gentoo auto-resync : 01:05:2024 - 00:00:04

20 files changed, 31 insertions, 31 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 93d82fa77140..c1eec181be8c 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/bfast/Manifest b/sci-biology/bfast/Manifest
index 1c2c90571e1c..9ea43db42657 100644
--- a/sci-biology/bfast/Manifest
+++ b/sci-biology/bfast/Manifest
@@ -2,5 +2,5 @@ AUX bfast-0.7.0a-C99-inline.patch 2316 BLAKE2B 744908af002c5d5af57358baffbaff75a
 AUX bfast-0.7.0a-autotools.patch 1268 BLAKE2B b5da950d0230322f0a95b7c1417aec5fc4774a7d40ce4576b10bbc66d21f8d4907e17f3020679f3074cfdbe10f7e69bc3d8b62371ad381a2fb7b17854f146e46 SHA512 d1b00230ef35e82fb633a063c32e48a50866d8c40889cb0e13fddb0866a5b5447ed0f41cc948811f7e50918544ed3d0758ace3e1060a97a33ff5a0c3ee12b29c
 AUX bfast-0.7.0a-test-sourcing.patch 1399 BLAKE2B 2cc246d437da36a28d6fd86fe8c4acb78ba06120672158c16305c108298f46f4cabf37193f793e9b32ecb8fddc022f076bc845d06564f23ed9f412f5d7c22378 SHA512 3257038564997ae1b2bdd814e893825951c9cc72934cc204d6a3cd1dd31c796d26b76b6801dca4722be3e10ac309e0d177ddf725a6b6a2c5fe01106bd35d5a5f
 DIST bfast-0.7.0a.tar.gz 2456617 BLAKE2B a841e7651e731dbb3faf22eb03dce5d2008c84f9a6198204d3c41aea26626058e3a23375bc0e7e8fc142d4898e09ddbb168016c71a7b79527e602e06ec329151 SHA512 16e7ec5101c478f0dfc171016cbacb2b9240773e43b2d40eeb42d0e47afcee50a6dd5838e043a0326fc1ca9a87d3e55b42326a7f17b7c5654ef9825913860836
-EBUILD bfast-0.7.0a.ebuild 595 BLAKE2B 257ddca11ba647f033b22f98afa4d718f1260687a17cf8386dec115f9e0dfc764a30f94af2cdb4f3f63057e1286e104bb9e3a666dfd44a4f004aa9c84b8f5e92 SHA512 5ce28ea79f9dc037eb432a23f742e7c9efb18be1317324c2200fa0a66f7e938526daa386c146922ae45a1b0f8c96460bdd2700db77c172b18935cd06dc1353eb
+EBUILD bfast-0.7.0a.ebuild 608 BLAKE2B eea76ad72a8017eddf0926670727b9f19c6f7e84ac3c1d1f74470e95c07a696769ad33c8393342b5d5132c8cf87a8df954180d17b7b6a6f1617764e26fc05b3e SHA512 a2e7c794d0e02240fefac07fa29ddece91010ee0677c2b5474c5541a24c4c33d5e33efcc07b9f16a2dc041eece726396f0eff54e53fd79f28e52facdc408982a
 MISC metadata.xml 347 BLAKE2B fda3b1b1f01d1cadeae82a76b136ff36dca51aa87133f2413169e8e42f9551a5982aa865638d0fcd62aacac988bfca1cb273b4fc631f645a017be4242c481f66 SHA512 56e5f098713a53961f0967972197ee5eee51175964a4299c4aa647f66a47abf882304384a5dac51134ab1f806d300c7278c4479912b723f0a7ab5d19b0fe0834
diff --git a/sci-biology/bfast/bfast-0.7.0a.ebuild b/sci-biology/bfast/bfast-0.7.0a.ebuild
index 6a48785022f4..dd4036c6030e 100644
--- a/sci-biology/bfast/bfast-0.7.0a.ebuild
+++ b/sci-biology/bfast/bfast-0.7.0a.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -7,7 +7,7 @@ inherit autotools
 
 DESCRIPTION="Blat-like Fast Accurate Search Tool"
 HOMEPAGE="https://sourceforge.net/projects/bfast/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
+SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.gz"
 
 LICENSE="GPL-2"
 SLOT="0"
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index 182f6a8c17fd..d8a1aac4fceb 100644
--- a/sci-biology/bowtie/Manifest
+++ b/sci-biology/bowtie/Manifest
@@ -1,5 +1,5 @@
 DIST bowtie2-2.4.4-source.zip 10515984 BLAKE2B be4ceb9d3155d2a9a1f580e5032251b04b89ce0c8c9c89fc3551b34fe3bd71a683362488be7aad6daef24734c6f95c19223f20e67f198f745c4432381243039c SHA512 1b5dadd7e41b90bb9b05f50bfa171fe219cfd03aa8bb6f800de4baaffeb975eef6efc4fb8b49cb0d18833f74a1741cbe1556b87388f59188e04a55dcee6a02da
 DIST bowtie2-2.5.1-source.zip 10528859 BLAKE2B 9dc22bfef4b3a1cfaa606cb235acd1d7688015678d82e8ca80d3d7cf269e1f45d6cb60bc29eb334fb6f0c25d5afd8202e83a83e53668c8965857b8885d2692c8 SHA512 31cc642e318ab50e7ef6035a9c2095024d46d92a317011ed0c3ac3ccb3d427a13bf724d0158d29a4f1e07115ddcb85229b95bcb2d4351164fcadd6568293565f
-EBUILD bowtie-2.4.4.ebuild 1207 BLAKE2B 4e89cd7884065637cba84784321100b90a0c0e561dca1519f843be418b33737f31d7db9cc74810a67b1211b9e69e0ac5e7b45548b5b8b0999d42a36a317e9491 SHA512 28473ddcd136172f0b35625cc2a79c4a9a5801c65df28aa0800ed6ea9552f2cf381377ef81504279764fecc7fc2e3c0566c1f7dbc98e2e578ef0452bc2c33653
-EBUILD bowtie-2.5.1.ebuild 1528 BLAKE2B eec523c39c69b9b0862696b0579441c79c028eb2465fdb3c5c153cd1dcaf403e43eb6596bbb64e41f2e7b1fbf27fa832d019720f6c31361d047d4d341e987a6a SHA512 1f7b179a376d0f6a89c223cdf8bc5804b13bef4b9cba3cf4364c109f4d622beba51c2b79f238f92ffb44922711530fbf199af1db36e93d7236b6ce23312e124c
+EBUILD bowtie-2.4.4.ebuild 1215 BLAKE2B 4d88c3ff6149289019301cbdf5b682da576feabe5a51f2a83fceccf2b2475e81ae69a9318e64453d16c4c2b713dc7858bf4f5c3e9306004e418d34f10099ac71 SHA512 2da6db5d4d96ea3e5eba3fb992e8ef350becdbd24ba4d0844a2c6127a357f458fb709ea833bb06bf464001872f45530f9fdc6b5682801aab7ac400641c42e1b1
+EBUILD bowtie-2.5.1.ebuild 1542 BLAKE2B b927f815c929a324c607df93479833079a0e5a8dd9b723755ad19d528e35601b796cdb0618c5d7787ce591c0d8e5c0be5b5d7217fc1a0393f070049451c3d9db SHA512 1ea410f3b1c0b5be41369f1f001f92f366cd3fec9f1518bfc9da32bda8f88c9b2bb57b73e6f2ec71e9144844cca7db47c747e4193ff243c78ca1304d4897b176
 MISC metadata.xml 342 BLAKE2B 7f98f1707e3f53e7c2e532427d6935c692cdcf45304701d28d245ba13b62e752d14d5c3a96925fdf5bceb87a9c291edad0ce715339a5bf92ca6de7ee839adced SHA512 b7f0359b22f70ab25737565bda08e500f6a79bf33052d39fe2013b085c3f636122d0f373430ce3f0b56f95051db9571cb6c79b6f58e30658f45ef752ec708df6
diff --git a/sci-biology/bowtie/bowtie-2.4.4.ebuild b/sci-biology/bowtie/bowtie-2.4.4.ebuild
index 7d28271d336b..de69bfadd825 100644
--- a/sci-biology/bowtie/bowtie-2.4.4.ebuild
+++ b/sci-biology/bowtie/bowtie-2.4.4.ebuild
@@ -1,15 +1,15 @@
-# Copyright 2021-2023 Gentoo Authors
+# Copyright 2021-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_{9..10} )
+PYTHON_COMPAT=( python3_10 )
 
 inherit python-single-r1 toolchain-funcs
 
 DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
 HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"
-SRC_URI="mirror://sourceforge/project/${PN}-bio/bowtie2/${PV}/bowtie2-${PV}-source.zip"
+SRC_URI="https://downloads.sourceforge.net/project/${PN}-bio/bowtie2/${PV}/bowtie2-${PV}-source.zip"
 S="${WORKDIR}/${PN}2-${PV}"
 
 LICENSE="GPL-3"
diff --git a/sci-biology/bowtie/bowtie-2.5.1.ebuild b/sci-biology/bowtie/bowtie-2.5.1.ebuild
index 353362fd6026..b30a2b920f4e 100644
--- a/sci-biology/bowtie/bowtie-2.5.1.ebuild
+++ b/sci-biology/bowtie/bowtie-2.5.1.ebuild
@@ -1,15 +1,15 @@
-# Copyright 2021-2023 Gentoo Authors
+# Copyright 2021-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_{9..11} )
+PYTHON_COMPAT=( python3_{10..11} )
 
 inherit python-single-r1 toolchain-funcs
 
 DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
 HOMEPAGE="https://bowtie-bio.sourceforge.net/bowtie2/"
-SRC_URI="mirror://sourceforge/project/${PN}-bio/bowtie2/${PV}/bowtie2-${PV}-source.zip"
+SRC_URI="https://downloads.sourceforge.net/project/${PN}-bio/bowtie2/${PV}/bowtie2-${PV}-source.zip"
 S="${WORKDIR}/${PN}2-${PV}"
 
 LICENSE="GPL-3"
diff --git a/sci-biology/maq/Manifest b/sci-biology/maq/Manifest
index 28258aa9b4e4..fd1038ce55de 100644
--- a/sci-biology/maq/Manifest
+++ b/sci-biology/maq/Manifest
@@ -5,5 +5,5 @@ AUX maq-0.7.1-gcc14-build-fix.patch 603 BLAKE2B a1c2722f4bc53014b5281fc8532573d5
 AUX maq-0.7.1-remove-64bit-flag.patch 787 BLAKE2B 2e94066962194133ccdae4095d3d6bf6f058f7a7d5d04f8737e03fc725508b3e291c76554418c6ff9a15969e332d340b86e11ae3cab90406ec60e9ea63361f5e SHA512 4864453afa79679c253b17a2b125bf0b44c1a05a6ae6341821382991217026b599437288a1c96625cdc2a1fad2cf73c79798a230bbfccef46e1c92012a6c3df1
 DIST calib-36.dat.gz 196371 BLAKE2B e4dab71e0830603a7c25bb4c8e15f92e4a5068eeeece451a3e0a2a9e2c4f65b87325e7ff4e4e5543b79f2c3d9dd43c9398cdb32241535bf44e66705bfdf683f7 SHA512 1033ad47b31882823f71f16054f366a6853b4b5e1fb286ab2c5f62c1409ed20e6dc0faec7e356350e91c71d25a198d8e0d7a521b3662b5e2fae22af44098e8b7
 DIST maq-0.7.1.tar.bz2 368645 BLAKE2B a7989ae2348a7332f17a75c6fccba55deb8bd9330863d0c5ab3bf997f2f07abd1ca89ebb41d034902f6571ee36365f63db9c8c84c1e5d3d788236279581b989e SHA512 acaba2d172f8f4ef7a2b1254bd220f134a5eb8e4936af16bf7fa6695d016e6b6fa9a5b00d073ec1ecc0ecc39dfb1c9700c38fd017edb5bd49a83de383cb0d30c
-EBUILD maq-0.7.1-r4.ebuild 827 BLAKE2B 1c5389612a5c79df5ab8321c8835b7933abb17136e60c14b85254ea9320b1a9d4b0e433f0df99c5158b3662b8fcb260c283c208e02db4503f47da154fff1a454 SHA512 a7e3ab88ea0b4c51f1f223f3e7c15930345ff614f6e6c468b3195843ff8e6007981bda055949e9c319c417b9fa0b2df0bd08622ea5b93dc7eba63cd7b50e7625
+EBUILD maq-0.7.1-r4.ebuild 853 BLAKE2B 566183a31390db572ed92eb1c12c9aab7709028c8bf7352f221a5dec036fb76196ad1994d798213e55e6a1ae83a01e10254fdba8700367920bd7677e4cdf2c04 SHA512 718bddb31f5d9884249dca88e2ec7b04a273be19b1557605af4206a6a1c550842673fe10ca28bac2efd6de55f8653dbde60af6b105529e7cf7df784ccb78aeb3
 MISC metadata.xml 345 BLAKE2B 3f590b0bf8c9f9fa9470f6b8ed3b20643c84fc92839740e6aebe720edd0a6e0b8bb5d2b74d4dcd8cf80a89c2769308b89e21f2f386a62fc28686f883eff56bbf SHA512 244600e6c19400a837eb859a09582fa78a670d81a58e6a461689d2695273b450df999334ffc44eecdfbed9232784af84e7cdcabe7ee045ae51a24509f2aabdcc
diff --git a/sci-biology/maq/maq-0.7.1-r4.ebuild b/sci-biology/maq/maq-0.7.1-r4.ebuild
index 8930c780cfa5..75a84d87b16c 100644
--- a/sci-biology/maq/maq-0.7.1-r4.ebuild
+++ b/sci-biology/maq/maq-0.7.1-r4.ebuild
@@ -8,8 +8,8 @@ inherit autotools
 DESCRIPTION="Mapping and Assembly with Qualities, mapping NGS reads to reference genomes"
 HOMEPAGE="https://maq.sourceforge.net/"
 SRC_URI="
-	mirror://sourceforge/${PN}/${P}.tar.bz2
-	mirror://sourceforge/${PN}/calib-36.dat.gz"
+	https://downloads.sourceforge.net/${PN}/${P}.tar.bz2
+	https://downloads.sourceforge.net/${PN}/calib-36.dat.gz"
 
 LICENSE="GPL-3"
 SLOT="0"
diff --git a/sci-biology/maqview/Manifest b/sci-biology/maqview/Manifest
index 304d8c466c41..b4077a64f00b 100644
--- a/sci-biology/maqview/Manifest
+++ b/sci-biology/maqview/Manifest
@@ -3,5 +3,5 @@ AUX 0.2.5-zlib.patch 1437 BLAKE2B c8a8908ca6586f3fdff730c2eca39e54b3d08e8fe07fd6
 AUX maqview-0.2.5-gcc14-build-fix.patch 337 BLAKE2B 8478ffbe452e25d663b452a2f562f2e7461fb211ebbe5c9401de3288534c6e3dfba599f42a833b156032b2a2ba299b229883f5fb7205fcfb727394b5c86deb56 SHA512 ac53e33dff1d9da5fd1b39e9e2c02e408809eb27059b08a42bf4568f8c4382d2e0e991ded1b33ff429617d881ca094aecd698821cda387cb0175415bb1c04695
 AUX maqview-0.2.5-gcc4.7.patch 575 BLAKE2B 8e461d07e0421e5dc1e209e83ed3fccfdcd541954481bbbb1f478cddb9ff045c3704a086a18d6e7a8b255d226a24eca7d791cde9e59673c842a4094d56f03ba0 SHA512 277086e1d6d536ae368083032421029d64d5173e643edaafbad2833d56e8ec283152a49d9874a7142333e0fee976d3600ed118b6beb0482ec7e0e95f4a36fba4
 DIST maqview-0.2.5.tar.gz 383410 BLAKE2B 7058f32e49267dfcc8b25da2ca2bbbd5134f66f0f9cbd10de7e876365d955d2e51cbab342af817f13018b7b1903872033c363fe077f10ce76e5fcc87da568dc1 SHA512 40bed0a1005ca96fdb12773cd9c22ddc926fe722c64652031609a17a50ff725a3dc117d51f4f27eda68b48861da78427469aaedff744f29921236b486396aed6
-EBUILD maqview-0.2.5-r5.ebuild 639 BLAKE2B 9260a2b388ff95f7ffe16b27d157373186efd497909d58fbf2aa9f459e9de7c69450679b225e0276666fd44ff4a522a38d2208c2d3605d922878668b47d5ceba SHA512 74da5046442b3bf9ec58c08a75ffdec93907739deb49647acf0ea49edb8a7998c3556a7b311c41f17d1302f59e474ffa9fc96375713002a0b5d95ce465bd0858
+EBUILD maqview-0.2.5-r5.ebuild 652 BLAKE2B a665a928f9d960df706b32a634cecba4f624bc4f98d5791b3f39e5e8d8aa3634ffa338b493bc646fa69c0bba8727b3f509628585b66355a0a0c101314f42cb7f SHA512 652b7fdedb9fc6666b0c27f3e536dd48866379838abf5d34f9feacad4518a0c0330f33801e6f71e3c482ad685a7a61dab941e55e0179b86a7dec11797871957e
 MISC metadata.xml 345 BLAKE2B 3f590b0bf8c9f9fa9470f6b8ed3b20643c84fc92839740e6aebe720edd0a6e0b8bb5d2b74d4dcd8cf80a89c2769308b89e21f2f386a62fc28686f883eff56bbf SHA512 244600e6c19400a837eb859a09582fa78a670d81a58e6a461689d2695273b450df999334ffc44eecdfbed9232784af84e7cdcabe7ee045ae51a24509f2aabdcc
diff --git a/sci-biology/maqview/maqview-0.2.5-r5.ebuild b/sci-biology/maqview/maqview-0.2.5-r5.ebuild
index 479d0c01af91..2ffe5fa8ecf6 100644
--- a/sci-biology/maqview/maqview-0.2.5-r5.ebuild
+++ b/sci-biology/maqview/maqview-0.2.5-r5.ebuild
@@ -7,7 +7,7 @@ inherit autotools
 
 DESCRIPTION="GUI for sci-biology/maq, a short read mapping assembler"
 HOMEPAGE="https://maq.sourceforge.net/"
-SRC_URI="mirror://sourceforge/maq/${P}.tar.gz"
+SRC_URI="https://downloads.sourceforge.net/maq/${P}.tar.gz"
 S="${WORKDIR}/${PN}"
 
 LICENSE="GPL-3"
diff --git a/sci-biology/mrbayes/Manifest b/sci-biology/mrbayes/Manifest
index 9f1764971060..537b1a58a681 100644
--- a/sci-biology/mrbayes/Manifest
+++ b/sci-biology/mrbayes/Manifest
@@ -1,6 +1,6 @@
 AUX mb_readline_312.patch 586 BLAKE2B 6505a8d9fc40c0470264b6e293f2f4e51a5d6b4a73dfeaff747e2f4acd122369d810cdc86ae0d7cead3a3741cfffc02080c07618c2847985553322a1c9bf79b5 SHA512 8427c83ccb98c0b57274914d8f0d0f539ace7dbc475eb10bd586762efa3465b595b91907b55d6809b94e6b9c4f65aa139bc16a7d81b1c76f7623eae46d495aa8
 DIST mrbayes-3.1.2.tar.gz 545968 BLAKE2B f4c5bbdde765fb9e596c17d5fd890b168c22cefb0d24b67c1c68623e1dcfa4df716a896fe120f7a1cac4234125b6ed524973506e47492ba3ec26e389783d618a SHA512 2fb0ee7224cbb69c1acf2ffb0c6c8974f63002cda4f39a626eadf80fad9cfc23861f8c03f5545970f3a81e02093d62b6a0549ab7d7f7080557e91e21b2c3ee14
 DIST mrbayes-3.2.7.tar.gz 9787214 BLAKE2B 2d0ebbc376712e15fc1ed146053d977ad1af96f44c31b8fd0fdbd47ef9bafc41cbb8904db94bc8d30c753c0267a1dcce0d08c73d8b35c20e0f15206bc8fef6ff SHA512 4dc869cd07cf384b3a3945ac8d91a7cc2982e8c5cd8d1f097b46a479a071cb71e71c60e152aa4fc01b0bb296295c5fa9f5a48aa8e913b920c33e30cbb3a6ed37
-EBUILD mrbayes-3.1.2-r2.ebuild 1333 BLAKE2B 035f7c449670674dcfdb158a6b6ea96a03df32d3e72ecf42ebde5b3f6756aafab4ec042bb36cc42826cb6cfd06bf0d4ea77924288d7adfab0af2b74116567875 SHA512 4091068e40f41a6a2bbc1b6e6d91f9f1d557d25890e3352f3584c84d0e821519ff7263c39dc454cb0f564e2d83c3b4d9552c4346ed59e5859805c5fba60e4a7a
+EBUILD mrbayes-3.1.2-r2.ebuild 1346 BLAKE2B ec92939e71b157c6bcc757d09462a6eb6ee2e725526697d5a4b800d5addd5d1f689bb657e3e64f07efe01a3af3573dac60b7738f779e120442db523f30b9f6aa SHA512 243d6fa5ad6339b1c944bcd177de6cc4e96af6184eb83800cbb9bafd14a7dd2238ae8586d83d2e29c685b912d93adba7b0d1a46ac97efde659f7e426f2b73776
 EBUILD mrbayes-3.2.7.ebuild 1518 BLAKE2B 1179623e2f7bb9f31d26713c7ead2b82b430a47ffc5a9b705c20999b82947da1e6d9ea7859ddf91802cc77d35a811a0ed70a322a88478871e1f2071e0d1fe197 SHA512 286bc8ea2cc8d9cb40c7e13a7bc7a2437aaffd4799bcf7a2825e6634dcf7c15044a3b0e71d665dd55b31f4475add8f233dba60bf9ed65fae4b339d6456e6242d
 MISC metadata.xml 964 BLAKE2B 6530733a29250579b0981a2712a8878094f1b347951d8c565449d46e1dcfd28459b9cfbc82d4cd6e79ee2e06d275673227c068a1b57bea3edec024dbbf3895bd SHA512 e5f7e98b69c437e3ffe18ca05d2dbefa1aaeee6b630e481b346576d46edd35784f174953b4616f7463d561bb8dae962288c9f9180967fc845c43bf29525aa47a
diff --git a/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild b/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild
index 1174d0de599e..3d9f683d4666 100644
--- a/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild
+++ b/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
@@ -7,7 +7,7 @@ inherit toolchain-funcs
 
 DESCRIPTION="Bayesian Inference of Phylogeny"
 HOMEPAGE="http://mrbayes.csit.fsu.edu/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
+SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.gz"
 
 LICENSE="GPL-2"
 SLOT="0"
diff --git a/sci-biology/mummer/Manifest b/sci-biology/mummer/Manifest
index 449d54fecfea..ee2e5ad9d81c 100644
--- a/sci-biology/mummer/Manifest
+++ b/sci-biology/mummer/Manifest
@@ -2,5 +2,5 @@ AUX mummer-3.23-fix-build-system.patch 10130 BLAKE2B 1c11e08dcc21daf26b14e13dac8
 AUX mummer-3.23-fix-c++-qa.patch 2615 BLAKE2B c4af27ae72445836a71ef6417f56b2feaf10483da70d38ff3cbda80d95db0947eb183ef3f34c3922397c759a7e424b1674b193495199c0f5b942af5c9efd77f8 SHA512 ca1a8156ecac367817f4678ed9fd0dd7e5f31cce0d8d167dd9245ea1e2ad4b4acad254277483f99764891a0cbad8ca6f879acc731b8e3e306e5644739c0f82d2
 AUX mummer-3.23-fix-shebangs.patch 2357 BLAKE2B 1a244047f55483240bc257892f2a607ab695624152613d665be5abecd85e02484a251e33f411fc67377dad3c49eb5ac32624acefa5cabeaadc8b5e3506dbb21c SHA512 d0ac58170232244385328d3a23e6b8203593d32dda30d75915b4da8ad935fc1dc447b2a7c7d982b0a86c9fe4ca6f8c2031fe7f81af8a72bfba4d56ae6d246235
 DIST MUMmer3.23.tar.gz 3160143 BLAKE2B 5be613e0b7bcdbd0c38bb6dd7ff8d5c220ceb596582d89e0c1b62bbb2b289ce3a1842cd7e335a62d612af55388e21b6f780254de06f59e9e49a7eeadd04b6d8e SHA512 f31d36ef3e07fa4ac017c76c1c8d5f53882a59b061742d201f1f7aafb29d16af8268985285398dd90e98d276b2513d2c611f9876069b23fe82b5da1d3ebc04d3
-EBUILD mummer-3.23-r1.ebuild 1122 BLAKE2B 3cc8490dabdfd892868789447d811b522fe2efca8ae30e73e43ba3be1d1af3affae47e10740c4ff941176ec99a0b37f67405efaa4043c32092ae0ca4c92bb27a SHA512 6f6ebee7bc3cbc8c69643dd25433ef270de2d99bafb11cf06ec325beaf408cdcb0efdd744474689fdad8cf2c288162e85e4f785362f1bc27935584e75e7e3465
+EBUILD mummer-3.23-r1.ebuild 1135 BLAKE2B ace3658a63ba02884bb12ebfd1e7eaacf5090091cda9a49af73b337816f26b942d991a044957e53f6f0d8a5ec48812c1305ae3dcdc8f41f5e03244281384c857 SHA512 9ffdec58ff6293848a62cd6f57359578c60fd2a1d4633586d3cbc1bed4dc0fee5a3ba7e3c23ce252056cec944d571fc69042491605e52713efd548955a17e1e8
 MISC metadata.xml 348 BLAKE2B 4f2a263ee7069564001bbbd3d68c710f9bb1dd0f34c2cd9ad2459b483c942bb4cf0785f57c60fa1a27b57a90b5f445fad1422025e424e70b596bb90fe4f64857 SHA512 17850f7126f24e9d1ae26c3034e679881686f775afddf916905da3108bc2d5e3ce0e6b2aa3f63427c62cd76f7cf232c4e9b24077e5341e9f022ebe1c7e6ee1d5
diff --git a/sci-biology/mummer/mummer-3.23-r1.ebuild b/sci-biology/mummer/mummer-3.23-r1.ebuild
index 59a66abe2f04..1359833dc21d 100644
--- a/sci-biology/mummer/mummer-3.23-r1.ebuild
+++ b/sci-biology/mummer/mummer-3.23-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
@@ -7,7 +7,7 @@ inherit flag-o-matic toolchain-funcs
 
 DESCRIPTION="A rapid whole genome aligner"
 HOMEPAGE="http://mummer.sourceforge.net/"
-SRC_URI="mirror://sourceforge/mummer/MUMmer${PV}.tar.gz"
+SRC_URI="https://downloads.sourceforge.net/mummer/MUMmer${PV}.tar.gz"
 S="${WORKDIR}/MUMmer${PV}"
 
 LICENSE="Artistic"
diff --git a/sci-biology/poa/Manifest b/sci-biology/poa/Manifest
index b867b628de1e..5956032f3413 100644
--- a/sci-biology/poa/Manifest
+++ b/sci-biology/poa/Manifest
@@ -2,5 +2,5 @@ AUX poa-2-clang16.patch 2406 BLAKE2B 24a49f9b9c3acc33541f7143250d871584c9bab2ec2
 AUX poa-2-fno-common.patch 357 BLAKE2B 5d239201e987f1fc45e82019a27b2c8e81015cd2b6b5b35f90838a8fff16bb08b51da5e6e9e1ac163bd6591341ba96a870fce4949a79e9ca558ce8c765d15ba4 SHA512 9d8f6552fd43a0f40da9cb7a5316e0e434df793fb9f7522b60e067061d14a7b27299feb02a8603cb4f6039b205723f562ea5c54c15ab3bd6582f2e6e7c223c43
 AUX poa-2-respect-flags.patch 874 BLAKE2B ee278cdbc6ec0603bc28087bd008caa70fe39668360a1473891ed997bde93f31ef7586acc9137a23a4d3123047ce5b600c3d6418a89e1e62ca70545b99a3112b SHA512 95e2e7c43ba18f9238b379ea13d3a6004cf580c75d484dbe43f01c823484f84eb93c3d2fe1ae3c98583c51c660ab24e6dc580d132649adedbf30d8675d8107b0
 DIST poaV2.tar.gz 62612 BLAKE2B 92f7b2926dd7fc93745411fc04c8dd3380c32e3e87cf89afa81aefe787a1aa0e7a416d08809cce531a21d5118398a9474a751a742ee1fca47e83bd907444e9c0 SHA512 2a54b025f0a74ff4c01828f3e4b9e8e135bffe26d08f651f981bc95a64196173b5d887ef988a25c1f5fbf89333b4771622d5dc93946d66e7ec9abacb6167595c
-EBUILD poa-2-r1.ebuild 891 BLAKE2B 4c0e42af595a527f95ce4248146774a322fe7d1e2d309664c6dcd37c588511f0bfc33a1274dd96d89fd4780f69fc61641e6c1a7cdd4d03c6d445fb12dd7d58f0 SHA512 d89e34e9733879d1bce07d4d2f357cf1fa7b10461c407ba89640c674d4557d5e3ec34fc2537e1e31ce484bbe6ec898ce248b9de3243eca0c91e123d9969f8cc0
+EBUILD poa-2-r1.ebuild 904 BLAKE2B 00dd57a15669c12f657d6a3fe35dffb8e201a7f48c1ab78b7055b0cec539aab4c62b4e9616d6e195b7378ca52595530479d9e2e48d11e737fb607cb7dd02810d SHA512 fc917491f5a980f133a1c617e48c95468bc639b3464fbfa5e9cc1699e11219ebf4f776fec24ffba27e3545837f36fb96594497c16e88a47cd73080afbc943f2f
 MISC metadata.xml 348 BLAKE2B a159034e493b50e7390db0516a4f478d14877323a256152eb9e596251cc71b161a38f9b740313f015ed2ef1757d0110d7e368eabf37b0e295d063d3770708ec7 SHA512 6452fa4eda03932e1ddfb7ac88b5b5dd4ea5429767ea06d1ac4db1df87e88159333a7c817f101b34975d20cb35d0b62f8947d658eba47ab917c0ecfa106f29d1
diff --git a/sci-biology/poa/poa-2-r1.ebuild b/sci-biology/poa/poa-2-r1.ebuild
index f6d9b756f3d5..8044b8f822bf 100644
--- a/sci-biology/poa/poa-2-r1.ebuild
+++ b/sci-biology/poa/poa-2-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -9,7 +9,7 @@ MY_P="${PN}V${PV}"
 
 DESCRIPTION="Fast multiple sequence alignments using partial-order graphs"
 HOMEPAGE="http://bioinfo.mbi.ucla.edu/poa/"
-SRC_URI="mirror://sourceforge/poamsa/${MY_P}.tar.gz"
+SRC_URI="https://downloads.sourceforge.net/poamsa/${MY_P}.tar.gz"
 
 # According to SF project page
 LICENSE="GPL-2"
diff --git a/sci-biology/primer3/Manifest b/sci-biology/primer3/Manifest
index 5e9995a11985..b949150879fe 100644
--- a/sci-biology/primer3/Manifest
+++ b/sci-biology/primer3/Manifest
@@ -1,5 +1,5 @@
 AUX primer3-2.3.7-buildsystem.patch 5855 BLAKE2B 74395e3ecaf16e10bce493337681f2ab7b2b6016bb784854777c2a00cb09f9ab1275d9955d622bdd2d887bb7763a5d2addd7064fafb00b4d2102463491a112d1 SHA512 4cc3492b1c93e2d736493fe04e18b544dc9487ded5e6ebb4bc64e19b38ca125aafa4732e80cfab83d6467ba4d8e11ca7c59342188c7e4464e9a674e7ac26c59f
 AUX primer3-2.3.7-gcc7.patch 421 BLAKE2B 3f861ecb493ce9673cdebac9ea224a0588bd3b758d72a7ef4e41d4efb929db444a8c2808a55ead42dcb174265a926c021a89dd83dc8a1e5ba4eb5ed26280be43 SHA512 c818cd80e4762ef46e4e52acd27f4eb966d676995154b3503c98d8defb545c3dd7ea307c8946b5b5c462dd7f5dee6abc254cea59e21e2229cb779a7178dec04d
 DIST primer3-2.3.7.tar.gz 1658090 BLAKE2B 0bc9a0faa19c4ac3b48680d65b0d91a13d8bdd651ad3a0d344b4f50ce8dc510fe7a22665192751fb2c8ff6282b560daf4540a02cc70482dba0fcc344f7727e37 SHA512 f227f80d395cb682a9d65e0ac3afdcacb8385d66e721b9163fda939a9c788a7c6907273f6223782702b48d7df66ea2331114f6303fcd29e3b3c50a2717da2fa7
-EBUILD primer3-2.3.7-r1.ebuild 1065 BLAKE2B 0a2ef28bc0882e40384746768783a39a0a07e19fdb962d60284fa97a1873414da2732efcd5ae4110672e2748606df9cbb67a9871b9fccf0048d1647b0cf5872a SHA512 e0dcd3bbe1ef50fafa42b160f103cb8d357ecd31f7313714c9fbc135b4ee12e289d267b4d5f09a93e027009fcb513786d4bf4234e4e24bc540a7c2b7f8a19d90
+EBUILD primer3-2.3.7-r1.ebuild 1078 BLAKE2B 5405a20c9eb45e4e356da5f942339d527760c707c3de8a8ea102e76320a682deda00cd7ed91193f659110269050582dce6c40bb76cecd2cabfff926e40ec1281 SHA512 dbbbb201eeb60405db1d53e4bff0362a1078211f8cfd8e08fbbf44b1af5a1e4212037994960b564b93c97be43d16d1877c5ca9ed9033a899d80c9b6e893733cf
 MISC metadata.xml 798 BLAKE2B b57850f7ea949d9e026fba81ffb483b542f725aa96477b013ac635ef058c42fa925cc104ccac89e07cb655939364effc5193c9665264145b6d892593c133856a SHA512 1f1541c1a632b9ad37359bb60cb7e4fa4e583d9eafa10f9ec43450c30ade6ae88289ca62c793ec63da376306ab383b399ff4ab89483bcc43588aab78249100f8
diff --git a/sci-biology/primer3/primer3-2.3.7-r1.ebuild b/sci-biology/primer3/primer3-2.3.7-r1.ebuild
index 3ce2c4fe5d39..498c564753bf 100644
--- a/sci-biology/primer3/primer3-2.3.7-r1.ebuild
+++ b/sci-biology/primer3/primer3-2.3.7-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
@@ -7,7 +7,7 @@ inherit toolchain-funcs
 
 DESCRIPTION="Primer Design for PCR reactions"
 HOMEPAGE="http://primer3.sourceforge.net/"
-SRC_URI="mirror://sourceforge/project/${PN}/${PN}/${PV}/${P}.tar.gz"
+SRC_URI="https://downloads.sourceforge.net/project/${PN}/${PN}/${PV}/${P}.tar.gz"
 
 LICENSE="GPL-2"
 SLOT="0"
diff --git a/sci-biology/sibsim4/Manifest b/sci-biology/sibsim4/Manifest
index f4f8bc0957bc..5b0612cce721 100644
--- a/sci-biology/sibsim4/Manifest
+++ b/sci-biology/sibsim4/Manifest
@@ -1,4 +1,4 @@
 AUX sibsim4-0.20-makefile.patch 603 BLAKE2B 1d5bf536aec1c8d6716a2feeefc19d9397c8a8446899d40bdc58abe577ed5b4e7234b21bd428a831fcccd9ed0cdf6da70e9fda0db3070e3d51506b91b4324d01 SHA512 d434cf369ec418e29df7d34b139acf06182d84d1e83a7aaafe2d5df2ee49884ff86ad7fd5b6697108e7d1dea865652c8755459ff4ec0ae6395b1ec8c46126e55
 DIST SIBsim4-0.20.tar.gz 32118 BLAKE2B 79b1f080d547732ee6a5996885c26f422f8a1590fa37d525f35cfa3dee353fd36ce9aa4677fe7e570f43e8283c26541c8c9e76ca03788a66d1c356adb3d649d5 SHA512 3802520095e83d3c691804b661696095a4198c4b2a16385c55ccdc8e4e836f82cc9c2251a5d37cb5918c2ee80aeb81737d751e6b065fbfe9c64f1aee3e0ea0c8
-EBUILD sibsim4-0.20.ebuild 519 BLAKE2B 5722f5be83f06fc155500fcf5baa4780874d9e84be2ed9e607fb1d5850c10af504ac62d807c5b3e4e905494d246dde0073262c3788f5c9e0873bb0368eef72f5 SHA512 ea2b8e53d2f12becd13e5fddcffa46e20ee05d1b88fc5cb1c756abc1ef7ead63d129abfb130761ae18b66b754a39fbfb66d6ebd6b3843bcc5a852c1290e1fcbf
+EBUILD sibsim4-0.20.ebuild 532 BLAKE2B 2876d538aca35a73afc491dd2805919a8fb30de3283c7d3eeece02e627486aed1e39e9c465ab3750afa5f58ec3b33570a6cb3798ff9392251a3811ee44a93261 SHA512 3a6db39a9af465862d90552b8c47c93231ef295d64b745c3ed52475c67029397d3195b50935cb4d68a22d4a50c1bf04ca98a206d2e01bf95755b0dbab9f29492
 MISC metadata.xml 349 BLAKE2B 67cc5ec26168241638acef4254a0b8682d9df46e574871b9aaa114a5ba8ecf3bf2e3a6bf5523c145df33415e1900faa95e8d65344b861c18e6e9ee800b2fca5f SHA512 ceea81611ac099beabf355230b2df7e61e96fdb8823e992bc283094f182ca8b2486f50d016242f1dd21c1b4148b832f73de4af9cba57a108122d714313a8b5f6
diff --git a/sci-biology/sibsim4/sibsim4-0.20.ebuild b/sci-biology/sibsim4/sibsim4-0.20.ebuild
index c90c13dce7ec..2c9d69ada02c 100644
--- a/sci-biology/sibsim4/sibsim4-0.20.ebuild
+++ b/sci-biology/sibsim4/sibsim4-0.20.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2023 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -7,7 +7,7 @@ inherit toolchain-funcs
 
 DESCRIPTION="A rewrite and improvement upon sim4, a DNA-mRNA aligner"
 HOMEPAGE="http://sibsim4.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/SIBsim4-${PV}.tar.gz"
+SRC_URI="https://downloads.sourceforge.net/${PN}/SIBsim4-${PV}.tar.gz"
 S="${WORKDIR}/SIBsim4-${PV}"
 
 LICENSE="GPL-2"