From 2997df5d95cb64694ec91d50c93407e92c68e2a8 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sat, 4 Feb 2023 21:14:48 +0000 Subject: gentoo auto-resync : 04:02:2023 - 21:14:48 --- sci-biology/Manifest.gz | Bin 19496 -> 19500 bytes sci-biology/augustus/Manifest | 4 +- sci-biology/augustus/augustus-3.4.0-r2.ebuild | 51 -------------------------- sci-biology/augustus/augustus-3.4.0-r3.ebuild | 51 ++++++++++++++++++++++++++ sci-biology/augustus/metadata.xml | 1 + 5 files changed, 54 insertions(+), 53 deletions(-) delete mode 100644 sci-biology/augustus/augustus-3.4.0-r2.ebuild create mode 100644 sci-biology/augustus/augustus-3.4.0-r3.ebuild (limited to 'sci-biology') diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz index c69bcbc42b0f..e776d8d7ee7b 100644 Binary files a/sci-biology/Manifest.gz and b/sci-biology/Manifest.gz differ diff --git a/sci-biology/augustus/Manifest b/sci-biology/augustus/Manifest index 68a832441ac2..274e7b36b36e 100644 --- a/sci-biology/augustus/Manifest +++ b/sci-biology/augustus/Manifest @@ -2,5 +2,5 @@ AUX augustus-2.5.5-sane-build.patch 5271 BLAKE2B 1ba799aa4d9611087f1455f334dc356 DIST augustus-3.4.0.tar.gz 221652100 BLAKE2B dfc8c98107f5a955f688f3d2976ca936faf2ef7004095f6b9d7c1902a36ca5d3c9aef59cab1b82b56cd5c2abc7b67195c5030111ed68557d53128814b1bf6bab SHA512 ca1df1016589f55527a883429edd5024cbc32c1b32036c81f9df5e0967a7d194f5b7a82109e924f380627427d9731caa478e63cad8cd804c01521aed76d8c4a6 DIST augustus.2.5.5.tar.gz 70826249 BLAKE2B 3f3f1537c5c614f00298e1835eeb7bbe968987c3e0dee13299e1e26b4abf198d8635a93121b11722d2c90b63ff54cf153c72716d01c3ca033481bb54357b7bcf SHA512 33eb05d5c90200d2fc17026743d3a25e73aa3e217b8546f0bed4c94bcb460597d853377a67896e52e45ead5d736d13ed3b2c91b31fed8216da2920c825e8c20f EBUILD augustus-2.5.5.ebuild 910 BLAKE2B 5cde42582b4873dbaabe4457a4b7b4f5305b928cbfd7afc3c067cbeb3ea042e82faa56810b4f72078d57f7b0ecd4c96eaa30cfde5ef73d67c26fd05d0035d84e SHA512 03103b4d5cec5dfd46971f1a089d0c02d3cc5ecf7647ee5589e8e297b3f60689c2c763b8c8f2137becfa0e11c0e3c7977186c466085c3065f88eaf5a469bcb9c -EBUILD augustus-3.4.0-r2.ebuild 1031 BLAKE2B 45a1ddd194df245043599abe15d9a104a7857f2592441f6aec1dff942c3d4b145e56204a6a7dbb1e714943797f38a5d13259e674b4ba6585c2c4eab9caee85f4 SHA512 f2740287ddb5de53ac1ba572b35849aa527d341044dd353d83387222d9e2a2f67c85f8e0bd07e2b077227730b241153af2f5d5d8c843d1b7999dc1927a8c62a4 -MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de +EBUILD augustus-3.4.0-r3.ebuild 1033 BLAKE2B 52d45534a5f9cc900d3a048926046fac00016a16f6dd8d65b530c24d99a0873ebdb177eff3d83ed74cb3cd6f1660a17ff0349217d073893d351d31b5ccfbe1d7 SHA512 6a0a337b6c4376412b7184fc6303b4c18da80936d8228ac35c8a106ab2e2070a2c998ee3ce28e2453275eeeecc82c7b4be4bdc0a031b5b47c820e6e76db5a867 +MISC metadata.xml 331 BLAKE2B 55a0917b78fc838f65b29d89a4e65e7be0143f0f867186e4af130e22c0950e688fc80af96374f63d0bae9369538c684cdce87e1ed09bc77be92075ea68c2c77d SHA512 40ab355fb770a0683028ab521777c6f89cc96b24ad04feb1ba45f473c39eaa74b81e63475573546019cfac059c2ccc0640b73962b2243963850a243f6cb1518e diff --git a/sci-biology/augustus/augustus-3.4.0-r2.ebuild b/sci-biology/augustus/augustus-3.4.0-r2.ebuild deleted file mode 100644 index 30b3d7d0a6f8..000000000000 --- a/sci-biology/augustus/augustus-3.4.0-r2.ebuild +++ /dev/null @@ -1,51 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DOCS_BUILDER="doxygen" -DOCS_CONFIG_NAME="doxygen.conf" -inherit docs toolchain-funcs - -DESCRIPTION="Eukaryotic gene predictor" -HOMEPAGE="https://bioinf.uni-greifswald.de/augustus/" -SRC_URI="https://github.com/Gaius-Augustus/Augustus/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" -S="${WORKDIR}/${P^}" - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-db/sqlite:3 - dev-db/mysql++:= - dev-db/mysql-connector-c:= - dev-libs/boost:=[zlib] - sci-biology/bamtools:= - sci-biology/samtools:0 - sci-libs/gsl:= - sci-libs/htslib:= - sci-libs/suitesparse - sci-mathematics/lpsolve - sys-libs/zlib -" -DEPEND="${RDEPEND}" - -src_compile() { - tc-export CC CXX - - emake LINK.cc="$(tc-getCXX)" - - docs_compile -} - -src_install() { - einstalldocs - # from upstream Makefile install: - dodir "opt/${P}" - cp -a config bin scripts "${ED}/opt/${P}" || die - local file - for file in bin/*; do - dosym "../${P}/${file}" "/opt/${file}" - done -} diff --git a/sci-biology/augustus/augustus-3.4.0-r3.ebuild b/sci-biology/augustus/augustus-3.4.0-r3.ebuild new file mode 100644 index 000000000000..7c662aead62f --- /dev/null +++ b/sci-biology/augustus/augustus-3.4.0-r3.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DOCS_BUILDER="doxygen" +DOCS_CONFIG_NAME="doxygen.conf" +inherit docs toolchain-funcs + +DESCRIPTION="Eukaryotic gene predictor" +HOMEPAGE="https://bioinf.uni-greifswald.de/augustus/" +SRC_URI="https://github.com/Gaius-Augustus/Augustus/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/${P^}" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-db/sqlite:3 + dev-db/mysql++:= + dev-db/mysql-connector-c:= + dev-libs/boost:=[zlib] + sci-biology/bamtools:= + sci-biology/samtools:0 + sci-libs/gsl:= + sci-libs/htslib:= + sci-libs/suitesparse + sci-mathematics/lpsolve:= + sys-libs/zlib +" +DEPEND="${RDEPEND}" + +src_compile() { + tc-export CC CXX + + emake LINK.cc="$(tc-getCXX)" + + docs_compile +} + +src_install() { + einstalldocs + # from upstream Makefile install: + dodir "opt/${P}" + cp -a config bin scripts "${ED}/opt/${P}" || die + local file + for file in bin/*; do + dosym "../${P}/${file}" "/opt/${file}" + done +} diff --git a/sci-biology/augustus/metadata.xml b/sci-biology/augustus/metadata.xml index ccdff086e20b..20555ec8076a 100644 --- a/sci-biology/augustus/metadata.xml +++ b/sci-biology/augustus/metadata.xml @@ -5,4 +5,5 @@ sci-biology@gentoo.org Gentoo Biology Project + Gaius-Augustus/Augustus -- cgit v1.2.3