diff options
Diffstat (limited to 'sci-biology/augustus')
| -rw-r--r-- | sci-biology/augustus/Manifest | 5 | ||||
| -rw-r--r-- | sci-biology/augustus/augustus-3.4.0-r3.ebuild | 6 | ||||
| -rw-r--r-- | sci-biology/augustus/augustus-3.5.0.ebuild | 93 | ||||
| -rw-r--r-- | sci-biology/augustus/files/augustus-3.4.0-missing-cstdint.patch | 39 |
4 files changed, 141 insertions, 2 deletions
diff --git a/sci-biology/augustus/Manifest b/sci-biology/augustus/Manifest index 759691acff14..0a483257cf09 100644 --- a/sci-biology/augustus/Manifest +++ b/sci-biology/augustus/Manifest @@ -1,6 +1,9 @@ AUX augustus-2.5.5-sane-build.patch 5271 BLAKE2B 1ba799aa4d9611087f1455f334dc35616979267bb546aa2ab16f6c8d3d528af84373da482840b455d4d0f0374af24cc3010f6925d4a93c0eb7abe524544fd408 SHA512 5afe12b51b8ce27ef32e8e66dd72be451022757228b4c86dec938b26870885bee06712438a22801a42944d2def8ae8bf4a2d7fdb82e12455c145abcd6f0c4aa1 +AUX augustus-3.4.0-missing-cstdint.patch 1102 BLAKE2B af80ef05823b7318db3c9b3440d8634dbbc532e57614ce51ac2be8950a7ee1f72984c3e2fdbc57b9328f84cf639b45625d974b176963deee2e13bb9c94389b16 SHA512 380da23de6489b9e27c83c2d87b3175f4cad1c301e5458c8eb8c6bc1e93a4ece467223408322c581cd5b50d03526f46a10d3a5ab8dea96eb47b06694798402fc DIST augustus-3.4.0.tar.gz 221652100 BLAKE2B dfc8c98107f5a955f688f3d2976ca936faf2ef7004095f6b9d7c1902a36ca5d3c9aef59cab1b82b56cd5c2abc7b67195c5030111ed68557d53128814b1bf6bab SHA512 ca1df1016589f55527a883429edd5024cbc32c1b32036c81f9df5e0967a7d194f5b7a82109e924f380627427d9731caa478e63cad8cd804c01521aed76d8c4a6 +DIST augustus-3.5.0.tar.gz 225918930 BLAKE2B 26e934f3d3f50d183fb0ee7874352c5ac9af9877eaa40a9a6195ae79cfd9a78a321bd9261e8bd3435b1d4984589d0bdd4e0821ba6600c717d6afd95f511702de SHA512 0869e54b3126b3ab2f6fb2c28ff07b779265a139968e5277352f5230d3c317415324ca61dce4a0cd6c3f1fb5399447ae815bec7732a285ce652cf44e6cd23e5d DIST augustus.2.5.5.tar.gz 70826249 BLAKE2B 3f3f1537c5c614f00298e1835eeb7bbe968987c3e0dee13299e1e26b4abf198d8635a93121b11722d2c90b63ff54cf153c72716d01c3ca033481bb54357b7bcf SHA512 33eb05d5c90200d2fc17026743d3a25e73aa3e217b8546f0bed4c94bcb460597d853377a67896e52e45ead5d736d13ed3b2c91b31fed8216da2920c825e8c20f EBUILD augustus-2.5.5.ebuild 911 BLAKE2B 92c56fcf261b64393440c92e0f01b9dae018e082b4addb5759cbfc807183944059775a8482fafcba5c3dc3fc4ca7568c93bd4be546b65a0bc446028a537c71f6 SHA512 a54cc943fa343179edb7d21c9cd841672d6abc548e5a2c6b56c054b85bd64684dc7bf145110c6eb51788d600a37bfcad60e8f4d8c982aa92213ee75ed95cc963 -EBUILD augustus-3.4.0-r3.ebuild 1033 BLAKE2B 52d45534a5f9cc900d3a048926046fac00016a16f6dd8d65b530c24d99a0873ebdb177eff3d83ed74cb3cd6f1660a17ff0349217d073893d351d31b5ccfbe1d7 SHA512 6a0a337b6c4376412b7184fc6303b4c18da80936d8228ac35c8a106ab2e2070a2c998ee3ce28e2453275eeeecc82c7b4be4bdc0a031b5b47c820e6e76db5a867 +EBUILD augustus-3.4.0-r3.ebuild 1098 BLAKE2B f8fd13b91ffeb4f5c2bae0ce51473275ad61a9ad25c548ce4f564dfea6462dfd7c83be9fb6395908a8b226472d7f0e29430910552da2f70e0d6ece8258ac794e SHA512 94507d41aeb7a64f046f7c76f9feb86b95db082c34b099a9470d17200540997a58ef1b445083c2ba486bf3c6267ecf56f80c90174c099bc095c60cfa5ac98cf8 +EBUILD augustus-3.5.0.ebuild 1794 BLAKE2B f850df5e8d1b48323f26541350f6a23c09c916a2136c41a377ea3ea40a7aede9d28732b45cd2219eb8373ec74695495dafefbef52ca7e8c831d16b3bf3259c5c SHA512 9c6f7ca416a30dbf4424d539a8fdfbb78c2d8ac715955515079978d55457001e5cfd366c384dfdd7718f723fd87f693dd978c8abacb2212ae39df3c8feedd082 MISC metadata.xml 360 BLAKE2B a2a37a6ac8535c7c1e48711fe6f330bddc6057a445afb33bced10e3137255bbe647d85a1c300af4cc802c2fdaa4a6d4ee169e82778ba4437e60824daf2485633 SHA512 7f3cc43067ed98c6fee8302eff2855b3594c2adc3e81d72c27aa20bd9e4477401607a4424e93368a3e501bcb90a44106bebdffd2ca0069e94b3b5d3e5fc2156e diff --git a/sci-biology/augustus/augustus-3.4.0-r3.ebuild b/sci-biology/augustus/augustus-3.4.0-r3.ebuild index 7c662aead62f..7f1bd71bdf41 100644 --- a/sci-biology/augustus/augustus-3.4.0-r3.ebuild +++ b/sci-biology/augustus/augustus-3.4.0-r3.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2025 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -31,6 +31,10 @@ RDEPEND=" " DEPEND="${RDEPEND}" +PATCHES=( + "${FILESDIR}"/augustus-3.4.0-missing-cstdint.patch +) + src_compile() { tc-export CC CXX diff --git a/sci-biology/augustus/augustus-3.5.0.ebuild b/sci-biology/augustus/augustus-3.5.0.ebuild new file mode 100644 index 000000000000..01f8dbc42621 --- /dev/null +++ b/sci-biology/augustus/augustus-3.5.0.ebuild @@ -0,0 +1,93 @@ +# Copyright 1999-2025 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DOCS_BUILDER="doxygen" +DOCS_CONFIG_NAME="doxygen.conf" + +PYTHON_COMPAT=( python3_{12..13} ) + +inherit docs python-any-r1 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}/${P^}" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +IUSE="test" +RESTRICT="!test? ( test )" + +RDEPEND=" + dev-db/sqlite:3 + dev-db/mysql++:= + dev-db/mysql-connector-c:= + dev-libs/boost:=[zlib] + sci-biology/bamtools:= + sci-biology/samtools:0 + sci-libs/gsl:= + sci-libs/htslib:= + sci-libs/suitesparse + sci-mathematics/lpsolve:= + sys-libs/zlib +" +DEPEND="${RDEPEND}" +BDEPEND=" + test? ( + ${PYTHON_DEPS} + ) +" + +PATCHES=( + "${FILESDIR}"/augustus-3.4.0-missing-cstdint.patch +) + +pkg_setup() { + use test && python-any-r1_pkg_setup +} + +src_compile() { + tc-export CC CXX AR + + emake + + # Vendored gtest + use test && emake -C src unittest + + docs_compile +} + +src_test() { + if use elibc_musl; then + # Upstream already does this for non-amd64 and non-linux environments + # Probably related https://github.com/Gaius-Augustus/Augustus/issues/247 + # bug #873025 + emake test TEST_COMPARE= TEST_HTML= + else + emake test + fi + + pushd src/unittests >/dev/null || die + if use elibc_musl; then + # Float issues + ./unittests --gtest_filter='-CodonEvoTest.CodonEvoRateReadWrite' || die + else + ./unittests || die + fi + popd >/dev/null || die +} + +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/files/augustus-3.4.0-missing-cstdint.patch b/sci-biology/augustus/files/augustus-3.4.0-missing-cstdint.patch new file mode 100644 index 000000000000..3c0095241636 --- /dev/null +++ b/sci-biology/augustus/files/augustus-3.4.0-missing-cstdint.patch @@ -0,0 +1,39 @@ +https://bugs.gentoo.org/895204 + +https://github.com/Gaius-Augustus/Augustus/commit/1ed97dc4ce2909c5f89737005b8ea4a664fbe728 +https://github.com/Gaius-Augustus/Augustus/pull/395 + +From 1ed97dc4ce2909c5f89737005b8ea4a664fbe728 Mon Sep 17 00:00:00 2001 +From: Kuoi <kuoi@bioarchlinux.org> +Date: Sun, 11 Jun 2023 23:47:49 +0800 +Subject: [PATCH] fix: gcc13 failed with this + +--- a/include/sqliteDB.hh ++++ b/include/sqliteDB.hh +@@ -11,6 +11,7 @@ + #include <string> + #include <vector> + #include <sqlite3.h> ++#include <cstdint> + + using namespace std; + + +https://github.com/Gaius-Augustus/Augustus/commit/3dbe752e4cf3f6778168166a2c662d02d8623f15 +https://github.com/Gaius-Augustus/Augustus/pull/395 + +From 3dbe752e4cf3f6778168166a2c662d02d8623f15 Mon Sep 17 00:00:00 2001 +From: Kuoi <kuoi@bioarchlinux.org> +Date: Mon, 12 Jun 2023 01:32:02 +0800 +Subject: [PATCH] fix: without it compile fail + +--- a/auxprogs/homGeneMapping/include/sqliteDB.hh ++++ b/auxprogs/homGeneMapping/include/sqliteDB.hh +@@ -13,6 +13,7 @@ + #include <string> + #include <vector> + #include <sqlite3.h> ++#include <cstdint> + + using namespace std; + |