From d99093fb4bb5652015c06274d64083daa2439e4f Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Wed, 3 Mar 2021 10:28:17 +0000 Subject: gentoo resync : 03.03.2021 --- sci-biology/Manifest.gz | Bin 22468 -> 22469 bytes sci-biology/bedtools/Manifest | 2 ++ sci-biology/bedtools/bedtools-2.30.0.ebuild | 49 ++++++++++++++++++++++++++++ sci-biology/finchtv/Manifest | 3 +- sci-biology/finchtv/finchtv-1.3.1-r2.ebuild | 29 ---------------- sci-biology/finchtv/finchtv-1.3.1-r3.ebuild | 2 +- 6 files changed, 53 insertions(+), 32 deletions(-) create mode 100644 sci-biology/bedtools/bedtools-2.30.0.ebuild delete mode 100644 sci-biology/finchtv/finchtv-1.3.1-r2.ebuild (limited to 'sci-biology') diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz index d374f3c80bc7..989c9575830c 100644 Binary files a/sci-biology/Manifest.gz and b/sci-biology/Manifest.gz differ 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}" -- cgit v1.2.3