git a/sci-biology/embassy-cbstools/Manifest b/sci-biology/embassy-cbstools/Manifest
index 562e4108ead2..cc9f49dc240f 100644
--- a/sci-biology/embassy-cbstools/Manifest
+++ b/sci-biology/embassy-cbstools/Manifest
@@ -1,4 +1,4 @@
-AUX embassy-cbstools-1.0.0.650_fix-build-system.patch 2944 BLAKE2B f33ea2bc9579a7a233064e562ae76ede11fa81d9c6c972338e944028192390e797deb13514b1d02a32b1b6b55925a8eeef15f8ed11598ab487e9deb3e7a6a14d SHA512 913542383cf0dcacdf7c18ee258b6bf37fcde77b41a548089e239c9e20e2087cbec0e5244eb946b511bb76ec5930a6a44142ea172d894061bfca5e1228e29047
+AUX embassy-cbstools-1.0.0.650_fix-build-system.patch 2944 BLAKE2B ef932cd3c779c5edcdd6bfec49bb84813d8d7e0b4d4d0998c939bebc25cafb1a0a7d889caed1832b1f69ad3d7a44aed512ae1fcda7e8726a879e8bbc9ccbca3b SHA512 e243358427240b1c009a360c4b5c5829822924d33a5a515244be706d4916eb8ba6cc9a8e814ef0875b84f5eeb266f2c5d0be2287335ec09fff1f2fa686d3f419
 DIST embassy-cbstools-1.0.0.660.tar.gz 452594 BLAKE2B 68d13e14b4805af7ba1742537e6ebd621553ba6c895cd4bb13a5c1e93e72e03916ba62833f31ec35e69fa9a4ab15d9348dbfe19eb55a82f3ecd86141726e6c01 SHA512 8f16f726220a36f998d8a0f1d8aec9ec6b2db8160b15bed7bafc5a65d57a937bd91ee831ecabe2e9aaa8cecaa18d050f16439a276a882730fde3fa4937bec384
-EBUILD embassy-cbstools-1.0.0.660.ebuild 349 BLAKE2B 3930b547938c8e72d8e058684c8808385c7dff42b3d6796e854da4f2401be95d652eba027c7c17e715e3a670eb4d8b31837a65d0d0dd285374ef169a8b87852f SHA512 c3354cf9907079e2870e1acf7c8ccfed1225da5c1eff6f97f144373b80ebdfdbb6d4b0fd95632e341e51edd42b15bce88bf7a10ed78a328a4907f86ba24a843d
+EBUILD embassy-cbstools-1.0.0.660-r1.ebuild 381 BLAKE2B 7a006d21648251649e0517046565e00b4a454c807a572914110736fd9b6a844ba8d84c7aa9ea290131a15f2be3567e87f8ac305d8d870744dd811c94cd945e61 SHA512 5ab338616a004b4e156b5f996039e825e627de7d455e8c9ed7781300bacad3fae6bc19619083a33b1e9cc8afb09010c103a8f13cd244e3590920ba26854b7be4
 MISC metadata.xml 348 BLAKE2B d71aba38f248b80e63e5805f1c0f710815220774a8a514f69a708666c647f061a3f295196da119cec9b5681648a54a1915073039302586d17540296855a255df SHA512 4f8c9238704b81e38abad62bc92e67ad08fe30907277794ee5a4265f4dd8e69fb1b4cabead1fc45c48888c3dbe30496b2c7df3b1c8fa2662f87a4deef32661cd
diff --git a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.660.ebuild b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.660-r1.ebuild
index 873b9cb64520..40dafb6bb62c 100644
--- a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.660.ebuild
+++ b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.660-r1.ebuild
@@ -1,15 +1,18 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
 EBO_DESCRIPTION="Applications from the CBS group"
 
-EBO_EAUTORECONF=1
-
-inherit emboss-r2
+inherit autotools emboss-r3
 
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 
 S="${WORKDIR}/CBSTOOLS-1.0.0.650"
 PATCHES=( "${FILESDIR}"/${PN}-1.0.0.650_fix-build-system.patch )
+
+src_prepare() {
+	default
+	eautoreconf
+}
diff --git a/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch b/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch
index bdaaaf98f23c..7ed96e5ff23b 100644
--- a/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch
+++ b/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch
@@ -1,5 +1,5 @@
---- a/configure.ac
-+++ b/configure.ac
+--- a/configure.in
++++ b/configure.in
 @@ -635,33 +635,6 @@
  
  
diff --git a/sci-biology/embassy-clustalomega/Manifest b/sci-biology/embassy-clustalomega/Manifest
index b91cfce1661d..b82af7d00ed7 100644
--- a/sci-biology/embassy-clustalomega/Manifest
+++ b/sci-biology/embassy-clustalomega/Manifest
@@ -1,4 +1,4 @@
-AUX embassy-clustalomega-1.1.0_fix-build-system.patch 2775 BLAKE2B 03c93a180b5bd19d74196a17e093df54a82ad70378222c04041274477f16a94bff901ff4d31b36df3597d6bb6a2e96750688a5e279d2f83b2e745cb82cd18549 SHA512 bbdf887e87e00c5f82f964ffda547ce0437795d13ecb73255901028c1e45def1a5a02decf5cd7be045985cf125669cafb00617def6cc2b5ec543aadae1dfb547
+AUX embassy-clustalomega-1.1.0_fix-build-system.patch 2775 BLAKE2B 6e007c46b5028201bb8105227114b48012e75b5bfd8089a3dc7e7a8a75f2bd93a14dae810e949d8924dfb9d3a23bfcd435b52325fe4ffc8775f6db15bb92b1ac SHA512 94a7a9782ba2c5586860eb402201fbe81088337f191a7d17171e438ef29a6d298b8ea7a6a20345d1e29877991cf32b101bc03fa8d801b50aec3247d62b0cfbce
 DIST embassy-clustalomega-1.1.0.660.tar.gz 618177 BLAKE2B 5d3f300a0dd825c92c3f953219b2ae8be271a7d89a1237980571b3f9a9027d6a0191ad9e61be87d1ad3334ddd56f9ff11c05d3e277683dc8cdfe511ef3739877 SHA512 fc16f9505e0300ae184e292fb1d96ce6b90eaf80298f847769466a84726d10ea58e3f4c14ed21a9e2c36d7fa533c7ad248b4995bf41c8abbd0fed1faf1fd4801
-EBUILD embassy-clustalomega-1.1.0.660.ebuild 381 BLAKE2B 35ffd764e71b73b85110065818095193d822955fa9890e5e9076e09cade350980d1bcf41ee38b56b363c6dea6ca081dbf0f55ae75c474e08c7ef5555d5a330a0 SHA512 58e8112f9d645a058bc40523b6690673dfc0c0870b8b5495dd8121acd5209896a5ee3ac8c89799188635366df4a50631baeffc2d29ab5278c2e52c46e5736bfa
+EBUILD embassy-clustalomega-1.1.0.660-r1.ebuild 413 BLAKE2B ade112ccd4e0742db333bae5f33c016181f456381cf81cb9db0190202f92c627cc0c716ce505402ba4b339971939cddb4776e2f455c9b9620a54b0831758e67c SHA512 fbb97ff3a4c57da0844122924f5cb83a2361ec7828ef0f2c29d40f64994517513822e019569daaee039cd6d16c37284596c482e4d834fbe38ce78602f8cbaad0
 MISC metadata.xml 348 BLAKE2B d71aba38f248b80e63e5805f1c0f710815220774a8a514f69a708666c647f061a3f295196da119cec9b5681648a54a1915073039302586d17540296855a255df SHA512 4f8c9238704b81e38abad62bc92e67ad08fe30907277794ee5a4265f4dd8e69fb1b4cabead1fc45c48888c3dbe30496b2c7df3b1c8fa2662f87a4deef32661cd
diff --git a/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.660.ebuild b/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.660-r1.ebuild
index 93092e9f884e..600b75769e5f 100644
--- a/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.660.ebuild
+++ b/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.660-r1.ebuild
@@ -1,13 +1,11 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
 EBO_DESCRIPTION="Clustal Omega - Multiple Sequence Alignment"
 
-EBO_EAUTORECONF=1
-
-inherit emboss-r2
+inherit autotools emboss-r3
 
 KEYWORDS="~amd64 ~x86 ~x86-linux"
 
@@ -15,3 +13,8 @@ RDEPEND="sci-biology/clustal-omega"
 
 S="${WORKDIR}/CLUSTALOMEGA-1.1.0"
 PATCHES=( "${FILESDIR}"/${PN}-1.1.0_fix-build-system.patch )
+
+src_prepare() {
+	default
+	eautoreconf
+}
diff --git a/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch b/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch
index 7f92130fb501..024f8bfc3a09 100644
--- a/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch
+++ b/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch
@@ -1,5 +1,5 @@
---- a/configure.ac
-+++ b/configure.ac
+--- a/configure.in
++++ b/configure.in
 @@ -635,33 +635,6 @@
  
  
diff --git a/sci-biology/embassy-domainatrix/Manifest b/sci-biology/embassy-domainatrix/Manifest
index 1c63220b2918..022550b63979 100644
--- a/sci-biology/embassy-domainatrix/Manifest
+++ b/sci-biology/embassy-domainatrix/Manifest
@@ -1,4 +1,4 @@
-AUX embassy-domainatrix-0.1.650_fix-build-system.patch 2775 BLAKE2B cfe8ec8c3bd62ebaa789d1f3ee63b961f0ab7c41ef44c78faa7b4913945d84da1fa082dc31ebeb92b105762a25992e2d68b56988177aed9ff444743942687d43 SHA512 505a92947e8f50a2a22ea8888a326723fe47584cab4f2414d703753201daecd0e8030cfe41ff53274a0ca08a6cf9c110557e902d7a038ef7f2baffe046093e2a
+AUX embassy-domainatrix-0.1.650_fix-build-system.patch 2775 BLAKE2B c8b736cc72532023c94b74cb33ca2c73a889ed99fe8d2e4d10a5f65597fb9bf51d63569174ce9b03c919278446db992318d45b140607f7e4583a0d73afd95627 SHA512 25034b508e638246850708ad522f1aca2b7f5347d6baf6c30284bb244136bb3913985825b6e0043d0f2607132bf9255b9324b7f20a31167310b0bae3a2304ae6
 DIST embassy-domainatrix-0.1.660.tar.gz 474066 BLAKE2B ac5e081ac1a18d8abfbcdf687a43d4a09436c83fd54bed8c75487f8ed74852979adc96fa592df9f86c161fc8b398f1225ec44e565b470c59a5c2268898943270 SHA512 151e026445abb171a9141ae5576442307121646c66dc811320a6f73be1103203bf04d37b813e5c95ef0873be261cd474835f4dffd042f33f99d7dd4fda19be7b
-EBUILD embassy-domainatrix-0.1.660.ebuild 342 BLAKE2B f4c97aaa3fa9fb33a060b7973d64308bd90caa10e57497d31d3401e5d87d737a353ee5665ae0ee563f994d972e402090ef2bdbf333b4696886aadaa69136cf88 SHA512 178adf2159cc20c5e23a13b4420bf7ecd77a7b82b1047f4f499abbc9e93b1c6cce1acc6e6e27719bf767077c407de314f0d0c9e8ea93ad985944e7c3eedb452e
+EBUILD embassy-domainatrix-0.1.660-r1.ebuild 374 BLAKE2B d51978b1cfc0121ce8c6b55e3e081824d02c3ea13ea9c0cd6a4ff7f78401b19db694c9e1ff7687cec678c5c422c669c22eceafff7be21f20cf5c35b0f36409de SHA512 934d77e536685638e18bf79c419baa54be2590a1106766c282ae831d766b982fe4ec7b6cfa316a25f044be701472665957403e22662eac5d8b93ca41c3b38ccf
 MISC metadata.xml 348 BLAKE2B d71aba38f248b80e63e5805f1c0f710815220774a8a514f69a708666c647f061a3f295196da119cec9b5681648a54a1915073039302586d17540296855a255df SHA512 4f8c9238704b81e38abad62bc92e67ad08fe30907277794ee5a4265f4dd8e69fb1b4cabead1fc45c48888c3dbe30496b2c7df3b1c8fa2662f87a4deef32661cd
diff --git a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.660.ebuild b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.660-r1.ebuild
index 03e728926cb6..affd53e8a3b4 100644
--- a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.660.ebuild
+++ b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.660-r1.ebuild
@@ -1,15 +1,18 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
 EBO_DESCRIPTION="Protein domain analysis add-on package"
 
-EBO_EAUTORECONF=1
-
-inherit emboss-r2
+inherit autotools emboss-r3
 
 KEYWORDS="~amd64 ~x86 ~x86-linux"
 
 S="${WORKDIR}/DOMAINATRIX-0.1.650"
 PATCHES=( "${FILESDIR}"/${PN}-0.1.650_fix-build-system.patch )
+
+src_prepare() {
+	default
+	eautoreconf
+}
diff --git a/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch b/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch
index 1cd2a1b29b09..849da318d245 100644
--- a/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch
+++ b/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch
@@ -1,5 +1,5 @@
---- a/configure.ac
-+++ b/configure.ac
+--- a/configure.in
++++ b/configure.in
 @@ -635,33 +635,6 @@
  
  
diff --git a/sci-biology/embassy-domalign/Manifest b/sci-biology/embassy-domalign/Manifest
index cd83b75904c8..c65714e46a66 100644
--- a/sci-biology/embassy-domalign/Manifest
+++ b/sci-biology/embassy-domalign/Manifest
@@ -1,4 +1,4 @@
-AUX embassy-domalign-0.1.650_fix-build-system.patch 2809 BLAKE2B 01ae7488b764f3d3853d8f6e4fc2f2115d381decbac3d20922d26c079d0242622f553359dab2401481be3cdf28f25495c567682c1b9d2140f3686f312cbc20f5 SHA512 09444e7ee2b263b56177275c4fe9452344720e641acb721e1630696941a3f077c9790357f9d8b775bff4f5df595973f59d1e9f4c3f66b54fa31f53db4e32ce58
+AUX embassy-domalign-0.1.650_fix-build-system.patch 2809 BLAKE2B 91dbf0f57f811e264a2002309dc2d4172f84baf383c9a59b693ee67fe73dfb9b3c426bada6a6d53cc2a800d82f733bb9a0e3a71f5ea09d87c77859d0473bb57e SHA512 59a6518f65e40e4233d16ad0a97696563ab2af83cd7ad3fe95aef5e1259ef0e1919c2edc81b1e5a6a685acf9bb7b7047f940943a8137a9e75170f636666cb883
 DIST embassy-domalign-0.1.660.tar.gz 498669 BLAKE2B d21352b28ca046c1bfe8600a7eba641d670e232571f95f9c75b47486a63f2a2b02516191706c0688e81bc33cda90ebf88a9ce800535dce9a955ccc15e25dd20a SHA512 14e86664e9038acc60fbec92fa218e218921fb1e51cc2e482fb1760ccd9ea16041dc8a2a9f5f320fca3340b7efdc48ea9d753b048a43966fc3431acdaddc7846
-EBUILD embassy-domalign-0.1.660.ebuild 340 BLAKE2B 8e42cd3a864fe7b85628901b37eba3e72b2d7efcf48ac3b7b48c65735b0983a68d47dd525ed7972e2be9c9b15723c6409de10017718e5945cd7c231153be022a SHA512 236b004af2c4a2e84eebc72f8363af05c757e0251417c8f2971ec4902a067669754980cc65f358a3295a05ea0e3c4a43a9e2b2a7e9e6010632c73ac06c281ed6
+EBUILD embassy-domalign-0.1.660-r1.ebuild 372 BLAKE2B c18a3e36d562234e9916009fe4237a4f287839e74dc650e4d9e5bffff8f95db18bc4275a5751a7f942609f3061053d01b668c1790f3a3336095375614af94653 SHA512 09bf7d9e06394544cad847712cb0dedd49debc2a960b4c718b567382140e75aea9c48e1e352dab279322fb886b57a443cb8b39a8fa35a3c339df6bb363a8e9cd
 MISC metadata.xml 348 BLAKE2B d71aba38f248b80e63e5805f1c0f710815220774a8a514f69a708666c647f061a3f295196da119cec9b5681648a54a1915073039302586d17540296855a255df SHA512 4f8c9238704b81e38abad62bc92e67ad08fe30907277794ee5a4265f4dd8e69fb1b4cabead1fc45c48888c3dbe30496b2c7df3b1c8fa2662f87a4deef32661cd
diff --git a/sci-biology/embassy-domalign/embassy-domalign-0.1.660.ebuild b/sci-biology/embassy-domalign/embassy-domalign-0.1.660-r1.ebuild
index 331bd7e05a71..106fbd13912b 100644
--- a/sci-biology/embassy-domalign/embassy-domalign-0.1.660.ebuild
+++ b/sci-biology/embassy-domalign/embassy-domalign-0.1.660-r1.ebuild
@@ -1,15 +1,18 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
 EBO_DESCRIPTION="Protein domain alignment add-on package"
 
-EBO_EAUTORECONF=1
-
-inherit emboss-r2
+inherit autotools emboss-r3
 
 KEYWORDS="~amd64 ~x86 ~x86-linux"
 
 S="${WORKDIR}/DOMALIGN-0.1.650"
 PATCHES=( "${FILESDIR}"/${PN}-0.1.650_fix-build-system.patch )
+
+src_prepare() {
+	default
+	eautoreconf
+}
diff --git a/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch b/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch
index 079850c2bcc3..873deaa645ab 100644
--- a/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch
+++ b/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch
@@ -1,5 +1,5 @@
---- a/configure.ac
-+++ b/configure.ac
+--- a/configure.in
++++ b/configure.in
 @@ -635,33 +635,6 @@
  
  
diff --git a/sci-biology/embassy-domsearch/Manifest b/sci-biology/embassy-domsearch/Manifest
index 3d8c2451a9bc..5ce32bfe51e2 100644
--- a/sci-biology/embassy-domsearch/Manifest
+++ b/sci-biology/embassy-domsearch/Manifest
@@ -1,4 +1,4 @@
-AUX embassy-domsearch-0.1.650_fix-build-system.patch 2806 BLAKE2B 44cfc67f34b7d4112cf0247231eb82db7433a1aecfffaf1723b4fcd5e186c0d7dd683db52bbc006027b305c2551b760c98116e5fab3eb874bd1a843f38ef2e71 SHA512 73bc497c5e7974d50a1ecd1ea537b923e5670ac1abafe9877b8fb98e4e94688fe7c77d233e4df45952da6f39013f0fa87d80791cdc79d3ed005e3f8070484144
+AUX embassy-domsearch-0.1.650_fix-build-system.patch 2806 BLAKE2B 6c3deb1ef0ac8732e3f50ffe419cf9fcaaeb46d0dc528ee18fb65f4b2f4a5fda85327ba1595930f3a7442458e76308ffd021ce8f9b2c0fc5f87f7ae5d3ce068d SHA512 60595ee48a01f1be6f51dfa3e828fecb83dbf51983c6f833439bda08a860680d9b6c44d231608ed93fccebf232f804e45ef2b9bc05460854b211ba8ad5d6037d
 DIST embassy-domsearch-0.1.660.tar.gz 504183 BLAKE2B 598ba359558519967d0e8d895bca453aaeffef3d8a62c3d77b6b2f321118e890ec70c3baa3dd3acc03fc9a19cc380909cf3f14e5569c4ae90d3d5e88817d6e6d SHA512 a242100dc7b4b1f4a838dbf65dffb0475b6b890c7d68efae6a74beb3d4784d031f92365a50a41c0d7ea7d1b4be5e65a298626a798970c74df0d5f85427a51589
-EBUILD embassy-domsearch-0.1.660.ebuild 338 BLAKE2B 90d616ea192ce84a7cd8806425ecddbb8cb1c475900616c0aeb7f629ceb9294a05620a23df512a694c606af4e90f4968ddf0643a9800c13adde6556d6382a268 SHA512 64cb26ac31b6dee716132a3ec575e8c19d703e8ba023db382e1ade34ecda2227d2663fc18aa7ef5b5de9bedbb6ff103d2f6ac1a33c1c50e60e18523d54132351
+EBUILD embassy-domsearch-0.1.660-r1.ebuild 370 BLAKE2B a242babea0ada2fe20ec51a78f6fd8f1d3e55d67ccda2720630127a28b851f48a3368abc9187040f6b9cef29fd9ee8bd8982bfe250b1fb1fc5408057e33675f8 SHA512 2faa6f8481f2182d0adc32c589514874cf7f0f7389a07994f3a6713a9acd3c56c15c8e319777b0783cc2b8e2ec096b48123c6ecbddda1b7320b6bac6e29a41f9
 MISC metadata.xml 348 BLAKE2B d71aba38f248b80e63e5805f1c0f710815220774a8a514f69a708666c647f061a3f295196da119cec9b5681648a54a1915073039302586d17540296855a255df SHA512 4f8c9238704b81e38abad62bc92e67ad08fe30907277794ee5a4265f4dd8e69fb1b4cabead1fc45c48888c3dbe30496b2c7df3b1c8fa2662f87a4deef32661cd
diff --git a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.660.ebuild b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.660-r1.ebuild
index e4c37b996653..07a16e7e2272 100644
--- a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.660.ebuild
+++ b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.660-r1.ebuild
@@ -1,15 +1,18 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
 EBO_DESCRIPTION="Protein domain search add-on package"
 
-EBO_EAUTORECONF=1
-
-inherit emboss-r2
+inherit autotools emboss-r3
 
 KEYWORDS="~amd64 ~x86 ~x86-linux"
 
 S="${WORKDIR}/DOMSEARCH-0.1.650"
 PATCHES=( "${FILESDIR}"/${PN}-0.1.650_fix-build-system.patch )
+
+src_prepare() {
+	default
+	eautoreconf
+}
diff --git a/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch b/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch
index ecc702edcb66..2fe1803f8452 100644
--- a/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch
+++ b/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch
@@ -1,5 +1,5 @@
---- a/configure.ac
-+++ b/configure.ac
+--- a/configure.in
++++ b/configure.in
 @@ -635,33 +635,6 @@
  
  
diff --git a/sci-biology/embassy-emnu/Manifest b/sci-biology/embassy-emnu/Manifest
index 91a18d61b862..c57fbf87201b 100644
--- a/sci-biology/embassy-emnu/Manifest
+++ b/sci-biology/embassy-emnu/Manifest
@@ -1,4 +1,4 @@
-AUX embassy-emnu-1.05.650_fix-build-system.patch 3844 BLAKE2B b77be3d3917db4cdfcfce201089595a80b970575f77dffbc366c77ae27010b9a78582b035728008b20ae11b0c7c18b7b20a5fdfcd59b840f85f54a1db2fc5496 SHA512 1836ba79762f62f9e27a770a35b89ae5f2821c4d23dc93b1ab3505404105280256f1c43287471385a5be71659fbe614f5f7f97d78a4743b3b1b90b303a25f674
+AUX embassy-emnu-1.05.650_fix-build-system.patch 3844 BLAKE2B 8b59525070af4962da9419c41d217a8f7b9f52eb783cbcf865d661296d8ce8e8e56dd8a815c3166c258d75e6fe73930a419e4a47ad3fe11f7bb0b6de04fb2555 SHA512 ca6b3b7b0e7964b002aa8cba1a8057f50b8687700790741617f920a7014f4e96084a7ddcf9b4e64741c999561199db0e6ef35eb93c445222d72d6872cccb8b3e
 DIST embassy-emnu-1.05.660.tar.gz 425595 BLAKE2B ed6ab4a0572ac4b57cf0f0b75a3894b1f950f7f373a7c6797ea0c34ba1b0d0e044f2c6951aec7c084340c6b207aa4c8b386055e92ceb9fc83c920fc70e83e665 SHA512 0cb0dafd53c4fd410409430dc12353989d2c226191acace26e81b457602b6b6c60f8eb1d0d9b36ea90b2420010c1a3e887a2458e8487008a36775961e378d0dd
-EBUILD embassy-emnu-1.05.660.ebuild 530 BLAKE2B 063882fbbb297ea4bf5b70dd82cc7d4625f027fd87ecf3ff28e34a5d20834e20db39a8750bd3e6738e829f8c727211c1d3d47c47f2a77ffa436f925dcc8f08c0 SHA512 d4caec2280558dcbdbf7e2a5a2d3d658845781d8f05588fcedb7f7ab33fda937f1aac4e97627ae7a6744258d2384d9859a7dc0ea7af968f60f5f8739f070c296
+EBUILD embassy-emnu-1.05.660-r1.ebuild 562 BLAKE2B eb6c82dbd8f3ca972db40002a3993d06bc8cd43a63921330c724d897241f0173dec59b39202c2fd2e0ad8416662c16ff52f5f86c1f313ea50de124a01af7ae2d SHA512 8e89c29d7e66bf923fd096f373375c835b97445992c1854bec9b42c282a6fec5792e8ae7de9d75f8cbdeacc143f42a2abb79ed7b3036f9d19971da154bf27c3a
 MISC metadata.xml 348 BLAKE2B d71aba38f248b80e63e5805f1c0f710815220774a8a514f69a708666c647f061a3f295196da119cec9b5681648a54a1915073039302586d17540296855a255df SHA512 4f8c9238704b81e38abad62bc92e67ad08fe30907277794ee5a4265f4dd8e69fb1b4cabead1fc45c48888c3dbe30496b2c7df3b1c8fa2662f87a4deef32661cd
diff --git a/sci-biology/embassy-emnu/embassy-emnu-1.05.660.ebuild b/sci-biology/embassy-emnu/embassy-emnu-1.05.660-r1.ebuild
index dfff5eb5de26..8f26aee861c1 100644
--- a/sci-biology/embassy-emnu/embassy-emnu-1.05.660.ebuild
+++ b/sci-biology/embassy-emnu/embassy-emnu-1.05.660-r1.ebuild
@@ -1,13 +1,11 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
 EBO_DESCRIPTION="Simple menu of EMBOSS applications"
 
-EBO_EAUTORECONF=1
-
-inherit emboss-r2
+inherit autotools emboss-r3
 
 KEYWORDS="~amd64 ~x86 ~x86-linux"
 
@@ -17,8 +15,13 @@ DEPEND="${RDEPEND}"
 S="${WORKDIR}/EMNU-1.05.650"
 PATCHES=( "${FILESDIR}"/${PN}-1.05.650_fix-build-system.patch )
 
+src_prepare() {
+	default
+	eautoreconf
+}
+
 src_configure() {
 	# --disable-curses is not a thing,
 	# EMNU hard depends on ncurses really, #752216
-	emboss-r2_src_configure --enable-curses
+	emboss-r3_src_configure --enable-curses
 }
diff --git a/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch b/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch
index ecd7f928da3a..3039ac9c83f0 100644
--- a/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch
+++ b/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch
@@ -1,5 +1,5 @@
---- a/configure.ac
-+++ b/configure.ac
+--- a/configure.in
++++ b/configure.in
 @@ -635,33 +635,6 @@
  
  
diff --git a/sci-biology/embassy-esim4/Manifest b/sci-biology/embassy-esim4/Manifest
index c2bff794bc86..8abc6902fbba 100644
--- a/sci-biology/embassy-esim4/Manifest
+++ b/sci-biology/embassy-esim4/Manifest
@@ -1,4 +1,4 @@
-AUX embassy-esim4-1.0.0.650_fix-build-system.patch 2944 BLAKE2B 19712a0b6fb79a37e990bfbf91471c7a08e1e22c01ae97850ed6c09f7c81272ddf841bd834b88f798598297c4df526f4cb12cb29d6db28f0d0ae1db6d05ce116 SHA512 846197536cf1f308f51ae96bb8186198f1c720ad05fb16c94e36b1aadbc3dbf50b21ddecdb2a52acc0444e0c0db980653f3d90f01b43d334d1cd995868888da8
+AUX embassy-esim4-1.0.0.650_fix-build-system.patch 2944 BLAKE2B 92dacc9399084c4a53e9e95ca25962fabf115c49986ec65edc15c3586f1969556ba5053082bc5a1da746b7f33cffa31b36fefc525c91ba58c60f8c0ebfdbed0e SHA512 05fd07e2e4252b1336a96cdb771d3d58fea7e01ed954c24387e94859d77e74886dcc2e7da96ed83640915a0d146c6516c622773540eabb0d6df45587a7bf89e2
 DIST embassy-esim4-1.0.0.660.tar.gz 473261 BLAKE2B d15029b0723dd739fa9208f9b0ffd7814cbddc630ca2ff15955412f493f7983753acf82bcc8a3fc6ddfd49abe630982ead377e6941dcbff44ddc5d8ab4e7d6e5 SHA512 623b241915217ffb314e3fc4ca6aed5e1683b78b6c76f899b67c4e5d48ce83c9920d79b1c5a1508d61856c332e614020d0804b7252c535d9622f9623f29cd152
-EBUILD embassy-esim4-1.0.0.660.ebuild 342 BLAKE2B 2e9c56d305a5e31d2376695e89236d7f64751a9bb922dae565e457fc44230e199e767c12208da0bae8f40be23957fcc788139a1d2e25d499e3da1ad0820e7a78 SHA512 082006d670e565b734711759cedc3ea84229c7b13ccf48a1dd823fc8918ea4e2f1d1568b1599ea2587ae0c5a4eb6e6753311df68d8a82b5b55e77dbf5733fa4c
+EBUILD embassy-esim4-1.0.0.660-r1.ebuild 374 BLAKE2B a80f736ff608fb351157fcdb7bc00d5efe94baf12ab735fe6aced51d9207f46b673f05c8c1b5186f5e0a8a5e218f824e90b49cca449d98568ace07161b854593 SHA512 1991b3962967038eb2d3b0a36213be5c8f8c43bf2259b2fc2c0566f31c2d7a5341203785e2565083684537f7d4e31e02084e86d70121768fbdcf693c4e1ba324
 MISC metadata.xml 348 BLAKE2B d71aba38f248b80e63e5805f1c0f710815220774a8a514f69a708666c647f061a3f295196da119cec9b5681648a54a1915073039302586d17540296855a255df SHA512 4f8c9238704b81e38abad62bc92e67ad08fe30907277794ee5a4265f4dd8e69fb1b4cabead1fc45c48888c3dbe30496b2c7df3b1c8fa2662f87a4deef32661cd
diff --git a/sci-biology/embassy-esim4/embassy-esim4-1.0.0.660.ebuild b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.660-r1.ebuild
index 2538510c6bd3..ab0fee10dc58 100644
--- a/sci-biology/embassy-esim4/embassy-esim4-1.0.0.660.ebuild
+++ b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.660-r1.ebuild
@@ -1,15 +1,18 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
 EBO_DESCRIPTION="sim4 - Alignment of cDNA and genomic DNA"
 
-EBO_EAUTORECONF=1
-
-inherit emboss-r2
+inherit autotools emboss-r3
 
 KEYWORDS="~amd64 ~x86 ~x86-linux"
 
 S="${WORKDIR}/ESIM4-1.0.0.650"
 PATCHES=( "${FILESDIR}"/${PN}-1.0.0.650_fix-build-system.patch )
+
+src_prepare() {
+	default
+	eautoreconf
+}
diff --git a/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch
index 7a85b4f7bf81..7ffa00c52f75 100644
--- a/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch
+++ b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch
@@ -1,5 +1,5 @@
---- a/configure.ac
-+++ b/configure.ac
+--- a/configure.in
++++ b/configure.in
 @@ -635,33 +635,6 @@
  
  
diff --git a/sci-biology/embassy-hmmer/Manifest b/sci-biology/embassy-hmmer/Manifest
index 1fd74b1d1e06..812023a3654e 100644
--- a/sci-biology/embassy-hmmer/Manifest
+++ b/sci-biology/embassy-hmmer/Manifest
@@ -1,5 +1,5 @@
-AUX embassy-hmmer-2.3.2.650_fix-build-system.patch 2775 BLAKE2B 70ac87074b81a15a4f8641a9c98136b23ef8ad78c2ee17b3762a624366638023e147efaef478b1c79f5a5f1d09a882cb3fecb1eec4131307bc585b08855aae6b SHA512 b0ff185fecd52e5452d3257b2e5bd6f1268d84b491f529d66025534d9353f57ddecefa81a69ae3299ad687b1d3480964c4a1df609c2e77b0db1a511207ac49b6
+AUX embassy-hmmer-2.3.2.650_fix-build-system.patch 2775 BLAKE2B c553c7c7a842445d36645ab3c3dcba8c36b3b1d74b4d8a8974c0c5ddbee9f48cc9c316328206d2b1e6f222eee4b6aac9f5df7908602215a95a5b4712dc0c751e SHA512 0b0344712859f5512699b6e99b0ff912841afab3f44303d6bb1f26a6fee12bdc6251cfae6bd138535177b24d93d72343fbfafec55952b080f7eb7fe059ee8594
 AUX embassy-hmmer-2.3.2.660-slotted-hmmer2.patch 3392 BLAKE2B 56da7becf8da8195016cb98518a19fc34394d98400dca6bb499d43c57172ed76ec81d5a9216b4a1b5e67b33520431ce87ed1327db99f3f924a36d80ff8c9e0c3 SHA512 18d1595b7cd6091917f9657310b286d2f0d1f6a61c045840b1c551b66162142997b837cc50b47a3a5fa7efec4ffa78e5b9b52804e3c4d41efeed9b4edb6e5507
 DIST embassy-hmmer-2.3.2.660.tar.gz 587775 BLAKE2B ae7f7c8722bb06d4e28333837b082045e48179a596026a76c2a42f7905c7ebc42f98dd4f36915e4603322bb6d976ac4fa4e8ce6246cdee025b39ecfcb250bd10 SHA512 eb2c037fec70f4113b9ab59cc4eca9a608e8d0971a7bcc4612d60b1e28556444dd3ecdea4ff7b8f8b34711ad9f655334857e7510e89060459c81994a3abcc02a
-EBUILD embassy-hmmer-2.3.2.660.ebuild 498 BLAKE2B 7f319b02c38423cd0bcb6fa7f5833ec4c781c04ce52cf18db847406d5934ffb8957cb1a39e712fd3314bb78e08823b8442809c45b4c8b5d5e0c6e638451fadf7 SHA512 cff995afdb31de78ec2feb8e8b0fcc3f4e51f5214b3fd443c5b24a2f4a7dd3ac9e0a712f400734128bce52d7cc80b2fd71882716d7d1ed9007ccaa6a31710ee2
+EBUILD embassy-hmmer-2.3.2.660-r1.ebuild 530 BLAKE2B c5472cdafe2b6e60ee955eea5fb320b4b1e94342d3276767b4910ce947b980afbd64f202b1399a43ae84e088e58eb4607db6ca9c00ad1180afd88b1b122dca8e SHA512 75d495c8fc57fbbbc48feb9e93b18ac21d04311e0476ebf5a8a0eeaeab168cc0c38c35f04cf4ecc55d78176363e5ea9e1344baa610f46f7bded09f2de5441fd9
 MISC metadata.xml 348 BLAKE2B d71aba38f248b80e63e5805f1c0f710815220774a8a514f69a708666c647f061a3f295196da119cec9b5681648a54a1915073039302586d17540296855a255df SHA512 4f8c9238704b81e38abad62bc92e67ad08fe30907277794ee5a4265f4dd8e69fb1b4cabead1fc45c48888c3dbe30496b2c7df3b1c8fa2662f87a4deef32661cd
diff --git a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.660.ebuild b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.660-r1.ebuild
index c22ff4141c2f..964e637d657c 100644
--- a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.660.ebuild
+++ b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.660-r1.ebuild
@@ -1,13 +1,11 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
 EBO_DESCRIPTION="HMMER wrapper - sequence analysis with profile HMMs"
 
-EBO_EAUTORECONF=1
-
-inherit emboss-r2
+inherit autotools emboss-r3
 
 KEYWORDS="~amd64 ~x86 ~x86-linux"
 
@@ -19,3 +17,8 @@ PATCHES=(
 	# sci-biology/hmmer:2 has renamed commandline program names
 	"${FILESDIR}"/${PN}-2.3.2.660-slotted-hmmer2.patch
 )
+
+src_prepare() {
+	default
+	eautoreconf
+}
diff --git a/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch
index 303aacda46cd..dd1660dfbd5b 100644
--- a/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch
+++ b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch
@@ -1,5 +1,5 @@
---- a/configure.ac
-+++ b/configure.ac
+--- a/configure.in
++++ b/configure.in
 @@ -635,33 +635,6 @@
  
  
diff --git a/sci-biology/embassy-iprscan/Manifest b/sci-biology/embassy-iprscan/Manifest
index bd85e005f1fc..24ad1ce4b824 100644
--- a/sci-biology/embassy-iprscan/Manifest
+++ b/sci-biology/embassy-iprscan/Manifest
@@ -1,4 +1,4 @@
-AUX embassy-iprscan-4.3.1.650_fix-build-system.patch 2944 BLAKE2B 0342606ad758dc533186f455062b7019a04a0b7e8d49ca61214de09caf0518bec6b63f0dcc69652eb24bbb8704047cf0f8739cb9c8b8f2883e525176b389aa1a SHA512 98431bf56317a987083fe936f6b5d0d00c5f773bbdab5e3ee4dab6d1d6b6edb5448c4602c11f79aeed05a5642838cae7c3ab692661b18d1d15fdc9793604c856
+AUX embassy-iprscan-4.3.1.650_fix-build-system.patch 2944 BLAKE2B 369b0febb9263c646eb342838f55f1e7eafa4c734cea42093afedca05a35ee67ac70d74bb6bc2ff4ac9385e050df69540caf8b7ac0c5565954dc2d8ede68ca13 SHA512 91574d93ef5f3f16e380bab42f1fe2c952ed4cb423e05556b0f2499a6dd3c63b0e82845584b95284b539fe5eff61acf3fdf0620b9187882e563798c31c53ac4a
 DIST embassy-iprscan-4.3.1.660.tar.gz 406720 BLAKE2B a7e5a20b8fd1eb1ba562b5db6643542d5062b270d69a2c53aa66f5cb58f48f1d3a480ae062e53341a884eb497fff22d546df42256cdc131afb183067166fa8b6 SHA512 eed75693557f141331dfb6bec6961a8f6eab93780cad3b629d547b8635be2df6ec85e5ae0e9646d174a562a0f6d31c3c487a4dacac9efdd393a7144cd5716878
-EBUILD embassy-iprscan-4.3.1.660.ebuild 360 BLAKE2B c4cc140e02c9eced5cff9976734fcbccde4a61d259cf1787a0a744f0639ea12c27d173e8badfc649f7779dd18978523dc1acf86174e1eccf697351c839fa4c9e SHA512 5e4a54bd7fb3d0522bee736678a7e8e590b07635137089487412c23c2717c6fe9b6aa1075fcf2b8c94656388fe2594c78f5c0f7c9eef91807c355809d82ca527
+EBUILD embassy-iprscan-4.3.1.660-r1.ebuild 392 BLAKE2B e878bd7a924ebabec06e597403d9da47f8f8cdc7e8a2fc930c79127a361957d404ae4e7386429d14a1e20ed902908e9e93daae5e97f92a71cbdab8f0ac2f5d2e SHA512 340ecc929102942ddd3f4c7471fa55c00386fd88fffc9a99b6ecc9fbd99e71f8545b55c099a17058c4b59e6fc3406995d7cd0793e1819482e848c5f2b70ac1aa
 MISC metadata.xml 348 BLAKE2B d71aba38f248b80e63e5805f1c0f710815220774a8a514f69a708666c647f061a3f295196da119cec9b5681648a54a1915073039302586d17540296855a255df SHA512 4f8c9238704b81e38abad62bc92e67ad08fe30907277794ee5a4265f4dd8e69fb1b4cabead1fc45c48888c3dbe30496b2c7df3b1c8fa2662f87a4deef32661cd
diff --git a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.660.ebuild b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.660-r1.ebuild
index 351ecd1df3f8..4dd5c3cb354e 100644
--- a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.660.ebuild
+++ b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.660-r1.ebuild
@@ -1,15 +1,18 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
 EBO_DESCRIPTION="InterProScan motif detection add-on package"
 
-EBO_EAUTORECONF=1
-
-inherit emboss-r2
+inherit autotools emboss-r3
 
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 
 S="${WORKDIR}/IPRSCAN-4.3.1.650"
 PATCHES=( "${FILESDIR}"/${PN}-4.3.1.650_fix-build-system.patch )
+
+src_prepare() {
+	default
+	eautoreconf
+}
diff --git a/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch b/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch
index ab627c323253..7af8ae2f9ca5 100644
--- a/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch
+++ b/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch
@@ -1,5 +1,5 @@
---- a/configure.ac
-+++ b/configure.ac
+--- a/configure.in
++++ b/configure.in
 @@ -635,33 +635,6 @@
  
  
diff --git a/sci-biology/embassy-mse/Manifest b/sci-biology/embassy-mse/Manifest
index 0bebb593f522..13d152a70843 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 3968 BLAKE2B 97999702bc800bb02c0c77969e17f4ab36e6491d494ff09c3fbb20624f75db7392a5c1dbe91d977e3596855a89ccb70525c01cf7952364fb4bac4a8f403ea5d0 SHA512 8abaabce2566d42209e6863c30c6cbb392afc900d52f819e975662699651b7114257a372a50657419355d0af69f1dea80501fe2b3cf57ce1c8ca731d1b7557e4
+AUX embassy-mse-3.0.0.650_fix-build-system.patch 3968 BLAKE2B 93a61bae2ec37053f3c014634181bae9859e68c92bb2d5fe99fda09d5f083d19a2b3c8cdcf0117d8dfc34f6d892c44f1817115f2619a47909bc26e0f766a5429 SHA512 4824292eb41cb75ca038be63a8b4985b119a80426333f42a83c9316b69bc6431355d5637d3a30e6b42307ec4cc7603e53250bda9ef3fabbd00e3885a5252e73a
 DIST embassy-mse-3.0.0.660.tar.gz 491747 BLAKE2B 7d072458577a90fc367c5b6ed72d1d36592e42b83b3a4e31126b925ddc76f1946fba14e22b7410f66eb837f686f848bdb1033f3b62084f1423543d7605c4f6b9 SHA512 4ae34de71566464e4352ff7b3bbd19b8bf0571013f34253495cf5cc57240bac9c75192c302eb0231763db1745a7e3e79ebcdcb006e36ea4621a886b213eb96d3
-EBUILD embassy-mse-3.0.0.660.ebuild 539 BLAKE2B 91a33c56fb6a4d36f5d4ea39d0c2da09790e4020113c08ee9b4f994882ae20ffae9aa2a5c02d016c5fd01dbc1c389417cc7be138404c71118ce26b8868c2501b SHA512 471381ef53268938a0b166904e070ca12ef4c541900f62205300531c70b67c419fba6b312649b25c3b7a68b493ba84eb0c9b05239b927ff029bc8e7156f92388
+EBUILD embassy-mse-3.0.0.660-r1.ebuild 570 BLAKE2B d5ec39363a6682dca1070762f22c9ba34fbc98282204b78dcb369753a394a17fd69866cbe57acc2a9e73211bdf1397abaadb1130ec2d96ddc333837e07fa89e9 SHA512 49298c9f723e5cfc03f098c971781d483f2311d62a6f077bd6897a3fde3b37e26132267110c00ba9ee9de7f894b7ee2a4cb0755afe7ed8bea19f9a47f5a9a5aa
 MISC metadata.xml 338 BLAKE2B acd164074e32c1d0d2b3806e491017e350b45603515e368127fe6c1d9aefd305873d9dda8ed181da325f975043411aee91bebd2d8554c31976f618f6324e9456 SHA512 8cf0ad2755a86551c8bfdde159e2c25a1048a04f0f32c37b29a526ca29233d7eb76ad1704c70194745cf167b359f23529cbba5bfeb8003b833e6f22e0d4a333e
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-r1.ebuild
index cd9425254fb0..a806410e6366 100644
--- a/sci-biology/embassy-mse/embassy-mse-3.0.0.660.ebuild
+++ b/sci-biology/embassy-mse/embassy-mse-3.0.0.660-r1.ebuild
@@ -1,28 +1,31 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
 EBO_DESCRIPTION="MSE - Multiple Sequence Screen Editor"
-EBO_EAUTORECONF=1
 
-inherit emboss-r2
+inherit autotools emboss-r3
 
 KEYWORDS="~amd64 ~x86 ~x86-linux"
 
-RDEPEND="sys-libs/ncurses:0="
+RDEPEND="sys-libs/ncurses:="
 DEPEND="${RDEPEND}"
 
 S="${WORKDIR}/MSE-3.0.0.650"
-
 PATCHES=( "${FILESDIR}"/${PN}-3.0.0.650_fix-build-system.patch )
 
+src_prepare() {
+	default
+	eautoreconf
+}
+
 src_configure() {
-	emboss-r2_src_configure --enable-curses
+	emboss-r3_src_configure --enable-curses
 }
 
 src_install() {
-	emboss-r2_src_install
+	emboss-r3_src_install
 
 	insinto /usr/include/emboss/mse
 	doins h/*.h
diff --git a/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch
index 23e656dc0a86..72d7932a188d 100644
--- a/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch
+++ b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch
@@ -9,8 +9,8 @@
  
  CKITSRC = datafiles.c next.c seqentry.c strings.c gcg.c pir.c \
  seqspec.c ttyinterface.c nextseqentry.c \
---- a/configure.ac
-+++ b/configure.ac
+--- a/configure.in
++++ b/configure.in
 @@ -635,33 +635,6 @@
  
  
diff --git a/sci-biology/embassy-phylipnew/Manifest b/sci-biology/embassy-phylipnew/Manifest
index f750851e5b3e..04367b5bf202 100644
--- a/sci-biology/embassy-phylipnew/Manifest
+++ b/sci-biology/embassy-phylipnew/Manifest
@@ -1,5 +1,5 @@
 AUX embassy-phylipnew-3.69.650-fno-common.patch 16289 BLAKE2B 346f5d704be918503a80ab224e1892953a2d1d6ef642e6ced95fcb1476954e09d983bd0eef1d6afe71d2c4e043a05a99dd92748151e337ac5d3646d91008c2e9 SHA512 0ea1f10865832a44647f0888eabef1df6e5baadace9fda782f171d52eef70fc7d8ef80317d46eaeb029896b8b0b4ca0d845561ae761daf406f7c26e18ebd1341
-AUX embassy-phylipnew-3.69.650_fix-build-system.patch 3019 BLAKE2B 39c2d7843ffac8c0a04c70d307d5651f2e53cc386c3a9b1f312d4fd53a9b9ba235a02931c4812a750da8711988e262b1c9a51a7152da20f61cd56c0d21607a89 SHA512 7d46280ffadcbc07e01d09a49a7896539a5c0c271979fcb3e1ffdf385051812adeaabec186c73e2105a710eee2fd340d89bbcbd4ecfa112879fb00cbc58c2dfe
+AUX embassy-phylipnew-3.69.650_fix-build-system.patch 3019 BLAKE2B 94bdca3ee696570f1f6c82cdc3e948d8e48621ed3537c98f681e953a0ce88fe790b2a8ef60cc836cd2d9c303348cf13b2bc27ccb411714880da98af9ff0d42c8 SHA512 3ce374ac3d2537fd307e310357c6efa8b66330475c6fd383dd83a7507fe179796cbfb4c25036b3254731467a0dd5798b9024e9b6009c905df3990a168a528a6b
 DIST embassy-phylipnew-3.69.660.tar.gz 1741298 BLAKE2B 58a2c66ffb9c447fa17462bf54d7b8e65702701d74c1f16ec6906a3acaf076ebcab30982befe6334101bc483901132069a71ffa0e2334aaee0da02a30276b7f2 SHA512 b41a31285e05a418e4fbfae7241c3658fe458e3d5d84bff472d98b7c145340a55bee1d744b5c056d0e88407074947b5f37b2182c9cb800c8a8d43dfa76d026d5
-EBUILD embassy-phylipnew-3.69.660.ebuild 409 BLAKE2B 52d2e35042acda08f96cab28de1d0dd2c31c6824df7541b195644f67a8325b35b4ce34d8eab9710f0239466feeaa4c0f5f20017891812e702671710797fd0315 SHA512 7511f44570ab985948b8daf6b9267235a930d0c70fc17cff754393e3c2d9028db5360dc60642398a5fd951ae412a70d6d5610a0008137ef646040ccd1904ba27
+EBUILD embassy-phylipnew-3.69.660-r1.ebuild 441 BLAKE2B 773748fdfc603bd1134d4324f3e24ff49bfd2f4cf4f6a033aaa708aea2c3475f20a1467becbb3a965b07b2b77ec6dd2a1e6ae0d3f3ad1c4fe0e8ee6512b588fd SHA512 b075fe9ae13b226dba97252706cec3d5da279cf9be3225a29c7d673a21dcff4fb05d860d75a59f2b7a611c2c640df9d8c34272f72ae25f2b8be475255ff8a034
 MISC metadata.xml 348 BLAKE2B d71aba38f248b80e63e5805f1c0f710815220774a8a514f69a708666c647f061a3f295196da119cec9b5681648a54a1915073039302586d17540296855a255df SHA512 4f8c9238704b81e38abad62bc92e67ad08fe30907277794ee5a4265f4dd8e69fb1b4cabead1fc45c48888c3dbe30496b2c7df3b1c8fa2662f87a4deef32661cd
diff --git a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660-r1.ebuild
index 129b42870a79..d7dc57a64fc8 100644
--- a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild
+++ b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660-r1.ebuild
@@ -1,13 +1,11 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
 EBO_DESCRIPTION="The Phylogeny Inference Package"
 
-EBO_EAUTORECONF=1
-
-inherit emboss-r2
+inherit autotools emboss-r3
 
 LICENSE+=" free-noncomm"
 
@@ -18,3 +16,8 @@ PATCHES=(
 	"${FILESDIR}"/${PN}-3.69.650_fix-build-system.patch
 	"${FILESDIR}"/${PN}-3.69.650-fno-common.patch
 )
+
+src_prepare() {
+	default
+	eautoreconf
+}
diff --git a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch
index 95951e632188..589408ed4a9e 100644
--- a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch
+++ b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch
@@ -1,5 +1,5 @@
---- a/configure.ac
-+++ b/configure.ac
+--- a/configure.in
++++ b/configure.in
 @@ -635,33 +635,6 @@
  
  
diff --git a/sci-biology/embassy-signature/Manifest b/sci-biology/embassy-signature/Manifest
index 168fa527c1c5..ad0a3f25318f 100644
--- a/sci-biology/embassy-signature/Manifest
+++ b/sci-biology/embassy-signature/Manifest
@@ -1,4 +1,4 @@
-AUX embassy-signature-0.1.650_fix-build-system.patch 2775 BLAKE2B ca267498e98a294546429cac0c4276fe7c3dbdfc199d151bb7fc758e805a0f7b6de25094a2f9ec00e21b52a617176a8d45d20424cfbb37276bdc4a0000fb8ed8 SHA512 5e4f72d2960f17a2c758f6bee15f9ddd317e55ae338c46f2b915beba334729d837f573833b54310284db59fa1f1b397d8981ab4b91671cc95bcea7d441820911
+AUX embassy-signature-0.1.650_fix-build-system.patch 2775 BLAKE2B 969924f19b592fca784d4084a3a991bd3502fd312732588358fa5bccd41946b707a3ab0a7fc5622f1ec9019c5aa24f716d87c7d04f54044f34da028fe3cda028 SHA512 0117673cc5ea57e807486270c51b57bc262a47613e067ded557963929e3eec9a6087eeb3c34138b64104cfb20969c5826dade028d395201da2936422f99ba2a9
 DIST embassy-signature-0.1.660.tar.gz 622294 BLAKE2B 8d495b164d7aa18b4bc2db14d12e3f3ef46f2d9c6d9f98e46bebd888781ee71e7ddf88dbdb37c7be52fdd1182337ea7c70cca1247489a14f652b86918e58c46a SHA512 4989693b17c29ece16f94934e1b2f5e62f31c345bc8cbac938450db0d8f5d56ae37be6090c46e96725e63621c5951f8a65461cd36d4aafb1b509f3f554b4e952
-EBUILD embassy-signature-0.1.660.ebuild 334 BLAKE2B 3102c22d5f604cb3241730df137049d99fda38cd1f02a4120c58669c388c2881c6ecc9b9abbe47be05f58a8b6fe0c0fee9fc210eaaf73044aa7987de26cd609c SHA512 d1414951385d7301aa45881866f55433a37f9938e5be14de9d2056a8b87e16767c45421a0e0462c8609806afb379114578b0b3d4908008ca16a780638d8ab9e1
+EBUILD embassy-signature-0.1.660-r1.ebuild 366 BLAKE2B 144bec25d93cf62c18bd1b5095b38540928821e8a52b0da5340dec29583a36a4021261a6817fc9999b70f410cedd2cb7da04c94bdbd6ba5ef47af6f477d6edb4 SHA512 6b0a9086d99bce3e7f7b25b5faf6659468d6af0cc06269ddeb77a915cc4789c9e76bfbc5ee53ee003cea0e1ac5efeeb0af141461a87069d22371753f8970e91a
 MISC metadata.xml 348 BLAKE2B d71aba38f248b80e63e5805f1c0f710815220774a8a514f69a708666c647f061a3f295196da119cec9b5681648a54a1915073039302586d17540296855a255df SHA512 4f8c9238704b81e38abad62bc92e67ad08fe30907277794ee5a4265f4dd8e69fb1b4cabead1fc45c48888c3dbe30496b2c7df3b1c8fa2662f87a4deef32661cd
diff --git a/sci-biology/embassy-signature/embassy-signature-0.1.660.ebuild b/sci-biology/embassy-signature/embassy-signature-0.1.660-r1.ebuild
index 4d873a69a69a..6f04a1432d9b 100644
--- a/sci-biology/embassy-signature/embassy-signature-0.1.660.ebuild
+++ b/sci-biology/embassy-signature/embassy-signature-0.1.660-r1.ebuild
@@ -1,15 +1,18 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
 EBO_DESCRIPTION="Protein signature add-on package"
 
-EBO_EAUTORECONF=1
-
-inherit emboss-r2
+inherit autotools emboss-r3
 
 KEYWORDS="~amd64 ~x86 ~x86-linux"
 
 S="${WORKDIR}/SIGNATURE-0.1.650"
 PATCHES=( "${FILESDIR}"/${PN}-0.1.650_fix-build-system.patch )
+
+src_prepare() {
+	default
+	eautoreconf
+}
diff --git a/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch b/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch
index 10bee217bab1..a453b25bde66 100644
--- a/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch
+++ b/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch
@@ -1,5 +1,5 @@
---- a/configure.ac
-+++ b/configure.ac
+--- a/configure.in
++++ b/configure.in
 @@ -635,33 +635,6 @@
  
  
diff --git a/sci-biology/embassy-structure/Manifest b/sci-biology/embassy-structure/Manifest
index 05300119825b..ceaea7a0ce8a 100644
--- a/sci-biology/embassy-structure/Manifest
+++ b/sci-biology/embassy-structure/Manifest
@@ -1,4 +1,4 @@
-AUX embassy-structure-0.1.650_fix-build-system.patch 2775 BLAKE2B 2ef40db164efb8fa5dc3bbe06f5edbd7b2dcc9249e5a58ad3ec21feca8fcabbc78e317a1ea9a7939a4947088abe315c1cc6714fda0c20449a4cd527c1c112cff SHA512 19f51e9f1bc69f0807ee7f3d6bf8d2d21563c0a21eb08bee38cc0d9e68fb0cc1b8035402933cb8e5c12626d5b6a0b7e470518c503eaa5b1d34cc7548bccd6b21
+AUX embassy-structure-0.1.650_fix-build-system.patch 2775 BLAKE2B 15b9f5fb9855259f389259842cfcb8b078154e9208fb9b8faeeeb2581a3164cc75e433f8ba2c9cd1e70281d715325f7a2b4265406feba922881b36101de8e185 SHA512 8e77c1d98189162b964d8e2107ff4df1b9bc96096b1b90d510db3492617af59ae742e9083bcd4cffa20ff029da65edfa22fb4434bef0e10c588d347a661735a0
 DIST embassy-structure-0.1.660.tar.gz 588118 BLAKE2B 2723eebc309c81cc94fea687819de2c76d30ce87bb7c6dac12e9964c73fd18b497a31db07d12803d87799e42063b73d406520434482bcdb29f23a14756d11750 SHA512 56fb0ed975bfd95b1fbbccaf694e0617ec23971d53bdc230eeb6ca177907e784805697193e7630e4a513f1b4ee7a1a7974136520963557c452185be4ed22b641
-EBUILD embassy-structure-0.1.660.ebuild 334 BLAKE2B 53e652e9d8c396dc29f76a4142c64488918d01b73d94af8d06356440d1b1e99641941c7d6771b1d53f42448802f56592ad20f0ce8d50be32c1feafdbae1cb31f SHA512 9001c1dd9cc59c5d266b7945153b9cb0092a30654ca42d32e7ba0712231d44fa96c1d74f639f61c360a2576d224fc601ab4714c665d860f4c053b6a2dc36a978
+EBUILD embassy-structure-0.1.660-r1.ebuild 366 BLAKE2B ee9302a4bf087a146c1d37cc488280c9453c09e0d7a7ba7d91d293f3a05ed73ec42a3ab02668716f1a66e8deac2688e1e9829cc609936b3c8565a5b5e67d7707 SHA512 8eec442f750b145e2df45f35297ce5cabe9504becdccc2b184166c2667b4f458143cbf9a4b80212491f2ec2a3f4141bc713c7b8cce7613c74182f9c27934918e
 MISC metadata.xml 348 BLAKE2B d71aba38f248b80e63e5805f1c0f710815220774a8a514f69a708666c647f061a3f295196da119cec9b5681648a54a1915073039302586d17540296855a255df SHA512 4f8c9238704b81e38abad62bc92e67ad08fe30907277794ee5a4265f4dd8e69fb1b4cabead1fc45c48888c3dbe30496b2c7df3b1c8fa2662f87a4deef32661cd
diff --git a/sci-biology/embassy-structure/embassy-structure-0.1.660.ebuild b/sci-biology/embassy-structure/embassy-structure-0.1.660-r1.ebuild
index 1c5bb1e9a967..ba0b94964d2f 100644
--- a/sci-biology/embassy-structure/embassy-structure-0.1.660.ebuild
+++ b/sci-biology/embassy-structure/embassy-structure-0.1.660-r1.ebuild
@@ -1,15 +1,18 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
 EBO_DESCRIPTION="Protein structure add-on package"
 
-EBO_EAUTORECONF=1
-
-inherit emboss-r2
+inherit autotools emboss-r3
 
 KEYWORDS="~amd64 ~x86 ~x86-linux"
 
 S="${WORKDIR}/STRUCTURE-0.1.650"
 PATCHES=( "${FILESDIR}"/${PN}-0.1.650_fix-build-system.patch )
+
+src_prepare() {
+	default
+	eautoreconf
+}
diff --git a/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch b/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch
index a67bc80f2a23..32826f8ebbbe 100644
--- a/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch
+++ b/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch
@@ -1,5 +1,5 @@
---- a/configure.ac
-+++ b/configure.ac
+--- a/configure.in
++++ b/configure.in
 @@ -635,33 +635,6 @@
  
  
diff --git a/sci-biology/embassy-topo/Manifest b/sci-biology/embassy-topo/Manifest
index 20e01db138f3..74dcd9ddaf1a 100644
--- a/sci-biology/embassy-topo/Manifest
+++ b/sci-biology/embassy-topo/Manifest
@@ -1,4 +1,4 @@
-AUX embassy-topo-2.0.650_fix-build-system.patch 2944 BLAKE2B c9535f630899346a43a993c3563e202792610c751940a2aed3d41fc633fcffb53c372c702c19104fd709dda6b6093c4897d19336028312757135ccacec3cd8af SHA512 981326c4b27a0db091494da5a2d6215dbdac31544b33601765329c7b4e817ccdcc39e795cdc14719211a8726cb7761d070e83e234e878ac7f82bd226851ad1be
+AUX embassy-topo-2.0.650_fix-build-system.patch 2944 BLAKE2B 8668e8af9160f8da216abf570dc010445e6660bc03b4109ed045a9b720bf0384eb5a96ae8ed805d1053a677d4727536a03e2e6d3f7b9e09f9d6d2331db8a5cf1 SHA512 afa5434267d6b21f5e7cb472784b5d12fa8f320d0c167af250c0a9f108a6d33ebdfbefbc62f20eae02126fc17f76d2c314fc65c6685bb2345cf194843264e149
 DIST embassy-topo-2.0.660.tar.gz 443510 BLAKE2B ba49debdfb9f13051bd32d0d14de3b446a8fde83923e6927df52fd989460c60b5d3023aeaa84d3ab920533c40607f7ba274f64827cefa611a1513f203e08316c SHA512 8ef157a61ac47680734bed3d07cfe2bcd86730998453daa704b74aad667944ad6b0cc6f7fce36be4566cb19a626f1648d5f6793ce227cf57939fcfd0d10690a8
-EBUILD embassy-topo-2.0.660.ebuild 339 BLAKE2B 97a0643d61e7dd61025ee0ea1b2b0429bc843737dbed7e53ac955c60c2540a0372b1ad15f8a00d884943e7b791c4e98eb5c04a4fcb1992f031c9a40d1011860c SHA512 50f5b9a761e053206a6a3d1021e5cdbf9f1d557c300185e3d42353f593c2e653263f4a640c536fee938c74ac4924ef54eae9a9df233b32900f544f3512ce46e5
+EBUILD embassy-topo-2.0.660-r1.ebuild 371 BLAKE2B ec403fedc655b43d201c30319434a6adc4511e94fbeb79deeff4fbca64f14fc90343493dc1d5d53e20f6e6775029cebbd29fab4bb8e6beced84381d9e52d1197 SHA512 208ca5300b57744c6ba124d3749b5f29ccb215d38a8e863579bf965aaa552310af76c583deb3a5b40a3d552f280f32db0a5094052c15522b16d255224b17d961
 MISC metadata.xml 348 BLAKE2B d71aba38f248b80e63e5805f1c0f710815220774a8a514f69a708666c647f061a3f295196da119cec9b5681648a54a1915073039302586d17540296855a255df SHA512 4f8c9238704b81e38abad62bc92e67ad08fe30907277794ee5a4265f4dd8e69fb1b4cabead1fc45c48888c3dbe30496b2c7df3b1c8fa2662f87a4deef32661cd
diff --git a/sci-biology/embassy-topo/embassy-topo-2.0.660.ebuild b/sci-biology/embassy-topo/embassy-topo-2.0.660-r1.ebuild
index 3c16f7bf4fa4..583d93297669 100644
--- a/sci-biology/embassy-topo/embassy-topo-2.0.660.ebuild
+++ b/sci-biology/embassy-topo/embassy-topo-2.0.660-r1.ebuild
@@ -1,15 +1,18 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
 EBO_DESCRIPTION="Transmembrane protein display"
 
-EBO_EAUTORECONF=1
-
-inherit emboss-r2
+inherit autotools emboss-r3
 
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 
 S="${WORKDIR}/TOPO-2.0.650"
 PATCHES=( "${FILESDIR}"/${PN}-2.0.650_fix-build-system.patch )
+
+src_prepare() {
+	default
+	eautoreconf
+}
diff --git a/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch b/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch
index 600e38928aff..e1a2439b713b 100644
--- a/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch
+++ b/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch
@@ -1,5 +1,5 @@
---- a/configure.ac
-+++ b/configure.ac
+--- a/configure.in
++++ b/configure.in
 @@ -635,33 +635,6 @@
  
  
diff --git a/sci-biology/embassy-vienna/Manifest b/sci-biology/embassy-vienna/Manifest
index a79bc4c310b6..29303d58262b 100644
--- a/sci-biology/embassy-vienna/Manifest
+++ b/sci-biology/embassy-vienna/Manifest
@@ -1,5 +1,5 @@
 AUX embassy-vienna-1.7.2.650-C99-inline.patch 1457 BLAKE2B 0911b395427e1564d89557a1312e54fb414d0413aa368a8d93fe71dd821af828127c387ba561135e2ba4e16a9e1f9cdeac18e9b0c750844fc8eea3ea65c7e6b9 SHA512 c9a2e8004a7a0ae4e7078ccc223f0b2c16386c56a6458596c32de0afbdd6498cc9a01514a70f137ad0d12cffbc0a237762ae5440cce604f86428fe319983efeb
-AUX embassy-vienna-1.7.2.650_fix-build-system.patch 3349 BLAKE2B c6d12bee84b5bc5bb987929a1d606c28cab1d5bb318fdf294f01569d90ae4736c818ddf3d5d2fd506fe3d012c35d320c74c0b3185540e19a03b0e7dbcac9e0d6 SHA512 4da6e09711974bf10259558f78208d207f3e07b0156488acfce788d83f05a6872246d6acf3c318195285e1d84b3788aec65d82f989c682b56129c4dfb6df8eae
+AUX embassy-vienna-1.7.2.650_fix-build-system.patch 3349 BLAKE2B 5fd926d703e0d842a568ab17b2d106d22973585dd13b0cfadb4d1e2d01d874091d90c46f6e183cbfca412c6137456216e0c15279fa1dc66a169bf78ebc60c9e2 SHA512 a2e08357e3ca326979ad933520739512b536bf49b9f863836fbc49b041cc2daa33362ad0737a6e5fa584cbe8e256f00ef6fa4f59a71df277a9b056189b0f803e
 DIST embassy-vienna-1.7.2.660.tar.gz 873165 BLAKE2B 46e976e52ad65490237563af09e483c212a6170c8c79fac8a2f2609040ee6a4cf60c04b00159c4c33d8c2a10f6e457e412287409fc0ea5724c5687dbd65ff06c SHA512 1484ca419ebcb7776d8f92dd633d4fda1a752a73ccb5189b58f7417a5611e015e9b42cbb37b51f4d5c7a27df0d5cab2cdf1e95ebd70a8359ffc8fa1633d28103
-EBUILD embassy-vienna-1.7.2.660.ebuild 397 BLAKE2B 9f190749fed69294abeec16e993515ade0b94d5c99b00a47775ac702cedb1c01d789dc9b34e54dd64ae0e3b692e7d36a267b6e3a801de64b4dd77479ed2fd1e0 SHA512 b27a9747ec96c704ad6eebf9a122dc97f9d2995f97a44195641573fabd0cd69c6ca9e5dca58a77cc525e8175230a8e86898bcc328089fc04f3cb97cc5516e8c7
+EBUILD embassy-vienna-1.7.2.660-r1.ebuild 429 BLAKE2B 59062d9524c586694b647f8032319dd0ade9ba48e7f292dd879395a712100ec197b47ec49ba07dc8d084eed6f7bb98c71a705fcbbd892c2743649f9f89d8e003 SHA512 476bca0e3470a90273ebfe990236cbc8a3e8a4cb44142df158e0d34fb2256095934cd434db6a0f63cf663983c2dd7c16f4db770b212f95144621eb7843481732
 MISC metadata.xml 348 BLAKE2B d71aba38f248b80e63e5805f1c0f710815220774a8a514f69a708666c647f061a3f295196da119cec9b5681648a54a1915073039302586d17540296855a255df SHA512 4f8c9238704b81e38abad62bc92e67ad08fe30907277794ee5a4265f4dd8e69fb1b4cabead1fc45c48888c3dbe30496b2c7df3b1c8fa2662f87a4deef32661cd
diff --git a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660.ebuild b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660-r1.ebuild
index 35143accb01a..241194af375e 100644
--- a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660.ebuild
+++ b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660-r1.ebuild
@@ -1,13 +1,11 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
 EBO_DESCRIPTION="Vienna RNA package - RNA folding"
 
-EBO_EAUTORECONF=1
-
-inherit emboss-r2
+inherit autotools emboss-r3
 
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 
@@ -16,3 +14,8 @@ PATCHES=(
 	"${FILESDIR}"/${PN}-1.7.2.650_fix-build-system.patch
 	"${FILESDIR}"/${PN}-1.7.2.650-C99-inline.patch
 )
+
+src_prepare() {
+	default
+	eautoreconf
+}
diff --git a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch
index 8bd816b0e672..ea96e9d47fa9 100644
--- a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch
+++ b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch
@@ -1,5 +1,5 @@
---- a/configure.ac
-+++ b/configure.ac
+--- a/configure.in
++++ b/configure.in
 @@ -649,33 +649,6 @@
  
  
diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest
index 5ba17fa64771..5dbcc22ef285 100644
--- a/sci-biology/emboss/Manifest
+++ b/sci-biology/emboss/Manifest
@@ -1,5 +1,5 @@
 AUX README.gentoo 1522 BLAKE2B 566213e78e6c74fc6c8745391fbdbc477c9d1793f74e68fb0465ba4f842203e1670dd6216c4181326a4ccbf0c051daa99a376a15dd5b0714473f84ed8404e8f7 SHA512 a5441a056ebb11d24b83b8bfb9182f0753b85ec5ba126a123eb97c55fc665dadff2cc5f16c8e4314535f1b6a206c200324c0c5d5db6af109c841ee68ac76bb07
 DIST EMBOSS-6.6.0.tar.gz 117962028 BLAKE2B 91bf3c680290bd975d2ddb5251089d7f75f8a44a26e1247e93d2c9cf2f23e6b89c4218022ba1af0c940136ff56782f40d2c4604dc756b400ae23f223da7f3cca SHA512 2d28a03381f7dc98d205aa50202fbbac02ad218fc775d86579d310296be124403623484b1907154d915f15cd32a9f8cf16ecfaa6c4a28b362e24dc8e6380b75a
-DIST emboss-6.6.0-patches.tar.xz 5408 BLAKE2B ec1c55c90a64b1c27645804411b44e413ae881b1637ad2b8dfcff172e15b841cc3d2807039761f8307b0b5a29ab5b1a2c840e189f326091aa9ce25317ec9cda6 SHA512 942681df428f6254c1711902f667c6e8c71babf3e9b0c73b8b7d2fbfa5e8856ce5817560280948e588f6037011ad7055a3af5b88a58fc2b14349869927c889eb
-EBUILD emboss-6.6.0-r1.ebuild 1827 BLAKE2B 4e8b0902b12d390abadbf5c9a9e2824a94bc5513aadb87959eb2faf245ad75246ee3080f75e2ebfb34792471e65350a3cee2a7f08837402b43d7e5608eb181d7 SHA512 e5297ce7678262a91c8749217f094a944b87eb157893542fe89fa6ffb770726959dfe8fd1a1f84aa349432a636419cf2cba6950e83bcc1a6c0156c97144b075e
+DIST emboss-6.6.0-patches-r1.tar.xz 5384 BLAKE2B 7899141862880d000e1624e9df914b1918cd02645c0d14128bcffd41d76e3669404a718f25471795268e4a00d610377186b7cb73a126e30f74df80d04d22faf9 SHA512 95825a3bcaa6340d26fde65f3b77574e42fd424440ee48f2fad94b6e696346fe4f6e4ab48c7dcfe1e9c3311a8a7750defc004c2db40cc36f42e980a19e6bd0bd
+EBUILD emboss-6.6.0-r2.ebuild 1855 BLAKE2B 1d280f09c2a691759c3cd675e678f2bee3deb618f8fdd2078ceb802af82d0c7b6dd81f5bbcb8cfe6b9eb391c26ffcfc06e74c6ebec67411feda2e165eeed2418 SHA512 2ff60e56bd90140cd608e97897e0bb7e40eeced3636a69b263312ec88fabbc21dd7dfa607d1649f07e7119a189e7a23ea0fafa7382f5c96077d80fd0b520e47c
 MISC metadata.xml 1097 BLAKE2B 76363bb35212d819328fc6ef0fe303ed3819ebd3c1742039af2863ffc1fd4c7c5cff20b6451aa92b8718487ec1a7d2a2fff8236088b8bd945b1c439a4de09115 SHA512 4b1afa15e346442138361754f9ec176a36194c6b77d002f26cadf16f1ba0f57219274144e41125ef37668f5d9e892ae370cc98e6b6ee0ded83a233ace417a0ee
diff --git a/sci-biology/emboss/emboss-6.6.0-r1.ebuild b/sci-biology/emboss/emboss-6.6.0-r2.ebuild
index 766dd6a61b0c..01af5e2fa977 100644
--- a/sci-biology/emboss/emboss-6.6.0-r1.ebuild
+++ b/sci-biology/emboss/emboss-6.6.0-r2.ebuild
@@ -1,16 +1,14 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
-EBO_EAUTORECONF=1
-
-inherit emboss-r2 readme.gentoo-r1
+inherit autotools emboss-r3 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
-	https://dev.gentoo.org/~soap/distfiles/${P}-patches.tar.xz"
+	https://dev.gentoo.org/~soap/distfiles/${P}-patches-r1.tar.xz"
 S="${WORKDIR}/${P^^}"
 
 LICENSE+=" Apache-2.0 GPL-3+ CC-BY-3.0"
@@ -39,13 +37,18 @@ PATCHES=(
 	"${WORKDIR}"/patches/${P}-Wimplicit-function-declaration.patch
 )
 
+src_prepare() {
+	default
+	eautoreconf
+}
+
 src_install() {
-	emboss-r2_src_install
+	emboss-r3_src_install
 
 	readme.gentoo_create_doc
 
 	# Install env file for setting libplplot and acd files path.
-	newenvd - 22emboss <<- EOF || die
+	newenvd - 22emboss <<- EOF
 		# ACD files location
 		EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd"
 		EMBOSS_DATA="${EPREFIX}/usr/share/EMBOSS/data"
diff --git a/sci-biology/fasta/Manifest b/sci-biology/fasta/Manifest
index a9a197a0cebd..bdbbddf97625 100644
--- a/sci-biology/fasta/Manifest
+++ b/sci-biology/fasta/Manifest
@@ -1,4 +1,4 @@
-AUX fasta-36.3.5e-ldflags.patch 2781 BLAKE2B e6d4e0984b4dadfc9d38504ab215d769084edc6c79cfe641b6b3fba8264a40add1665027295ec4afa19d26277036bfe1a5103ecdf72ef91a1139542ac8272954 SHA512 5424bb8385def72ff75701c2da153f697520cbec82f36cbed8de0e98f93d399de660e79da7700ab0ff688fd5388cf9f42a30ccc4359335ae02042bf8cbb3aae7
-DIST fasta-36.3.5e.tar.gz 943763 BLAKE2B 6234d0aee76af6614e6d25ebcfbdfae080db5bc5adf611aeb6edc53ed7c6cb6cef257bf852ed39bc286527cec4175c251765ce23ea5ff39d12ff8947dba97ac6 SHA512 ddfcae36dadd7e2ed5c8c8c0bda2eed077e9f6cd55e4ebf507690671af156358e9da4e7cb1406d2b8713c326c54a9d829fc25e668b16dfa6df48d18e3a009812
-EBUILD fasta-36.3.5e.ebuild 1632 BLAKE2B 6165b7f1fc3440d94b337c13c0d520e5848d14b95720a27d941594355d70233af1c9db75e30603e4ae817ba2d2f3b1f5f7711dbcf37a2881effaade2608bc175 SHA512 f4c5cf2cb35e653d14c6afc8fd56743c8f7afb6302dd6227aec04bd8cb3efa9846fe32b6078b1b3dda94359857a214ec1580a2905aacb4ea9ed5234e2667b51c
+AUX fasta-36.3.8h-ldflags.patch 2291 BLAKE2B 61c0b7d82a4c138e82148f354576fbeadf38362337ae6d2ecdb23aea5c4dbb3719f3889a0479ea2b48de8e2c3e19c5b61a7b9508507fd7f61289205b93e899ed SHA512 a34021b398e077a409bd31508b0736e7a0fda533d86b26efe998227ce628414796a0dfd88b0010154e25ef79148b1b9acac4cd94cb7aa72a59fbcbd1fbbb6726
+DIST fasta-36.3.8h.tar.gz 1257682 BLAKE2B e6bd9087563150355fed6edf52a24a0b31ef0658b1e95c3df6d5b5711fc4d137ddd773fb8b3b2fa82fe3f5c310689b2f89668f5b51654eed41ed71f9ef140f99 SHA512 30d160ad083a605397c6c35d2b28f6064cd96f51f99b3664b424ec1dbbbd09772c72e89731a7257306ab58c4ad4b877e229873abd0e09407c64fae643bc04391
+EBUILD fasta-36.3.8h-r1.ebuild 1707 BLAKE2B 73197e61355b74a56ded2f3ff9feb3301d5831fc732419a8450db33a60b78473e6875ae6fff33e86996b255ddf9a6383e28ca66a1bfef105fab31320a6f8a554 SHA512 f3525c06e2937462f66dadda89c43cd4dd4b57b9b8ac0d37d34c3d4b8addd3f515f973af23644ea44f823e1855edecf98e94f1350acbe96e81b5aac57dd9e680
 MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de
diff --git a/sci-biology/fasta/fasta-36.3.5e.ebuild b/sci-biology/fasta/fasta-36.3.8h-r1.ebuild
index c4c94d0e7f21..1c396edf4586 100644
--- a/sci-biology/fasta/fasta-36.3.5e.ebuild
+++ b/sci-biology/fasta/fasta-36.3.8h-r1.ebuild
@@ -1,13 +1,16 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=8
 
-inherit epatch flag-o-matic toolchain-funcs
+inherit flag-o-matic toolchain-funcs
+
+MY_PV="${PV}_04-May-2020"
 
 DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package"
 HOMEPAGE="https://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml"
-SRC_URI="http://faculty.virginia.edu/wrpearson/${PN}/${PN}36/${P}.tar.gz"
+SRC_URI="https://github.com/wrpearson/fasta36/archive/refs/tags/v${MY_PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}36-${MY_PV}"
 
 LICENSE="fasta"
 SLOT="0"
@@ -15,8 +18,7 @@ KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos"
 IUSE="debug cpu_flags_x86_sse2 test"
 RESTRICT="!test? ( test )"
 
-DEPEND="test? ( app-shells/tcsh )"
-RDEPEND=""
+BDEPEND="test? ( app-shells/tcsh )"
 
 src_prepare() {
 	CC_ALT=
@@ -43,17 +45,17 @@ src_prepare() {
 	export CC_ALT="${CC_ALT}"
 	export ALT="${ALT}"
 
-	epatch "${FILESDIR}"/${P}-ldflags.patch
+	eapply "${FILESDIR}"/${P}-ldflags.patch
 
 	sed \
 		-e 's:-ffast-math::g' \
 		-i make/Makefile* || die
 
+	eapply_user
 }
 
 src_compile() {
-	cd src || die
-	emake -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS} -o" all
+	emake -C src -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS} -o" all
 }
 
 src_test() {
@@ -62,18 +64,18 @@ src_test() {
 }
 
 src_install() {
-	local bin
 	dobin bin/*
 
-	pushd bin > /dev/null || die
-	for bin in *36; do
-		dosym ${bin} /usr/bin/${bin%36}
-	done
-	popd
+	pushd bin >/dev/null || die
+		local i
+		for i in *36; do
+			dosym ${i} /usr/bin/${i%36}
+		done
+	popd >/dev/null || die
 
 	insinto /usr/share/${PN}
-	doins -r conf/* data seq
+	doins -r conf/. data seq
 
 	doman doc/{prss3.1,fasta36.1,fasts3.1,fastf3.1,ps_lav.1,map_db.1}
-	dodoc  FASTA_LIST README doc/{README.versions,readme*,fasta*,changes*}
+	dodoc FASTA_LIST README* doc/{README*,readme*,fasta*,changes*}
 }
diff --git a/sci-biology/fasta/files/fasta-36.3.5e-ldflags.patch b/sci-biology/fasta/files/fasta-36.3.8h-ldflags.patch
index a6eeabfdf46c..40070d50fe76 100644
--- a/sci-biology/fasta/files/fasta-36.3.5e-ldflags.patch
+++ b/sci-biology/fasta/files/fasta-36.3.8h-ldflags.patch
@@ -1,14 +1,7 @@
- make/Makefile.pcom   | 8 ++++----
- make/Makefile.pcom_s | 8 ++++----
- make/Makefile.pcom_t | 8 ++++----
- 3 files changed, 12 insertions(+), 12 deletions(-)
-
-diff --git a/make/Makefile.pcom b/make/Makefile.pcom
-index 9c5f801..33fc001 100644
 --- a/make/Makefile.pcom
 +++ b/make/Makefile.pcom
-@@ -209,14 +209,14 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c
- 	$(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M)
+@@ -216,14 +216,14 @@
+ 	$(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c pssm_asn_subs.c $(LIB_M) $(LIB_DB)
  
  map_db : map_db.c uascii.h ncbl2_head.h
 -	$(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c
@@ -26,12 +19,10 @@ index 9c5f801..33fc001 100644
  lav2svg : lav2plt.o lavplt_svg.o
 -	$(CC) -DUNIX -o $(BIN)/lav2svg  lav2plt.o lavplt_svg.o -lm
 +	$(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg  lav2plt.o lavplt_svg.o -lm
-diff --git a/make/Makefile.pcom_s b/make/Makefile.pcom_s
-index dc53001..8a45044 100644
 --- a/make/Makefile.pcom_s
 +++ b/make/Makefile.pcom_s
-@@ -143,14 +143,14 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c
- 	$(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M)
+@@ -149,14 +149,14 @@
+ 	$(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c pssm_asn_subs.c $(LIB_M) $(LIB_DB)
  
  map_db : map_db.c uascii.h ncbl2_head.h
 -	$(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c
@@ -49,12 +40,10 @@ index dc53001..8a45044 100644
  lav2svg : lav2plt.o lavplt_svg.o
 -	$(CC) -DUNIX -o $(BIN)/lav2svg  lav2plt.o lavplt_svg.o -lm
 +	$(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg  lav2plt.o lavplt_svg.o -lm
-diff --git a/make/Makefile.pcom_t b/make/Makefile.pcom_t
-index 8a71438..5b08a50 100644
 --- a/make/Makefile.pcom_t
 +++ b/make/Makefile.pcom_t
-@@ -164,14 +164,14 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c
- 	$(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M)
+@@ -171,14 +171,14 @@
+ 	$(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c pssm_asn_subs.c $(LIB_M) $(LIB_DB)
  
  map_db : map_db.c uascii.h ncbl2_head.h
 -	$(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c
diff --git a/sci-biology/foldingathome/Manifest b/sci-biology/foldingathome/Manifest
index f05ea2de4408..c7cb1fd9d18a 100644
--- a/sci-biology/foldingathome/Manifest
+++ b/sci-biology/foldingathome/Manifest
@@ -1,4 +1,6 @@
 AUX 7.3/folding-conf.d 339 BLAKE2B 93a0b3672777ad737ce27694aaca547634c375e180ad3c28c3adb9cae2cb1c054ff9458ee1fe04b70fe9841ae67d41198bcecfc4826d05d5de8df2759bd80910 SHA512 6fd10dc938262c05831e68176e93a24869bb6991508bcc48ece487b701788026561d073025bd347cd77ede13ca26f6b284861f30b07becf72ea77e4db22867b3
 DIST fahclient_7.6.13-64bit-release.tar.bz2 3951134 BLAKE2B 2748b7c1987d166bdda08caf5ff2f331523ff519e24768cd7e111c6d3a93f54c10c88d8adbf733230b6c51547360135dbcb272e5d43fd06d01918481601382a1 SHA512 f39f2990d78d075e1061ceaff9453b703a000770a3422965b7b8a91d1814f8804837628d8a34be5afd914228ef787f699f2488523baad295a8d9c1e3bb4f35cf
+DIST fahclient_7.6.21-64bit-release.tar.bz2 4081015 BLAKE2B b47f99bb2c568ee78dfb8998f6faa6c19aa78492a7882d128917596fa51ca7fb9f02dc0a822b6859ee4b333812f961cbcba504b9b188a3a16e7c5c9489cbfbdb SHA512 b52d97c0169eea8686ac3e52a713bb8513ae2b33a853fbf88a0311569aee22681e9ac87bcc01acdaf31d5af5c3641bd5611d34fcbdbb6c1f0ebbb3fc1efeabdb
 EBUILD foldingathome-7.6.13-r1.ebuild 4368 BLAKE2B 987b6022e43c2a39338ec8269e3ac001f9c0667237384814183d100fa2191dd91aaf57cfa86407d3bac0e4cee7bd12e022a967d5045e6888ba57622873500d2d SHA512 5225fcec1fb2e5d29b6628a0b06ec1f9f588f74feee6282ff7ee910fb87fba29512880707219ef77e63d0c7584858f50d0a1262ee88eea624c8dedce7df5d873
+EBUILD foldingathome-7.6.21.ebuild 4389 BLAKE2B c06064b68a21d31445d946097f574d3a42d114682633b406ca672cfa65e83a6af9bd0cdce7e5d5c20757f8a65f44727bf72954bdcea2510cdec173ddcca1ce90 SHA512 4028dca370a7935ac03c3bb117f66a831c4ea57e058c21807a08adc58ede17a4649ab8db9e89bb18764fb50a6c05f35734c9be76b1aac14dd59906f83be05c31
 MISC metadata.xml 258 BLAKE2B 51009df26b3682090e316b4cf4a3afad84001705063be6c74a28fb11bacde48b758dc280bf9d4d049c69e728d9660e737072674ad5ff8068da4f6a49f1f4e203 SHA512 05153e39b77e8b1437a0ba80b66b6bb1b4837d719765cb157b23d5425a625ddb4056422dcbf28d182e039583a0b3863e8429efe80da85a035c96f4c4788ced6d
diff --git a/sci-biology/foldingathome/foldingathome-7.6.21.ebuild b/sci-biology/foldingathome/foldingathome-7.6.21.ebuild
new file mode 100644
index 000000000000..04b1ff468a1e
--- /dev/null
+++ b/sci-biology/foldingathome/foldingathome-7.6.21.ebuild
@@ -0,0 +1,138 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit systemd
+
+DESCRIPTION="Folding@Home is a distributed computing project for protein folding"
+HOMEPAGE="https://foldingathome.org/"
+SRC_URI="https://download.foldingathome.org/releases/public/release/fahclient/centos-6.7-64bit/v$(ver_cut 1-2)/fahclient_${PV}-64bit-release.tar.bz2"
+S="${WORKDIR}/fahclient_${PV}-64bit-release"
+
+LICENSE="FAH-EULA-2014 FAH-special-permission"
+SLOT="0"
+KEYWORDS="~amd64"
+RESTRICT="mirror bindist strip"
+
+# Expressly listing all deps, as this is a binpkg and it is doubtful whether
+# i.e. uclibc or clang can provide what is necessary at runtime
+DEPEND="dev-util/patchelf"
+RDEPEND="
+	acct-group/foldingathome
+	acct-group/video
+	acct-user/foldingathome
+	app-arch/bzip2
+	|| (
+		dev-libs/openssl-compat:1.0.0
+		=dev-libs/openssl-1.0*:*
+	)
+	sys-devel/gcc
+	sys-libs/glibc
+	sys-libs/zlib
+"
+
+QA_PREBUILT="opt/foldingathome/*"
+
+pkg_setup() {
+	elog ""
+	elog "Special permission is hereby granted to the Gentoo project to provide an"
+	elog "automated installer package which downloads and installs the Folding@home client"
+	elog "software. Permission is also granted for future Gentoo installer packages on the"
+	elog "condition that they continue to adhere to all of the terms of the accompanying"
+	elog "Folding@home license agreements and display this notice."
+	elog "-- Vijay S. Pande, Stanford University, 07 May 2013"
+	elog ""
+	elog "(ref: http://foldingforum.org/viewtopic.php?f=16&t=22524&p=241992#p241992 )"
+	elog ""
+}
+
+src_install() {
+	patchelf --set-rpath "${EPREFIX}/opt/foldingathome" FAHClient || die
+	patchelf --set-rpath "${EPREFIX}/opt/foldingathome" FAHCoreWrapper || die
+
+	dosym "../../usr/$(get_libdir)/libssl.so.1.0.0" /opt/foldingathome/libssl.so.10
+	dosym "../../usr/$(get_libdir)/libcrypto.so.1.0.0" /opt/foldingathome/libcrypto.so.10
+
+	exeinto /opt/foldingathome
+	doexe {FAHClient,FAHCoreWrapper}
+
+	insinto /opt/foldingathome
+	doins sample-config.xml
+
+	newconfd "${FILESDIR}"/7.3/folding-conf.d foldingathome
+	cat <<EOF >"${T}"/fah-init || die
+#!/sbin/openrc-run
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+start_stop_daemon_args="--chdir \"${EPREFIX}/opt/foldingathome\""
+command="${EPREFIX}/opt/foldingathome/FAHClient"
+command_args="\${FOLD_OPTS}"
+command_user=foldingathome
+command_background=1
+pidfile="\${PIDFILE}"
+EOF
+	newinitd "${T}"/fah-init foldingathome
+
+	cat <<EOF >"${T}"/fah-init.service || die
+[Unit]
+Description=Folding@Home V7 Client
+Documentation=https://foldingathome.org
+
+[Service]
+Type=simple
+User=foldingathome
+Group=foldingathome
+Nice=19
+WorkingDirectory=${EPREFIX}/opt/foldingathome
+ExecStart=${EPREFIX}/opt/foldingathome/FAHClient --fork=false --pid=false --respawn=false --service=false
+NoNewPrivileges=yes
+PrivateTmp=yes
+ProtectControlGroups=yes
+ProtectSystem=full
+RestrictRealtime=true
+ProtectControlGroups=yes
+
+[Install]
+WantedBy=multi-user.target
+EOF
+	systemd_newunit "${T}"/fah-init.service foldingathome.service
+
+	fowners -R foldingathome:foldingathome /opt/foldingathome
+}
+
+pkg_postinst() {
+	elog "To run Folding@home in the background at boot:"
+	elog "(openrc)\trc-update add foldingathome default"
+	elog "(systemd)\tsystemctl enable foldingathome"
+	elog ""
+	if [ ! -e "${EPREFIX}"/opt/foldingathome/config.xml ]; then
+		elog "No config.xml file found -- please run"
+		elog "emerge --config ${P} to configure your client, or specify"
+		elog "all necessary runtime options in FOLD_OPTS within"
+		elog "${EPREFIX}/etc/conf.d/foldingathome"
+		elog ""
+	fi
+	if [[ -n ${REPLACING_VERSIONS} ]]; then
+		elog "NOTE, the 'initfolding' helper script has been dropped, please"
+		elog "use emerge --config ${P} or run FAHClient --configure directly"
+		elog "and adjust file permissions and ownership yourself"
+		elog ""
+	fi
+	elog "Please see ${EPREFIX}/opt/foldingathome/FAHClient --help for more details."
+	einfo ""
+	einfo "The original package maintainer encourages you to acquire a username and join team 36480."
+	einfo "http://folding.stanford.edu/English/Download#ntoc2"
+	einfo ""
+}
+
+pkg_postrm() {
+	elog "Folding@home data files were not removed."
+	elog "Remove them manually from ${EPREFIX}/opt/foldingathome"
+}
+
+pkg_config() {
+	cd "${EPREFIX}"/opt/foldingathome || die
+	su foldingathome -s /bin/sh -c "./FAHClient --configure" || die
+}
diff --git a/sci-biology/repeatmasker-libraries/Manifest b/sci-biology/repeatmasker-libraries/Manifest
deleted file mode 100644
index dcc95a8bcc86..000000000000
--- a/sci-biology/repeatmasker-libraries/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST repeatmaskerlibraries-20120418.tar.gz 28059668 BLAKE2B 0683305f0d3045ff1bcb9f1c952d3c12e92a3003f79ba18a16334805049a64e0b307fac2cf7fad236c9b0cab80e3317ebb1d93bf6487bafd9d45de2455565879 SHA512 254d47faeee72ee62e6854ebc389578691d66e99d9d5e2a0c2462bf752ac5b4d2171c9e6b45d4f87f548a96b62753bb9c37c2d2c00e06544e91dd09fe2bbfe32
-EBUILD repeatmasker-libraries-20120418.ebuild 741 BLAKE2B 5226277bfa19b7642ab426572f799318e54e823728297371b580038b60c3d9c6226156e889e8562c546fd06e1fb443811354062344d78a80addf84a7ff322dba SHA512 e72c9eb08d6cbf11199e3aaeb9b847afcc764857f9624a2c8d5e228160a5a058bf6d0e1521ddfb82c43104084a397f10a5164009598a25f06ae54d121908e7a2
-MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de
diff --git a/sci-biology/repeatmasker-libraries/metadata.xml b/sci-biology/repeatmasker-libraries/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/repeatmasker-libraries/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20120418.ebuild b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20120418.ebuild
deleted file mode 100644
index 9445ce8e5278..000000000000
--- a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20120418.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="A special version of RepBase used by RepeatMasker"
-HOMEPAGE="http://repeatmasker.org/"
-SRC_URI="repeatmaskerlibraries-${PV}.tar.gz"
-S="${WORKDIR}/Libraries"
-
-LICENSE="all-rights-reserved"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-RESTRICT="fetch"
-
-pkg_nofetch() {
-	einfo "Please register and download repeatmaskerlibraries-${PV}.tar.gz"
-	einfo 'at http://www.girinst.org/'
-	einfo '(select the "Repbase Update - RepeatMasker edition" link)'
-	einfo 'and place it into your DISTDIR directory.'
-}
-
-src_install() {
-	HTML_DOCS=( README.html )
-	einstalldocs
-
-	insinto /usr/share/repeatmasker/Libraries
-	doins RepeatMaskerLib.embl
-}
diff --git a/sci-biology/repeatmasker/Manifest b/sci-biology/repeatmasker/Manifest
deleted file mode 100644
index d43f4216b5ad..000000000000
--- a/sci-biology/repeatmasker/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST RepeatMasker-open-4-0-1.tar.gz 84077910 BLAKE2B 45598d46ef1c0e1233ed5ce10c2d29e4b2ef1a6843846970df2d0f997a22657eeed7dd7c851418d6f751468b22327b47f3b72105fdcfa56bbebe97395946ab37 SHA512 6b710a02b2964bca6acb25cc918bd56f7caba7b80b3b683972f0584180bf0fd3704f657d7ee341187a4ac86d9883e62eb4f09da237fa8ef1b481137d1a89963e
-EBUILD repeatmasker-4.0.1.ebuild 1501 BLAKE2B c8a6bef25b5e9cfbf4be2d5336b7b9960872c16368c470dd720be2a76529e894077ee2875999cfbce66b954f3ec059de0a9e98e605e3c4b17338f520a43580f2 SHA512 a90a31bd066e05384f6583a04f2e8bb4624f84e2125b25eebc3b253ceca1e9bf1090e11ddbdda824f1e9a939b4fbe8f900335e14c6604d1f947ab6083191df5d
-MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de
diff --git a/sci-biology/repeatmasker/metadata.xml b/sci-biology/repeatmasker/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/repeatmasker/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild
deleted file mode 100644
index bf6097df1f68..000000000000
--- a/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-MY_PV=${PV//\./-}
-
-DESCRIPTION="Screen DNA sequences for interspersed repeats and low complexity DNA"
-HOMEPAGE="http://repeatmasker.org/"
-SRC_URI="http://www.repeatmasker.org/RepeatMasker-open-${MY_PV}.tar.gz"
-
-LICENSE="OSL-2.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="
-	sci-biology/rmblast
-	sci-biology/trf
-	sci-biology/repeatmasker-libraries"
-
-S="${WORKDIR}/RepeatMasker"
-
-src_configure() {
-	sed -i -e 's/system( "clear" );//' \
-		-e 's|> \($rmLocation/Libraries/RepeatMasker.lib\)|> '${D}'/\1|' "${S}/configure" || die
-	echo "
-env
-/usr/share/${PN}
-/usr/bin
-2
-/opt/rmblast/bin
-Y
-5" | "${S}/configure" || die "configure failed"
-	sed -i -e 's|use lib $FindBin::RealBin;|use lib "/usr/share/'${PN}'/lib";|' \
-		-e 's|".*\(taxonomy.dat\)"|"/usr/share/'${PN}'/\1"|' \
-		-e '/$REPEATMASKER_DIR/ s|$FindBin::RealBin|/usr/share/'${PN}'|' \
-		"${S}"/{DateRepeats,ProcessRepeats,RepeatMasker,DupMasker,RepeatProteinMask,RepeatMaskerConfig.pm,Taxonomy.pm} || die
-}
-
-src_install() {
-	exeinto /usr/share/${PN}
-	for i in DateRepeats ProcessRepeats RepeatMasker DupMasker RepeatProteinMask; do
-		doexe $i
-		dosym /usr/share/${PN}/$i /usr/bin/$i
-	done
-
-	dodir /usr/share/${PN}/lib
-	insinto /usr/share/${PN}/lib
-	doins "${S}"/*.pm
-
-	insinto /usr/share/${PN}
-	doins -r util Matrices Libraries taxonomy.dat *.help
-	keepdir /usr/share/${PN}/Libraries
-
-	dodoc README INSTALL *.help
-}
diff --git a/sci-biology/rmblast/Manifest b/sci-biology/rmblast/Manifest
deleted file mode 100644
index 1b59326510d7..000000000000
--- a/sci-biology/rmblast/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST rmblast-1.2-gcc47.patch.bz2 7803 BLAKE2B cd3bb1aa2b6eb9e188f28589d42ce91f027866d91013f2a6123ee61e7ce28f980b858e775bc15313cf1573f0bc827f9e663d46c1bd0d2fe218745cfbbc3781a1 SHA512 4cd72dd5c777ad866b9cf674384872de5424404b524ac536e58ab412b98b6601aa5f609d05ea2329b77f16e7aca215bbc6eb3531652e5fe81e48cf997b56d13b
-DIST rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz 10744076 BLAKE2B 6539ec8fcd345bcc1c3ecede6acec233cdc343c3df18748e195dc525f4a65fefeee8398471a26dc671bfed8612e010c26b7a8a66a3c7198f142c2e068ff72751 SHA512 e7c2ebd114aee045ea3f3f462cf2658440e13a2d1eb777648386e1c5eeda9f8083af383c019f9b5802d935d6eb2367eef20822afc45233ddb44a426b4dd7ddb6
-EBUILD rmblast-1.2-r1.ebuild 1191 BLAKE2B b096fcac217355ebecf8a33b1f145ae6482663e7437b78d1024858959d1653e2424f250d69fb238118751cb4133016fb17cc584f10a299bb6bcbae2a08806d53 SHA512 b2b4cd8e6eed2df9ff4a39783006515e57614dca8a14e38ae4335badb3af81056d4dad7aa377f78aafc659a06eb6cd8f184b60c4581771e2f6c077d3d635304a
-MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de
diff --git a/sci-biology/rmblast/metadata.xml b/sci-biology/rmblast/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/rmblast/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/rmblast/rmblast-1.2-r1.ebuild b/sci-biology/rmblast/rmblast-1.2-r1.ebuild
deleted file mode 100644
index 20a68f97763c..000000000000
--- a/sci-biology/rmblast/rmblast-1.2-r1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit epatch flag-o-matic toolchain-funcs
-
-MY_NCBI_BLAST_V=2.2.23+
-
-DESCRIPTION="RepeatMasker compatible version of NCBI BLAST+"
-HOMEPAGE="http://www.repeatmasker.org/RMBlast.html"
-SRC_URI="http://www.repeatmasker.org/rmblast-${PV}-ncbi-blast-${MY_NCBI_BLAST_V}-src.tar.gz
-	https://dev.gentoo.org/~mgorny/dist/${P}-gcc47.patch.bz2"
-
-LICENSE="OSL-2.1"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="dev-libs/boost"
-DEPEND="${RDEPEND}
-	app-arch/cpio"
-
-S="${WORKDIR}/${P}-ncbi-blast-${MY_NCBI_BLAST_V}-src/c++"
-
-src_prepare() {
-	filter-ldflags -Wl,--as-needed
-	sed \
-		-e 's/-print-file-name=libstdc++.a//' \
-		-e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \
-		-e "/DEF_FAST_FLAGS=/s:=\".*\":=\"${CFLAGS}\":g" \
-		-e 's/2.95\* | 2.96\* | 3\.\* | 4\.\* )/2.95\* | 2.96\* | \[3-9\]\.\* )/g' \
-		-i src/build-system/configure || die
-	epatch "${WORKDIR}"/${P}-gcc47.patch
-}
-
-src_configure() {
-	tc-export CXX CC
-
-	"${S}"/configure --without-debug \
-		--with-mt \
-		--without-static \
-		--with-dll \
-		--prefix="${ED}"/opt/${PN} \
-		--with-boost="${EPREFIX}/usr/include/boost" \
-		|| die
-}
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index e81f2187923a..2f378c0428d2 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,6 +1,8 @@
 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
 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
 MISC metadata.xml 409 BLAKE2B c94eab9ebda4844beb471694106e353ccbbaca53e69de680301c6cfab3f3b6224ec94fcd631c9de2811d309463e5ee6decf2e443bfc68921f3362c6a312cd3af SHA512 fb2d3686e1ee70e4e80266a26603b3e52b680b1537a4569493a3a0511b93e2acdb2be3136df7ae54905a9f86fb7e53fa054607262751ebd8f54903f1905dad24
diff --git a/sci-biology/samtools/samtools-1.15.ebuild b/sci-biology/samtools/samtools-1.15.ebuild
new file mode 100644
index 000000000000..74aee5acaaa2
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.15.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2022 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/seqan/Manifest b/sci-biology/seqan/Manifest
index 5264bf200470..161725918529 100644
--- a/sci-biology/seqan/Manifest
+++ b/sci-biology/seqan/Manifest
@@ -2,5 +2,7 @@ AUX seqan-2.4.0-cmake-add_library-static.patch 1542 BLAKE2B 08f006302c4b284bbbfc
 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
+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
 MISC metadata.xml 373 BLAKE2B 1fd7eb9978c4b1e8fee1edb30bef8e18de04fdbc6677f8442e0cb706512b7a49c0681737ade6b9c96f67e234907890694bafe8edfb6c35ef25cd570920ea07f7 SHA512 b273e12542b160e215945d85504a3e9ba9973b68e6870f9d27104024fb09b8e293d8f6f71f8a005ad35690a530cec608e5e01a5158b747e1003ce9c87add8486
diff --git a/sci-biology/seqan/seqan-3.1.0.ebuild b/sci-biology/seqan/seqan-3.1.0.ebuild
new file mode 100644
index 000000000000..fc9dd78e4233
--- /dev/null
+++ b/sci-biology/seqan/seqan-3.1.0.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake
+
+DESCRIPTION="C++ Sequence Analysis Library"
+HOMEPAGE="https://www.seqan.de/"
+SRC_URI="https://github.com/seqan/seqan3/releases/download/${PV}/seqan3-${PV}-Source.tar.xz"
+S="${WORKDIR}/seqan3-${PV}-Source"
+
+LICENSE="BSD GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~amd64-linux"
+IUSE="cpu_flags_x86_sse4_2"
+REQUIRED_USE="cpu_flags_x86_sse4_2"
+
+RDEPEND="
+	app-arch/bzip2:=
+	dev-cpp/range-v3
+	dev-libs/cereal
+	sci-libs/lemon
+	sys-libs/zlib:=
+"
+DEPEND="${RDEPEND}"
+
+src_install() {
+	cmake_src_install
+	dodoc -r doc/*
+}
diff --git a/sci-biology/vcftools/Manifest b/sci-biology/vcftools/Manifest
index 289dfe002b36..6495838a7c8d 100644
--- a/sci-biology/vcftools/Manifest
+++ b/sci-biology/vcftools/Manifest
@@ -1,4 +1,6 @@
 AUX vcftools-0.1.14-buildsystem.patch 1159 BLAKE2B 9eaa626c82b4d23e75f2d31ce31c6161996eb743efbdcb81ad4c3ba306b76a710c4b22670d68178da1b7d2e048d02aea44132f3009d5792dcf248368b53c3482 SHA512 838cade29bbeeee090ea52f546c37b68eee868f3329ceccb710da0dbcf0f14e1b18dcc7b05ceefdbf72d400f450374389649f56fc6981bd86f6e176469b054ea
 DIST vcftools-0.1.14.tar.gz 342369 BLAKE2B 14be867c0be41767e2c97c8be212f3cff495c1cb6699294fb8a26ac491901599cd1e400cb80c6d609dce36584ee5defdb3b3652657bd127e0c67c5b29a842cc5 SHA512 863a16b3b20d392deba7f04310af95f1ab21be537273692aa104e22d737af2eb1bc54a768af954f06188e0500e4f7a032d1189886eb3a439b108cb8189b14eb7
+DIST vcftools-0.1.16.tar.gz 480575 BLAKE2B 5c0bf67aef8ef4705f621485df4c556f6bace190311c308f0364f3e274cf4818f56f2186905fdfb7459dc4be9664a8b1ff631e2cecd03abd7aa82dcfc7e5aa64 SHA512 c4dd5ceb3ad0512e839154d8a05ef3e7a03cbe52c3099df48775b35460fce7ef10102819c2d1cefa33b98ad09e7bd1608e871978860ec9c0b0c2e781892b22e6
 EBUILD vcftools-0.1.14.ebuild 867 BLAKE2B f25ccc182927cd888c548f4eeb120c526716fc759dc7b8081baf76b9f4cd3a404a2828168577000ff816b02aa8d3e6fec52d883fdc2e6f2ec40f1a9712d024d1 SHA512 260555d8964cf329fe3710547b6ddb5600674525703d0b802d18c2a41d02271ff77c56c4d49bf9fb67966bce76a3d6addc88c5a1e86859425bf0574beecc2c34
+EBUILD vcftools-0.1.16.ebuild 818 BLAKE2B 7809d2b55b8e93fea1f4e32a302018e9d2f4b8f289f413be6ea0b34471e639e6f5857f9aeeda1de790abbf773881b63a8c8a31c4f40ba0d83a02363f6a534600 SHA512 e56916000bdcae78e7fd312f078020f2c1e8f007df842d2a0396f15b546dcd945e457fc1771495c7cc242a7c7e938302a9e25c56c884b7722889aa03b54ee550
 MISC metadata.xml 409 BLAKE2B 8b6096c95135edaa86244af0fa6c7da5eb131092dc6ff25108723c64183275727c49d9c1fd0f2c4805a3daebc780833e0d03127e58bb5cde3c6ee999b2fca68e SHA512 276a72290a191a7661f130b941ce81dd017242fad97f67efbbf84d9586d097bf5131b12f6fb4bf5f8dc18ee0babcd89d836692b2d912fea5bf90fed18e16885f
diff --git a/sci-biology/vcftools/vcftools-0.1.16.ebuild b/sci-biology/vcftools/vcftools-0.1.16.ebuild
new file mode 100644
index 000000000000..b06a81dd0a1a
--- /dev/null
+++ b/sci-biology/vcftools/vcftools-0.1.16.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit autotools flag-o-matic perl-functions toolchain-funcs
+
+DESCRIPTION="Tools for working with VCF (Variant Call Format) files"
+HOMEPAGE="http://vcftools.sourceforge.net/"
+SRC_URI="https://github.com/${PN}/${PN}/releases/download/v${PV}/${P}.tar.gz"
+
+LICENSE="LGPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="lapack"
+
+RDEPEND="sys-libs/zlib
+	dev-lang/perl:=
+	lapack? ( virtual/lapack )"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+src_prepare() {
+	default
+	eautoreconf
+}
+
+src_configure() {
+	perl_set_version
+
+	append-flags $($(tc-getPKG_CONFIG) --cflags lapack)
+	append-libs $($(tc-getPKG_CONFIG) --libs lapack)
+
+	econf \
+		$(use_enable lapack pca) \
+		--with-pmdir="${VENDOR_LIB#${EPREFIX}/usr}"
+}
author	V3n3RiX <venerix@koprulu.sector>	2022-03-20 00:40:44 +0000
committer	V3n3RiX <venerix@koprulu.sector>	2022-03-20 00:40:44 +0000
commit	4cbcc855382a06088e2f016f62cafdbcb7e40665 (patch)
tree	356496503d52354aa6d9f2d36126302fed5f3a73 /sci-biology
parent	fcc5224904648a8e6eb528d7603154160a20022f (diff)