gentoo resync : 03.03.2021

6 files changed, 53 insertions, 32 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index d374f3c80bc7..989c9575830c 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest
index 7e9ceaea378d..7ed1666c1527 100644
--- a/sci-biology/bedtools/Manifest
+++ b/sci-biology/bedtools/Manifest
@@ -2,5 +2,7 @@ AUX bedtools-2.29.2-buildsystem.patch 2002 BLAKE2B 7925c788858515ec4454ece382368
 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 406 BLAKE2B 5a16830031644c5087241b9e20afcb6315095c877e2b019eace76ee0602929c168c2273e27e99f03ca3c1a57db0bf728c2d8ccc39b7f80588bb215d1fd6a3ea6 SHA512 35a9b50a772503e6691faf1e2f1093bd6ffd5f6f5be08b1ad8581948f4f3e8fb7e54faa101cff757fc561ed71696253114c32fb6293df59cda3e8fd7c24d2bb0
diff --git a/sci-biology/bedtools/bedtools-2.30.0.ebuild b/sci-biology/bedtools/bedtools-2.30.0.ebuild
new file mode 100644
index 000000000000..3647f43dabe5
--- /dev/null
+++ b/sci-biology/bedtools/bedtools-2.30.0.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2021 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}"/${PN}-2.29.2-python.patch
+)
+
+src_configure() {
+	tc-export AR CC CXX RANLIB
+}
+
+src_install() {
+	default
+
+	insinto /usr/share/${PN}
+	doins -r genomes
+}
diff --git a/sci-biology/finchtv/Manifest b/sci-biology/finchtv/Manifest
index d98c46dbcab5..b8708a0f2395 100644
--- a/sci-biology/finchtv/Manifest
+++ b/sci-biology/finchtv/Manifest
@@ -1,4 +1,3 @@
 DIST finchtv_1_3_1.tar.gz 6706911 BLAKE2B 5aea60c2a107dc0d1d878b0416011f57bfcdb73b6e7c0da80be5b485ec5824aae7c610235057b74002765f5ab5e7bd250efec2a04a471b55abd046afc560ea38 SHA512 813217a6d44cbd60fff061da94f70adadcc803b77352b278246711bf1b952b592a0fdb6bfc9d74264d896cb816078e809bdc633981d4009c422f59f74aca5bc8
-EBUILD finchtv-1.3.1-r2.ebuild 610 BLAKE2B 4c58fdc546782232ea8c1fc5937ab83ba36000bbea56b83d813a9afd52cdc9caff0b946235f9d452c2ee287d11a228697c8a972e2bbbdaa94c640e4ac40c82eb SHA512 693cc060e91d2ed1ca9d4bc6ff6baaa9a3afe1a876d83d79e3cc3d4c416f8e7ddc878696e890e0b4e660ed5c017c0402bb8247e1b4d6d819f567292b5aa168a7
-EBUILD finchtv-1.3.1-r3.ebuild 720 BLAKE2B 1f3fb4ab17064186d094a1828f63e263619254974693df814dc19ca717c7ce555ba0788fd6d18fcc2d4b00655991d26f27b2fea940e3d77978371d6d73c0981f SHA512 511e0a9506d51cf765c89dd6dae1675be9e76cbbd264ba1bb559d137e9fed92ea97e1960683aa7d7ccef7c6cbab176a1ab11d6c3304ff0e54960fc85af16c5b9
+EBUILD finchtv-1.3.1-r3.ebuild 718 BLAKE2B 565eac2d89a9cf378309957a0a10b3aaf5b61311cec1651dd69307541cfcf067433d686fad48c340b47bc609484c475ffff1c5c5dfd6da1f89b61a7f0f4ac130 SHA512 06dd522e0ea7b6f5501b31162022d7eb9e3b75f3b7c1688a6ce5222d1726212e9f6e484a832686c3dce2676a72d20f2446c6c8c953482b63a071309e3d285dae
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/finchtv/finchtv-1.3.1-r2.ebuild b/sci-biology/finchtv/finchtv-1.3.1-r2.ebuild
deleted file mode 100644
index a08312d9033e..000000000000
--- a/sci-biology/finchtv/finchtv-1.3.1-r2.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-MY_PV="${PV//./_}"
-MY_P=${PN}_${MY_PV}
-
-DESCRIPTION="Graphical viewer for chromatogram files"
-HOMEPAGE="http://www.geospiza.com/finchtv/"
-SRC_URI="http://www.geospiza.com/finchtv/download/programs/linux/${MY_P}.tar.gz"
-
-LICENSE="finchtv"
-SLOT="0"
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-S="${WORKDIR}/${MY_P}"
-
-QA_PREBUILT="opt/bin/*"
-
-src_install() {
-	exeinto /opt/bin
-	doexe finchtv
-	dodoc ReleaseNotes.txt
-	dohtml -r Help/*
-	insinto /usr/share/doc/${PN}
-	doins -r SampleData
-}
diff --git a/sci-biology/finchtv/finchtv-1.3.1-r3.ebuild b/sci-biology/finchtv/finchtv-1.3.1-r3.ebuild
index f37355307e2d..60608c9aff2a 100644
--- a/sci-biology/finchtv/finchtv-1.3.1-r3.ebuild
+++ b/sci-biology/finchtv/finchtv-1.3.1-r3.ebuild
@@ -14,7 +14,7 @@ SRC_URI="http://www.geospiza.com/finchtv/download/programs/linux/${MY_P}.tar.gz"
 
 LICENSE="finchtv"
 SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
 
 S="${WORKDIR}/${MY_P}"