diff options
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/seqan/ChangeLog | 8 | ||||
| -rw-r--r-- | sci-biology/seqan/Manifest | 33 | ||||
| -rw-r--r-- | sci-biology/seqan/files/seqan-2.0.0-zlib.patch | 15 | ||||
| -rw-r--r-- | sci-biology/seqan/seqan-2.0.0.ebuild | 51 |
4 files changed, 91 insertions, 16 deletions
diff --git a/sci-biology/seqan/ChangeLog b/sci-biology/seqan/ChangeLog index 8061f95ad69e..deae422eb74f 100644 --- a/sci-biology/seqan/ChangeLog +++ b/sci-biology/seqan/ChangeLog @@ -1,6 +1,12 @@ # ChangeLog for sci-biology/seqan # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/seqan/ChangeLog,v 1.8 2015/02/19 22:03:53 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/seqan/ChangeLog,v 1.9 2015/02/24 16:47:47 jlec Exp $ + +*seqan-2.0.0 (24 Feb 2015) + + 24 Feb 2015; Justin Lecher <jlec@gentoo.org> +files/seqan-2.0.0-zlib.patch, + +seqan-2.0.0.ebuild: + Version Bump, #540692 19 Feb 2015; Justin Lecher <jlec@gentoo.org> seqan-1.4.2.ebuild: Prefix love, #540690; thanks Michael Schubert for the patch diff --git a/sci-biology/seqan/Manifest b/sci-biology/seqan/Manifest index 2f9b9d3e02c7..08c0310656cc 100644 --- a/sci-biology/seqan/Manifest +++ b/sci-biology/seqan/Manifest @@ -3,28 +3,31 @@ Hash: SHA512 AUX seqan-1.4.2-include.patch 552 SHA256 fb97f772388de6de381c7214b8b5167b2079e19d7f839673e281537c4bc80516 SHA512 b02ab4fe49a511494134e44855d865f0ff210392810970834deb304499b5017764ed1c04d8f8dbfb513c333ac302946e5c72c9160cd38a5ef5ad095a865cb6d0 WHIRLPOOL 26a3278707276b95197192c140589a2cc95cd5d487144975219bf4d918884434b57186093595f92ec009679dc5eb912422520c245691da6e1cc3cc441c284a5b AUX seqan-1.4.2-shared.patch 974 SHA256 3c704fa149d0d4b322f8bb1b5536dafca35c205e5931a149fce5e82cac1dfe05 SHA512 a509c243244b6b40b26700a73be267558ceb17c4e0079f3eca606835ecfe8d1417b88fd37719ca9cf226e6d2d33ee3e22790b20e39a86a300f722eb186cabaad WHIRLPOOL eb7a76bb6c82e7a312356d0db13b6f90bd0fadc021ce1e62e8f2c8708f25a84911842df4df20a8491f5971d62fda5a738527d863bd10c2f1167fbed82cd00dea +AUX seqan-2.0.0-zlib.patch 527 SHA256 e6ec043fc45c3436dbd86ab3bf4835d874ee325a3b8de2fcb024cbd25a9e9cab SHA512 ec7123b4f0ab5f99e66cc0ef025088df1b3e2b50e43bbaac5e543a7cfd86f969ed3246750c5caec8dd8ab7fafc4943b6025d46a184329184671fcfb1ac9744fa WHIRLPOOL 30b8eb0aa955f30ed3d8494c08ffc28ae2d000fef2acb97b37aa1a07de07ab6f49949692ea38e7b816cf1d2ffcaced9a05d103393f88eb0caabe65f351c08821 DIST seqan-1.3.1.zip 8787521 SHA256 87eebe73ace9ada2f4664a768ae212d4acc5fb3ce87702709c3d15bf2d153aeb SHA512 dafacccb4647fd0fc5a055d33390cb85f1c00ca74132e9b3839a739916acf9a2990db7db4f09e34f899b283cad8ccf6553a60cc7693164f250f08260c8ce8ae4 WHIRLPOOL 5a0a80d09e80285a4fc9fb9fb71adbea6b0b324a6a219cd7c9ef3d30e88133f5b25b3cf792b2b89e4ed07ff612f4aa347dc6f94e06974f947fe980c2e0a5d26b DIST seqan-src-1.4.2.tar.gz 120601994 SHA256 2b2c48572ea82fc2ac6a6e46bbd4204b6f8200fde717612797426af5ff6b82c3 SHA512 dbb56167c507b70111619a414054d9e70f1db42507bbfdf9e40c5dcbbe9489ad4187d882e638a675e96551c860c08f8203c929c4c9a558b19ea7d6059f50492a WHIRLPOOL 3c7f38e35d826adad94d53d359df8b5f1fb51746f3103457b12b41bd0bf161dc463d4a1932b0b23f2274d723c796116af0940260e1922ce806bb2466445788f0 +DIST seqan-src-2.0.0.tar.gz 115731415 SHA256 69cb39574e63de2f728715255ac7ffd26db6480d6ce33c8601eef05f282aed28 SHA512 9823b109c27fa770b86a72530ebb4f6ca4541f8f6cf979724730cd8c59809192c14178c01a9ec13ef0277c997c4c37f00c80bba1fef5ef57c367ae8285b0215a WHIRLPOOL afa5dd41106390f63523990ce876ef74952ce7787a2772c2116bafd564d466e588809e4c5812b5aa1137408a0291de739b70a9a1e116d212967f68f5246217f4 EBUILD seqan-1.3.1-r1.ebuild 979 SHA256 9feff642a58a7beec934130f8bfd0fa39ea614c22883bf7c832b6904d0f62b4b SHA512 cbf66445a3a3d862b8eb15c4bea8d3890c7a62f5aa6f295180d7899a2e7e9221fab726ac2e666faff78cb1fbf26d974505f1e41295aad80d247243d1a9b72114 WHIRLPOOL 0d303318d83105d64c22179b665a7235a3dcbf9ef8ef3362cdfcfdb32d74d011f5b751977d4f45a298ac0f79263f19385261a3649f9bab23b7e0e8cee5e7c729 EBUILD seqan-1.4.2.ebuild 1571 SHA256 3652a444818dc4d11998d0b728773e2b8d3a2057dfccdaa3db9e992fbbb92369 SHA512 d9abb95d890bc225af5dbf6bcc4c595f7639e389c0bf33bdd668037840eaef786ab56976bd5095e533960edac1dc13136ec8aae4a8d8f81c3612c0f1ebc54104 WHIRLPOOL f1be53239ab0267b0e6119185c1ce9bc5e9ed7ac4cecffbc3802e05d581478eb4e8177204b4e426e837ffe1513e80f8bb5ecfb43f8d6ee9d98059553d7934c7c -MISC ChangeLog 1247 SHA256 1a2eae89e900667ead4bd04fa6deb9ae3c7e1279325183f24c01d66d7e3f6d11 SHA512 3ec15fa4bcead179e2c4d62f2be90c15e2711b9c030e478c2515eb90b22ef7799cac7c2bd694ab721c4a732c217e99f0701f19f7b21555a404d9b0c53366f31b WHIRLPOOL 8e5ea3a176f873c7c630840682e2d64b8327b5cf62e17f5996caeab1d56a1e689d2691c277b0904ded21caf0d05f5623cb387a093644edb02180b3c828cc66a5 +EBUILD seqan-2.0.0.ebuild 1095 SHA256 1beadc530dabab02caa914f68cbea65fd836f3b31166c1877897488c1b20c058 SHA512 ddba4a6b9cc879f7c5d00282f2a996c83c60ec4512028aec7fb14ac548f345be6db8c1f2b52977080e552380629d2bd30511d444a4631acf3c9a46857abfc1b5 WHIRLPOOL 3109df9ae7495b45991f6bed460169438ba210a5cddffbbe1e69ddc4a2bc67de838e8b35e33b71fc2f1b20b448e49549694c66c6f48865fe08de4ffb629c6e25 +MISC ChangeLog 1401 SHA256 da38d2697f38a1e8f33c8396fa08e53725c73543c5adabbf1ff8b96505b4ea18 SHA512 6e2f090bf47b64aaaf97b6add5fecf48ea09a3cbe00637068e2e93ccf3202317d2a6dfb95ecb84591ee276bef58be4718e476486e90b247ac6557e4a7e333117 WHIRLPOOL c9ae8dd9b3d82fc7ff36c3c4c59209d205b7912a55ff9205f0efd832b741246f0018acc89b8b3b79182a0e63ee80c4cd56a1cd59c57caacf494e1a266f139c25 MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0 -iQJ8BAEBCgBmBQJU5l7QXxSAAAAAAC4AKGlzc3Vlci1mcHJAbm90YXRpb25zLm9w +iQJ8BAEBCgBmBQJU7Ks0XxSAAAAAAC4AKGlzc3Vlci1mcHJAbm90YXRpb25zLm9w ZW5wZ3AuZmlmdGhob3JzZW1hbi5uZXQyQ0JDQjFGMzBDQ0UxMjFGNENDNDgxMDdC -OUQ0RjIzMUJEMTU1OEFCAAoJELnU8jG9FVirmSEP/Ascot9tRKk84R/5NZwK2PAe 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a/include/seqan/stream/zipstream/zutil.h ++++ b/include/seqan/stream/zipstream/zutil.h +@@ -152,6 +152,7 @@ extern const char *z_errmsg[10]; /* indexed by 2-zlib_error */ + + /* functions */ + ++#define OF(x) x + #ifdef HAVE_STRERROR + extern char *strerror OF((int)); + # define zstrerror(errnum) strerror(errnum) diff --git a/sci-biology/seqan/seqan-2.0.0.ebuild b/sci-biology/seqan/seqan-2.0.0.ebuild new file mode 100644 index 000000000000..9ad67243c17f --- /dev/null +++ b/sci-biology/seqan/seqan-2.0.0.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/seqan/seqan-2.0.0.ebuild,v 1.1 2015/02/24 16:47:47 jlec Exp $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit cmake-utils flag-o-matic python-single-r1 + +DESCRIPTION="C++ Sequence Analysis Library" +HOMEPAGE="http://www.seqan.de/" +SRC_URI="http://packages.${PN}.de/${PN}-src/${PN}-src-${PV}.tar.gz" + +SLOT="0" +LICENSE="BSD GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="cpu_flags_x86_sse4_1" + +REQUIRED_USE="${PYTHON_REQUIRED_USE} cpu_flags_x86_sse4_1" + +RDEPEND="${PYTHON_DEPS} + dev-libs/boost:= + sci-biology/samtools" +DEPEND="${RDEPEND}" + +S="${WORKDIR}"/${PN}-${PN}-v${PV} + +PATCHES=( + "${FILESDIR}"/${P}-zlib.patch +) + +src_prepare() { + rm -f \ + util/cmake/FindZLIB.cmake \ + || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DBoost_NO_BOOST_CMAKE=ON + ) + cmake-utils_src_configure +} + +src_install() { + mkdir -p "${BUILD_DIR}"/docs/html || die + cmake-utils_src_install + chmod 755 "${ED}"/usr/bin/*sh || die +} |