diff options
| author | V3n3RiX <venerix@redcorelinux.org> | 2020-01-15 15:51:32 +0000 |
|---|---|---|
| committer | V3n3RiX <venerix@redcorelinux.org> | 2020-01-15 15:51:32 +0000 |
| commit | 21435953e16cda318a82334ddbadb3b5c36d9ea7 (patch) | |
| tree | e1810a4b135afce04b34862ef0fab2bfaeb8aeca /sci-biology | |
| parent | 7bc9c63c9da678a7e6fceb095d56c634afd22c56 (diff) | |
gentoo resync : 15.01.2020
Diffstat (limited to 'sci-biology')
33 files changed, 35 insertions, 378 deletions
diff --git a/sci-biology/HTSeq/HTSeq-0.9.1.ebuild b/sci-biology/HTSeq/HTSeq-0.9.1.ebuild index 8f27fec4c5a7..8e051640e6dd 100644 --- a/sci-biology/HTSeq/HTSeq-0.9.1.ebuild +++ b/sci-biology/HTSeq/HTSeq-0.9.1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 -PYTHON_COMPAT=( python2_7 python3_{5,6} ) +PYTHON_COMPAT=( python2_7 python3_6 ) inherit distutils-r1 diff --git a/sci-biology/HTSeq/HTSeq-9999.ebuild b/sci-biology/HTSeq/HTSeq-9999.ebuild index 8f27fec4c5a7..8e051640e6dd 100644 --- a/sci-biology/HTSeq/HTSeq-9999.ebuild +++ b/sci-biology/HTSeq/HTSeq-9999.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 -PYTHON_COMPAT=( python2_7 python3_{5,6} ) +PYTHON_COMPAT=( python2_7 python3_6 ) inherit distutils-r1 diff --git a/sci-biology/HTSeq/Manifest b/sci-biology/HTSeq/Manifest index 66c1a76c57df..8f1e4b2f2988 100644 --- a/sci-biology/HTSeq/Manifest +++ b/sci-biology/HTSeq/Manifest @@ -1,4 +1,4 @@ DIST HTSeq-0.9.1.tar.gz 596941 BLAKE2B 6865c36056bff2008ae8bf18d0ac81dbf721fb97cdcc8bbd9150356fc80ae99e0cb872033fac274b40df3d1c95e9bcfd83c4f7d033184725596ffc96081e26d1 SHA512 ec3e1ec9cf66918f2afacf7997ab5da02015896ddd97260f5abec8343a9013cf6e857872be38b2cd3bb5bde655abe602a3c22c32448190f32e1a8f1153a19344 -EBUILD HTSeq-0.9.1.ebuild 710 BLAKE2B 30f42cfd491af94a9f7adad9c99a74fa53607b0068bbae29f60197dad1fdb212e580ac8baa4878fb507ebd5be1b15fdd007fa07a110dd096cdc5cf1e274f0dd3 SHA512 d8e15adc39e65a8579853ef98faf1a77052d9d52532506f64d1028d1e60a185f4696bde425fcb5bcce7bffff6ad7863780f79ff47ae80bbe53e4dfb6538505fb -EBUILD HTSeq-9999.ebuild 710 BLAKE2B 30f42cfd491af94a9f7adad9c99a74fa53607b0068bbae29f60197dad1fdb212e580ac8baa4878fb507ebd5be1b15fdd007fa07a110dd096cdc5cf1e274f0dd3 SHA512 d8e15adc39e65a8579853ef98faf1a77052d9d52532506f64d1028d1e60a185f4696bde425fcb5bcce7bffff6ad7863780f79ff47ae80bbe53e4dfb6538505fb +EBUILD HTSeq-0.9.1.ebuild 706 BLAKE2B fd026fa4d29c04606e7895c199ce08093e9e2380e32096475feca351287e6a49383437ca23f5c06e99da5f3b3bc9393f04e29d9d327017d1d1103ead00ab09fa SHA512 1c5f968bb752a7941e2a0c4de16df1c13bd1d1668f464be9b58c2805e9b7cc3fc362213ab0528eedb8a8efc9e794cfd91b6c8abce042cc3be3005dd1ae64f5f2 +EBUILD HTSeq-9999.ebuild 706 BLAKE2B fd026fa4d29c04606e7895c199ce08093e9e2380e32096475feca351287e6a49383437ca23f5c06e99da5f3b3bc9393f04e29d9d327017d1d1103ead00ab09fa SHA512 1c5f968bb752a7941e2a0c4de16df1c13bd1d1668f464be9b58c2805e9b7cc3fc362213ab0528eedb8a8efc9e794cfd91b6c8abce042cc3be3005dd1ae64f5f2 MISC metadata.xml 555 BLAKE2B 9cb1b8a7b9beeeb137209a73b0f4687f3134f08ac17119daddcdff8f12c74b5724ea45e1de7a5259b1ffa39c06f103e1280065a72b26d73576bad377ed5c86b9 SHA512 a9402ce0e04f242a4509d6f8e3bfc998b32703a9e1ac619d618d761f03e76a92eb5ab625bba7b72dabf23d36d587d48815652764e9f62b317482495ecf59a97e diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz Binary files differindex 1b6cf94f7c86..08f0df073601 100644 --- a/sci-biology/Manifest.gz +++ b/sci-biology/Manifest.gz diff --git a/sci-biology/bamtools/Manifest b/sci-biology/bamtools/Manifest index 3ae03b0b2c07..eaed3ef7be55 100644 --- a/sci-biology/bamtools/Manifest +++ b/sci-biology/bamtools/Manifest @@ -1,4 +1,4 @@ DIST bamtools-2.5.1.tar.gz 549750 BLAKE2B c00b42b10e074e2c6b06f8bc9277a57080b9e99cd10080b1ad9052d59a3db353b33ecf6c30642d1651897396ea65e1e19cb15db0d58a89d4375fe34a8ec38e55 SHA512 f2c761c5bf923cf2f3db3dc54e40b4781307106b9177784f930aab619bd11fae3b343f3cfd232524580d39f0526a2a2f18efcf820fe4d9c951406bdb6b953afb -EBUILD bamtools-2.5.1.ebuild 785 BLAKE2B 61817ce7752bc30d318b0e15bb69f8e6a43c30e6703fa782c85937f29e7cab09354d475e397622896f8d1b4cde28648b09d230813f0eb21f2e463b3aab0381fc SHA512 b1591b8d207e6a97b2e5189197b184203dc61f1a3da6ac94016ce75f6eeb65872f2ff0a16a150c0372d49f475199abb21f2b15a03ada0dc3ecb33b069efe0659 -EBUILD bamtools-9999.ebuild 785 BLAKE2B 61817ce7752bc30d318b0e15bb69f8e6a43c30e6703fa782c85937f29e7cab09354d475e397622896f8d1b4cde28648b09d230813f0eb21f2e463b3aab0381fc SHA512 b1591b8d207e6a97b2e5189197b184203dc61f1a3da6ac94016ce75f6eeb65872f2ff0a16a150c0372d49f475199abb21f2b15a03ada0dc3ecb33b069efe0659 +EBUILD bamtools-2.5.1.ebuild 773 BLAKE2B 58b5af7760648a6919a875736cc52e851e9ff30cb5b308bdfd69a014e67e74a857f8f5a46c5f9d8e398b25383b3b316bfddf3b0fa3b09ca845ef31d87aab3e76 SHA512 7be431719d95ee3e44e79e752d201a940974cc343d20cba8e743a9e6566d6958abefa93f72fafab020d354fc84a42ab68ff131253375c442b91949e175860ff6 +EBUILD bamtools-9999.ebuild 773 BLAKE2B 58b5af7760648a6919a875736cc52e851e9ff30cb5b308bdfd69a014e67e74a857f8f5a46c5f9d8e398b25383b3b316bfddf3b0fa3b09ca845ef31d87aab3e76 SHA512 7be431719d95ee3e44e79e752d201a940974cc343d20cba8e743a9e6566d6958abefa93f72fafab020d354fc84a42ab68ff131253375c442b91949e175860ff6 MISC metadata.xml 881 BLAKE2B e7feabf909d8dbccc784cd2e94d07882d700433e773ac51928b796f4bfd22a7e8de7a4d99268dd8ea0f8d36683f5bbe9f3c4fcba37fc85c284f49b9ad7d413e0 SHA512 4922e3edaa65c7981b8656245287e4c4d613f8ba6d6b63131fe9e5183f8119eab5501e354ad80d37d8f61f56d86513af2aedd2b086e5da3d1ab48b3aef57a18c diff --git a/sci-biology/bamtools/bamtools-2.5.1.ebuild b/sci-biology/bamtools/bamtools-2.5.1.ebuild index b5affe9f0fa9..78a0c3cd2553 100644 --- a/sci-biology/bamtools/bamtools-2.5.1.ebuild +++ b/sci-biology/bamtools/bamtools-2.5.1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 -inherit cmake-utils +inherit cmake DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files" HOMEPAGE="https://github.com/pezmaster31/bamtools" @@ -29,5 +29,5 @@ src_prepare() { # delete bundled libs, just to be safe rm -rf src/third_party/{gtest-1.6.0,jsoncpp} || die - cmake-utils_src_prepare + cmake_src_prepare } diff --git a/sci-biology/bamtools/bamtools-9999.ebuild b/sci-biology/bamtools/bamtools-9999.ebuild index b5affe9f0fa9..78a0c3cd2553 100644 --- a/sci-biology/bamtools/bamtools-9999.ebuild +++ b/sci-biology/bamtools/bamtools-9999.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 -inherit cmake-utils +inherit cmake DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files" HOMEPAGE="https://github.com/pezmaster31/bamtools" @@ -29,5 +29,5 @@ src_prepare() { # delete bundled libs, just to be safe rm -rf src/third_party/{gtest-1.6.0,jsoncpp} || die - cmake-utils_src_prepare + cmake_src_prepare } diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest index 5ceccbec9fa5..8dd3860d13c8 100644 --- a/sci-biology/bedtools/Manifest +++ b/sci-biology/bedtools/Manifest @@ -1,4 +1,4 @@ DIST bedtools-2.26.0-fix-buildsystem.patch.bz2 2584 BLAKE2B 550cd03a0c01217adb347587cb75bdc2ffa4e03ad6ad66535b22d423e6f030e237b0ccfd3d1bd3e434cb9cc2a007971517f03e9ceabc08b63c725bac786e23e8 SHA512 0a7835f560102ce6183736faea6a2be05609b69bb8efdaf98b9d7057e24aa1ebe9d6067118b95c76470ca341b151970db532094ee70ca333075aed7c47509ba3 DIST bedtools-2.26.0.tar.gz 19939711 BLAKE2B 8f6ee6ed755c638dbdd0a4750a5348c28a865f36eaafef6160e90f62912cb0a6b719713935ba68dad74bc591e3f37db49eab54a06a316dc00e4ec82a5dca71dc SHA512 b224adcc09322e90ef389e8172e14572b68f164185fe1a8814db1c47bb4f15656ca8c0ff0061017eb54d76affbe0d0f5793d893b8ab489b56eaf0818616a5def -EBUILD bedtools-2.26.0.ebuild 969 BLAKE2B 325dee5796741cfc37c28cde5a3202665ed9d4f66c5a5d6ce2e798126e46e5f22799ad4daaaa1fe94cf98302a7b1cb12f7d4d50c7c446f4d3da32f35e422f8cb SHA512 f7b320772c9f0cb99011e08bdcb9238757c11f31784c9b9bdf6f43498fd416dde3fb5cd617d7821b059c2d7f484a1bf379ddcba9cf634f61ab80eb5fa73b842a +EBUILD bedtools-2.26.0.ebuild 965 BLAKE2B d7bd87cd069734c20c2ead2fbe6ce889f0e348e35406f390eb7b6826a993f3866968599006c2dd918e017c17550005d630c3e843b15fe28f5a9ca140adcb0178 SHA512 a32f895d9fe683be0d62176eff4dc800cc5d4a32b6c3fe749062f96fd4183f97217781e171434ddb87e9b958135e6b8f980529a8aa6514b9d6aae69c0325f9a8 MISC metadata.xml 761 BLAKE2B 35d57919e32a4b8bd6070ab5a513f62578394d43098d9e7b9b0765fd57d684c049dad9ec1b315044518bf01535d505e9d9d3fee540308df40c0b70886db8e49f SHA512 2d98b9559ef00bee2b741f9e7d22645442ba161f3cadb32c6366b39fcd71b6eac52afd210f59ae709a15cba36a2d0a47341345740e0cab6a1f6bfdffed064770 diff --git a/sci-biology/bedtools/bedtools-2.26.0.ebuild b/sci-biology/bedtools/bedtools-2.26.0.ebuild index 0705d9f46645..0ad6f3eb354d 100644 --- a/sci-biology/bedtools/bedtools-2.26.0.ebuild +++ b/sci-biology/bedtools/bedtools-2.26.0.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 -PYTHON_COMPAT=( python{2_7,3_5,3_6} ) +PYTHON_COMPAT=( python{2_7,3_6} ) inherit flag-o-matic python-any-r1 toolchain-funcs diff --git a/sci-biology/biopandas/Manifest b/sci-biology/biopandas/Manifest index 2d7765d9adbc..b97f0c02282c 100644 --- a/sci-biology/biopandas/Manifest +++ b/sci-biology/biopandas/Manifest @@ -1,3 +1,3 @@ DIST biopandas-0.2.1.tar.gz 209379 BLAKE2B 839a6f569f12b95c9b1c75dc755d009c77d7ef8224e517aed5026ffa6c33bd3826fe3862fec03469e967005a500600782fc372951d61358e2fe3bb56af734228 SHA512 0ea7aec84251d8d6ec4736c4968228133bd8622afb17d6916287168cb9f9757c5a97a4d5a52ac0e2f30027bf0edf9d76413db142f70d606f1359b8a4e06de7c8 -EBUILD biopandas-0.2.1.ebuild 1088 BLAKE2B 8cc423a572181b72e827aa8a84b85fa37aed8db08036f80fd3ca12acc3cb0960a8529dffc94b26eb25c56a250a805f79eec759c8888905a672ec349a3198f973 SHA512 f3af16a98f8fa984a95678a894775b7eb2581ec9bf6e38beaf0e343410ab8f118a5d2f34b6d32fee3c12fde0c322b4d55daa68756888a6d9681081baa17c709b +EBUILD biopandas-0.2.1.ebuild 1084 BLAKE2B d8da20a97d3af92925e0cafe87010c0bea58f13c878a1bdac3d12ed05757b3dfc0ffb16b50e2f21364d6c6bb3085b24ebaa6224d11d5ae4bdc7318b9a2bf0a08 SHA512 ab0d7c4f036c7a7da3ba973a918025a21093784ddbf6c7254171ff5fc3d592ba6c112172969b81b4532d84745a74f8da605c3c3841403b074a32f9aff3eb3004 MISC metadata.xml 536 BLAKE2B e3cb776d0332fff486a7e1ea1353c54694ff687d4685bbb51728db0ed2025bb3d09d39cf7c9ea9f11546cbf9c4727661348e2f5fdfc13ffac2329ef6dfbe7450 SHA512 502803e30ecfac53516b56501a7bffeb49c3c0bc44ce5b3dd87aac5c745de614c235523ba3be374fcbede1a9a7bcf11c328abb27d82e087b275303f38b80b166 diff --git a/sci-biology/biopandas/biopandas-0.2.1.ebuild b/sci-biology/biopandas/biopandas-0.2.1.ebuild index bbbd43d92d26..c7a632cec277 100644 --- a/sci-biology/biopandas/biopandas-0.2.1.ebuild +++ b/sci-biology/biopandas/biopandas-0.2.1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 -PYTHON_COMPAT=( python2_7 python3_{5,6} ) +PYTHON_COMPAT=( python2_7 python3_6 ) inherit distutils-r1 diff --git a/sci-biology/bioperl-db/Manifest b/sci-biology/bioperl-db/Manifest index e094d7d2b73d..0366b2b51a3a 100644 --- a/sci-biology/bioperl-db/Manifest +++ b/sci-biology/bioperl-db/Manifest @@ -2,5 +2,4 @@ AUX bioperl-db-1.6.9-db.patch 1567 BLAKE2B 40a1ba874e745630d886d0531ab90385bb220 DIST BioPerl-DB-1.006900.tar.gz 492799 BLAKE2B fb923533ecdb74e868a3aef0c0c6ba8da419ae3c0e9d2e8c55297aad15563b135b6b00fd158481b31dcacd1125f7e10a557052bd4b04eed3a400c972653ff757 SHA512 e06b8b9aa4188a83128f910d7b4a031f69d36f75e4f2d7210357366379024ef39b58eca97112b5b419f141c82b7518086273cc97c9637382ee5e0ddb9ce28746 EBUILD bioperl-db-1.6.9-r1.ebuild 2024 BLAKE2B ca465f670dae58a8deea0c1ef3ce9deb9a4fe5515ffae41850db8e20c41b57960a7fa0d7ddc0aace635fbf56f469c45604e9386639458590548e8fe3aa14b3b5 SHA512 91814c0b622e2390ac3db18bed47d4ea5f02f7fe493a668bab9a5de4ec3735c64385d4b11ca21d34a05f476e30b7fce7100b3fab77d51607b78804f9b23451e0 EBUILD bioperl-db-1.6.9.ebuild 914 BLAKE2B 8c295e576c35b00754492c715255fd1816bde6d8477e068f2796b96dfa251d24f24f8f260362d89a8cda4881fd4fb1aba204315105422a6c024f0b6a9f083917 SHA512 0d555ef35d5a6e9fda3a48ffc3c7437ad52110c8c9f2a223f103c15c6a866c6c776b7c8d0b1c5c1848336263c64a6e79f80ba476d6205e8f3a90788236ff13e8 -EBUILD bioperl-db-9999-r1.ebuild 811 BLAKE2B 43a9cab7283b634b0f1a1aca1d2c37734169b0a97e2234ba56140cee04bbed7e60f8012093420f07e7c3f9f298464c80dd5f0d9507d4509ba885867be9f5edd5 SHA512 23c57f3cf36d0be73470941b408ef59e84457b9db37cb764ba9553bb38404c48498665982a827c981328b6e37b8e7429170644a51ef3d8e9bbd2fe468f8ca7d8 MISC metadata.xml 344 BLAKE2B 9a757119f1a9939d57a4f9517b8dd5d68732419d7365fda69af107719aa0dba15c79ac16c746cfe28ce36beb060aaa867bffb078175da25961f9f8b233634d34 SHA512 a477289255247669c332915665c4d414ba2857b5716a60e8aec1bf8d1c38009c9fcfb7421a02bdbd9ad566be32bf2b21f57fd21c745aa62185d5dcd13d78bf70 diff --git a/sci-biology/bioperl-db/bioperl-db-9999-r1.ebuild b/sci-biology/bioperl-db/bioperl-db-9999-r1.ebuild deleted file mode 100644 index 2575b8c6af71..000000000000 --- a/sci-biology/bioperl-db/bioperl-db-9999-r1.ebuild +++ /dev/null @@ -1,37 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI="5" - -inherit perl-module git-2 - -DESCRIPTION="Perl tools for bioinformatics - Perl API that accesses the BioSQL schema" -HOMEPAGE="http://www.bioperl.org/" -SRC_URI="" -EGIT_REPO_URI="https://github.com/bioperl/${PN}.git" - -LICENSE="Artistic GPL-2" -SLOT="0" -KEYWORDS="" -IUSE="" - -CDEPEND=">=sci-biology/bioperl-${PV} - dev-perl/DBI - sci-biology/biosql" -DEPEND="dev-perl/Module-Build - ${CDEPEND}" -RDEPEND="${CDEPEND}" - -S="${WORKDIR}/BioPerl-db-${PV}" - -src_configure() { - # This disables tests. TODO: Enable tests - sed -i -e '/biosql_conf();/d' \ - -e '/skip.*DBHarness.biosql.conf/d' "${S}/Build.PL" || die - perl-module_src_configure -} - -src_install() { - mydoc="AUTHORS BUGS FAQ" - perl-module_src_install -} diff --git a/sci-biology/bioperl-network/Manifest b/sci-biology/bioperl-network/Manifest index 916e8474b098..2edc92b69cbd 100644 --- a/sci-biology/bioperl-network/Manifest +++ b/sci-biology/bioperl-network/Manifest @@ -1,4 +1,3 @@ DIST BioPerl-Network-1.006900.tar.gz 2198089 BLAKE2B 67197ed356f642d9e85f779019f6854f4baa3963e059895b89c75ae56f8b5a075ca04b04ce5c7622d46a3a2f55e1c7d80af695085c607ed7fda5517c71c579f3 SHA512 d0a95af17cb024cbc615c784f1dbcddd7bfc5b54524163ab127f1077ded18df222fe067c085f3dd17dd416d6417b8f726526be164e1e33144991393f6b6d5842 EBUILD bioperl-network-1.6.9.ebuild 634 BLAKE2B 7cb788c94d5017434f0f81dc5adbd3d64c31980d12f4e739862fc5127dea25f40964f11b384d42e73022b3fa4031d69e78bcb9f8933bab867827144d83596a02 SHA512 491c8190c28b7add4c1263038534705a7798afd29fbdfc853267f4b663b1fd92c21acfe47330357b83323e4ac05e39e52f78fa526ae1ae0059701a002f7ce03c -EBUILD bioperl-network-9999-r1.ebuild 666 BLAKE2B cc26881e82203bdf13a7fe04229ac57d5fa23271674502114d5fea0daf89a770fd906a9c20b64bef56bda392392d22090362707b32f7c0d466349c5ae8fb8545 SHA512 24829c8d9199b9d559e978c3187d0db950fb112b4f20152ec790133770de9aa173b596653322f0d670df366c8075f2ffe4bcd420204ed00f238b485d8621c323 MISC metadata.xml 349 BLAKE2B 18f5a67acf0859a50cca897d39e3e1a200eba44198d5c2bb1176d29579dd97dfcaf8b2cb8ffa4baf9c2adc7072f24b0344701a986b7a4f5a8491cf85b4086579 SHA512 dc3b8e26619cb4ff0dffeb79aa91f402a35cb2f673ecfd0bdac9d3667be82c248dcdd246185a006e8b91c9b66157689eaaf8ee464e00c54227c2c78cd9827b63 diff --git a/sci-biology/bioperl-network/bioperl-network-9999-r1.ebuild b/sci-biology/bioperl-network/bioperl-network-9999-r1.ebuild deleted file mode 100644 index 6be8f1cd8509..000000000000 --- a/sci-biology/bioperl-network/bioperl-network-9999-r1.ebuild +++ /dev/null @@ -1,31 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI="5" - -inherit perl-module git-2 - -DESCRIPTION="Perl tools for bioinformatics - Analysis of protein-protein interaction networks" -HOMEPAGE="http://www.bioperl.org/" -SRC_URI="" -EGIT_REPO_URI="https://github.com/bioperl/${PN}.git" - -LICENSE="Artistic GPL-2" -SLOT="0" -KEYWORDS="" -IUSE="test" -RESTRICT="!test? ( test )" -SRC_TEST="do" - -CDEPEND=">=sci-biology/bioperl-${PV} - >=dev-perl/Graph-0.86" -DEPEND="dev-perl/Module-Build - ${CDEPEND}" -RDEPEND="${CDEPEND}" - -S="${WORKDIR}/BioPerl-network-${PV}" - -src_install() { - mydoc="AUTHORS BUGS" - perl-module_src_install -} diff --git a/sci-biology/bioperl-run/Manifest b/sci-biology/bioperl-run/Manifest index f00e990af1c5..3807c07be987 100644 --- a/sci-biology/bioperl-run/Manifest +++ b/sci-biology/bioperl-run/Manifest @@ -1,4 +1,3 @@ DIST BioPerl-Run-1.006900.tar.gz 14546677 BLAKE2B 9faf58796b9874b19b66e74abc51ed1d1b6e2928bcf9904506b2af6b2b7c1772a90eab24bf0e7c050fd4a2b120ba506ad5edb8a693496b7468fe7c8d05d11f0a SHA512 47f2b853885c604291ac0aba3269b897de59cf7da6f7d54a50ff950cca836338091309df550f32695159c620be23391306d0421d2bbc22eebbb61a9e280ad83c EBUILD bioperl-run-1.6.9.ebuild 931 BLAKE2B e956a7d12719560e9b4cc33800f8a53d8c590d739ecf694f8fd334ced2b01a6fc81fcbcaad61cf5c69f9ede5a02afd2dcfe1051cc99f7fbf93466bf427bf00a0 SHA512 b512b3fc62208ab6ef1c6f160d43c5e9b8a3f03131398144ec4e4e1ddb1973f45b121220e71724a0c621ff58ea33b5f639cd23dedd62e033f3e78118dde2e94e -EBUILD bioperl-run-9999-r1.ebuild 928 BLAKE2B 46d56d6b0c025c8db012acae41a355dbfc6d94810811b9950fac0ef151a6f4bfb562bba257627f73c877cc6c4530f0818275aedb6e74419d128fef9c1beba6f1 SHA512 42449a6ab99ccd3779899536eb525b6bf029fe477d65e5d8c66958b5803749180c06d068fdc4c06c3de0bbb9987751f6b5886ee446fdec92db5683f8e41a8e4d MISC metadata.xml 345 BLAKE2B 91a15324464d913875ad2c449052e2f26d7c48cac90e9e36a66d91ff43d02e424841b8758121ec06625402dbadbfd4455e7e39a17009832fc4b2655d381379ae SHA512 23370e5fb887d48f37f6ef1d3fa45092fb3b45e111f82488153ce5235bdd7671bed559093927ad92e3c7876f390e385d032fbf9e76a55cb00a0da7fa80bea2ad diff --git a/sci-biology/bioperl-run/bioperl-run-9999-r1.ebuild b/sci-biology/bioperl-run/bioperl-run-9999-r1.ebuild deleted file mode 100644 index 2052432904af..000000000000 --- a/sci-biology/bioperl-run/bioperl-run-9999-r1.ebuild +++ /dev/null @@ -1,40 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI="5" - -inherit perl-module git-2 - -DESCRIPTION="Perl wrapper modules for key bioinformatics applications" -HOMEPAGE="http://www.bioperl.org/" -SRC_URI="" -EGIT_REPO_URI="https://github.com/bioperl/${PN}.git" - -LICENSE="Artistic GPL-2" -SLOT="0" -KEYWORDS="" -IUSE="-minimal test" -#SRC_TEST="do" - -RESTRICT="test" - -CDEPEND=">=sci-biology/bioperl-${PV} - !minimal? ( - dev-perl/Algorithm-Diff - dev-perl/XML-Twig - dev-perl/IO-String - dev-perl/IPC-Run - )" -DEPEND="dev-perl/Module-Build - ${CDEPEND}" -RDEPEND="${CDEPEND}" - -S="${WORKDIR}/BioPerl-run-${PV}" - -src_install() { - mydoc="AUTHORS BUGS FAQ" - perl-module_src_install - # TODO: File collision in Bio/ConfigData.pm (a Module::Build internal file) - # with sci-biology/bioperl. Workaround: the "nuke it from orbit" solution :D - find "${D}" -name '*ConfigData*' -print -delete -} diff --git a/sci-biology/bioperl/Manifest b/sci-biology/bioperl/Manifest index 60c0ff81b7a9..d687d9661fee 100644 --- a/sci-biology/bioperl/Manifest +++ b/sci-biology/bioperl/Manifest @@ -1,4 +1,3 @@ DIST BioPerl-1.6.901.tar.gz 12284856 BLAKE2B 004947fde9d02355ac96f71b67a33a27d6d0163892c978ac9059e70e089fb83b473e21252c5217dfba8faaa65bc3d2eebb8826d03f29a13409e2b6d337316b42 SHA512 227387437c940da1435ed83fad6ec2168ca12a729c90dc557e84750c6474213874c23a8f23e50db4027909469627baee581faa11be6208c8e0a5453a01c7eca4 EBUILD bioperl-1.6.9.ebuild 1544 BLAKE2B 83878553b6badd2c209da398bfd83e1733b94e85f44af140ffe3acc6a2915f41643483751845a32c838889b3468c66bd20bc899248953848ce4d6a47d0bb083d SHA512 2e6167abb3ab729eef114ef9e38955e5d2b5353efaf86f5af16aa00348a661adc5b2297f22c2a77126c7f4f3f08f3db9c0af4210ddb3328653f11b1f5a782744 -EBUILD bioperl-9999-r1.ebuild 1793 BLAKE2B 4b6d953bbbe3b3f233ad3c26fd446a145026d372f932b04273b6bc8fca823cb074ce4353ef07c15c61fe49dade606926275fc8448571acabd7a47462d857cc7c SHA512 25459e6fdeacb6bded0c81a4bbd3a6d85f7cbae973b6f9b8a2ee1a44ab56b5a81556b1c6176e389e57efa660fdb35a6b61c71aca65f90e221bc04a0dda395e5c MISC metadata.xml 541 BLAKE2B c01f01fae7a659a708d0d3d6520e98f5bb8fd0e848fd82ae11ba7b6806f18c3ce271d76f94123f6a47c33ca88ea665689b1ec5664c114e28ec18443a87cb31de SHA512 0693aba25e02d3ad67f82c2c77f9987ae06cb6545bb58df2c57f076a22d5c2f6d15c7fdc11b0766748680d53c709c7682b53f866a4f45d7d8a875d1311277e5c diff --git a/sci-biology/bioperl/bioperl-9999-r1.ebuild b/sci-biology/bioperl/bioperl-9999-r1.ebuild deleted file mode 100644 index f166946c008f..000000000000 --- a/sci-biology/bioperl/bioperl-9999-r1.ebuild +++ /dev/null @@ -1,73 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI="5" - -inherit perl-module git-2 - -SUBPROJECTS="+db +network +run" - -DESCRIPTION="Perl tools for bioinformatics - Core modules" -HOMEPAGE="http://www.bioperl.org/" -SRC_URI="" -EGIT_REPO_URI="https://github.com/${PN}/${PN}-live.git" - -LICENSE="Artistic GPL-2" -SLOT="0" -KEYWORDS="" -IUSE="-minimal graphviz ${SUBPROJECTS}" - -CDEPEND=" - dev-perl/Data-Stag - dev-perl/libwww-perl - !minimal? ( - dev-perl/Ace - dev-perl/Bio-ASN1-EntrezGene - dev-perl/Spreadsheet-ParseExcel - dev-perl/Spreadsheet-WriteExcel - >=dev-perl/XML-SAX-0.15 - dev-perl/Graph - dev-perl/SOAP-Lite - dev-perl/Array-Compare - dev-perl/SVG - dev-perl/XML-Simple - dev-perl/XML-Parser - dev-perl/XML-Twig - >=dev-perl/HTML-Parser-3.60 - >=dev-perl/XML-Writer-0.4 - dev-perl/Clone - dev-perl/XML-DOM - dev-perl/Set-Scalar - dev-perl/XML-XPath - dev-perl/XML-DOM-XPath - dev-perl/Algorithm-Munkres - dev-perl/Data-Stag - dev-perl/Math-Random - dev-perl/PostScript - dev-perl/Convert-Binary-C - dev-perl/SVG-Graph - ) - graphviz? ( dev-perl/GraphViz )" -DEPEND="dev-perl/Module-Build - ${CDEPEND}" -RDEPEND="${CDEPEND}" -PDEPEND="!minimal? ( dev-perl/Bio-ASN1-EntrezGene ) - db? ( >=sci-biology/bioperl-db-${PV} ) - network? ( >=sci-biology/bioperl-network-${PV} ) - run? ( >=sci-biology/bioperl-run-${PV} )" - -S="${WORKDIR}/BioPerl-${PV}" - -src_configure() { - sed -i -e '/add_post_install_script.*symlink_script.pl/d' \ - -e "/'CPAN' *=> *1.81/d" "${S}/Build.PL" \ - -e "/'ExtUtils::Manifest' *=> *'1.52'/d" "${S}/Build.PL" \ - || die - if use minimal && use graphviz; then die "USE flags minimal and graphviz cannot be used together"; fi - perl-module_src_configure -} - -src_install() { - mydoc="AUTHORS BUGS FAQ" - perl-module_src_install -} diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest index acc4141192b8..f252db4b4e14 100644 --- a/sci-biology/biopython/Manifest +++ b/sci-biology/biopython/Manifest @@ -1,7 +1,3 @@ -DIST biopython-1.68.tar.gz 14445813 BLAKE2B 566931c4e522e95278f7f6a9dc07ecc091dc54b69cdea8bb07603339af4f1fd38e3df87482e97729acb776dd2df19a4e61d49ee7608ec5cb0f24966e28c2e3dd SHA512 0ca994475654bb68ff326c8e86cbd4547cd87b42e1633dda039ad668e1298884b22e169f6b25ab514e929861334a93b7db6d057a3486cea9997ca2de95c61a69 -DIST biopython-1.71.tar.gz 16031832 BLAKE2B 2062065b77fc35ea8a3f09ec967482c233a6e0bbfc7d09187ff5e892848b45fa7bd6d7b6027b38c3d4c9a9c601785521fa7edb91fa960b46c8e49aed91b1f5dc SHA512 003955e92295e98526c88abb573db9bdc37877fc41395551b541e7106ffa603327a36c6f4d999838c0be38b378901235c9dbd7cb7fc25c14a5d7001939fe23bd DIST biopython-1.73.tar.gz 15715102 BLAKE2B b2c40f9ed02681f19607c88f91b469784985acefc6e81770a54e5c13c715915344bc7fd72e4a88ae50879a2463965ac6d0d04c6d263908887028d1e065620b95 SHA512 d067330ef8e25ca6881b56f4e5e89e16a816c89760473e2f32a6236ab202f805294650aa944f0b098987425bcb65727317da7a26deb4d4937f02b00123ea9a8f -EBUILD biopython-1.68.ebuild 1634 BLAKE2B 43d435496fc239c847b19a4e66bf52f920454ee6fd810b94d0d32bde6381059abb9561f90d06e5d1ca83a80721958c6051f79d0c92e5b76dc8d930ed54254f78 SHA512 70b8d2a8f84f70edc6a6225a8958328d8657dbb8b01c0716b7b1c15320914e827129c30da32b670f6ba9ab4d24a8f6cf01ea728b5d14e1607e9cef5c35f7b47f -EBUILD biopython-1.71.ebuild 1616 BLAKE2B e1e4b60cfe88dd00ef28135f137657147112249bc60738d145c5036bab3d1436878834f9ac03c829aa39c40696d0350d9ea98040be43e7f393752f9baf63ac21 SHA512 ae8fa77eefe2bb67c430bd6351a60e2a5d1e0193be4c8e6330f81edbac90b4730d5ec59b1bd25baf04452a9d8ea4f9b7550b703ecf20b1af9c9473b6465b2e5a -EBUILD biopython-1.73.ebuild 1684 BLAKE2B c98e92b2e989b2a398912b1335049750565933b202cc1e1d77d83f1aa13071bb5dd1ce63ac37113a2bf03cc1394dcb7011fb2346728d3463c353460101b847a5 SHA512 b71c3acc6b6f97564b31b3bfc4a8fe47ad1c95fcd07f265964f3cf381ef3d2c2917d2bc2ef8446ef3290eaf447a1c77ff38fc7d1459694c8884dc45cd8350e9a +EBUILD biopython-1.73.ebuild 1671 BLAKE2B d899d54d6983bbbcc43e34a051cd5cfdbed4ff92d50dcc95fd38df84f60882bfdda7d95cf4a5fa84ece32e36e10e53010340cdceb2f50b37351b917afd0dc062 SHA512 3d648fe4b0a62f984fe4541c8b4298759dcf772ef0119ca7de42b207fc09994ed2c5d0b3a561fc647382c2e41f2ec1832fe388c7fdf1f8b8d83ee4565d0e20b1 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/biopython/biopython-1.68.ebuild b/sci-biology/biopython/biopython-1.68.ebuild deleted file mode 100644 index f76da59c1b84..000000000000 --- a/sci-biology/biopython/biopython-1.68.ebuild +++ /dev/null @@ -1,55 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 python3_5 pypy ) - -inherit distutils-r1 eutils - -DESCRIPTION="Python modules for computational molecular biology" -HOMEPAGE="http://www.biopython.org/ https://pypi.org/project/biopython/" -SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz" - -LICENSE="HPND" -SLOT="0" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" -IUSE="" - -RDEPEND=" - dev-python/matplotlib[$(python_gen_usedep 'python*')] - dev-python/networkx[$(python_gen_usedep 'python*')] - dev-python/numpy[$(python_gen_usedep 'python*')] - dev-python/rdflib[$(python_gen_usedep 'python*')] - dev-python/pygraphviz[$(python_gen_usedep 'python2*')] - dev-python/reportlab[$(python_gen_usedep 'python*')] - dev-python/pydot[$(python_gen_usedep 'python2*')] - " -DEPEND="${RDEPEND} - sys-devel/flex" - -DOCS=( CONTRIB DEPRECATED NEWS README Doc/. ) - -python_test() { - distutils_install_for_testing - cp -r "${S}"/{Doc,Tests} "${TEST_DIR}"/lib/ || die - cd "${TEST_DIR}"/lib/Tests || die - rm test_BioSQL_{psycopg2.py,MySQLdb.py,mysql_connector.py} || die - ${PYTHON} run_tests.py --offline --verbose || die -} - -python_install_all() { - distutils-r1_python_install_all - - dodir /usr/share/${PN} - cp -r --preserve=mode Scripts Tests "${ED%/}"/usr/share/${PN} || die -} - -pkg_postinst() { - elog "For database support you need to install:" - optfeature "MySQL" dev-python/mysql-python - optfeature "PostGreSQL" dev-python/psycopg - elog - elog "Some applications need extra packages:" - optfeature "EMBOSS (The European Molecular Biology Open Software Suite)" sci-biology/emboss -} diff --git a/sci-biology/biopython/biopython-1.71.ebuild b/sci-biology/biopython/biopython-1.71.ebuild deleted file mode 100644 index 8b9a0cd7112e..000000000000 --- a/sci-biology/biopython/biopython-1.71.ebuild +++ /dev/null @@ -1,57 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python2_7 python3_{5,6} ) - -inherit distutils-r1 eutils - -DESCRIPTION="Python modules for computational molecular biology" -HOMEPAGE="https://www.biopython.org/ https://pypi.org/project/biopython/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="HPND" -SLOT="0" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" -IUSE="" - -RDEPEND=" - dev-python/matplotlib[${PYTHON_USEDEP}] - dev-python/networkx[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/rdflib[${PYTHON_USEDEP}] - dev-python/pygraphviz[${PYTHON_USEDEP}] - dev-python/reportlab[${PYTHON_USEDEP}] - dev-python/pydot[${PYTHON_USEDEP}]" -DEPEND="${RDEPEND} - sys-devel/flex" - -DOCS=( CONTRIB DEPRECATED NEWS README Doc/. ) - -python_test() { - distutils_install_for_testing - cp -r "${S}"/{Doc,Tests} "${TEST_DIR}"/lib/ || die - cd "${TEST_DIR}"/lib/Tests || die - rm test_BioSQL_{psycopg2.py,MySQLdb.py,mysql_connector.py} || die - "${EPYTHON}" run_tests.py --offline --verbose || die -} - -python_install_all() { - # remove files causing ecompressdir to fail - rm Doc/examples/ls_orchid.gbk.bz2 || die - - distutils-r1_python_install_all - - dodir /usr/share/${PN} - cp -r --preserve=mode Scripts Tests "${ED}"/usr/share/${PN} || die -} - -pkg_postinst() { - elog "For database support you need to install:" - optfeature "MySQL" dev-python/mysql-python - optfeature "PostGreSQL" dev-python/psycopg - - elog "Some applications need extra packages:" - optfeature "EMBOSS (The European Molecular Biology Open Software Suite)" sci-biology/emboss -} diff --git a/sci-biology/biopython/biopython-1.73.ebuild b/sci-biology/biopython/biopython-1.73.ebuild index f0d335a5933a..94acdfc2a2cb 100644 --- a/sci-biology/biopython/biopython-1.73.ebuild +++ b/sci-biology/biopython/biopython-1.73.ebuild @@ -1,10 +1,9 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 -PYTHON_COMPAT=( python2_7 python3_{5,6,7} ) - +PYTHON_COMPAT=( python3_{6,7} ) inherit distutils-r1 eutils DESCRIPTION="Python modules for computational molecular biology" diff --git a/sci-biology/embassy-phylipnew/Manifest b/sci-biology/embassy-phylipnew/Manifest index 3916b19b3ec5..5fd9d2e68b89 100644 --- a/sci-biology/embassy-phylipnew/Manifest +++ b/sci-biology/embassy-phylipnew/Manifest @@ -1,4 +1,4 @@ AUX embassy-phylipnew-3.69.650_fix-build-system.patch 3255 BLAKE2B 9dfa7b3fb97508e7807b5b3d3ddfa48b1bb78cff3b8e658a0ca786e3c472f997267252c39bde9bbea4311f7b2192c2a0553617a7991e43aca3aa66db289dec41 SHA512 a0d4dcb3e7d4ce9b5cbd68168ebe7c8d248aa1166a6a52a0a77031291af8d2d32af0243571b669b9318426f753251d983ebb9b96eb1da81b594f4f4d20d7c249 DIST embassy-phylipnew-3.69.660.tar.gz 1741298 BLAKE2B 58a2c66ffb9c447fa17462bf54d7b8e65702701d74c1f16ec6906a3acaf076ebcab30982befe6334101bc483901132069a71ffa0e2334aaee0da02a30276b7f2 SHA512 b41a31285e05a418e4fbfae7241c3658fe458e3d5d84bff472d98b7c145340a55bee1d744b5c056d0e88407074947b5f37b2182c9cb800c8a8d43dfa76d026d5 -EBUILD embassy-phylipnew-3.69.660.ebuild 360 BLAKE2B da2ce56a2787d6446fac6b5d3b20b661d0d0bcdff2362ea8e856d18cc7d9c9625540b49c41f7f123a9228fe1d995194907322a7ff421371f87a22a3b6ade12c5 SHA512 cadc029f641b4303325f4d4110a130bc46b1e74b2c6246bb31cc07ff2bd8801adc6438cf2253897d3d6c28bf4fd6f9bad098b73d0e664b79bec5899157551e12 +EBUILD embassy-phylipnew-3.69.660.ebuild 361 BLAKE2B 46ace0d20506300a83a423edd19d0305d4e7a072348a7355271dce004e896d92ebd04f2ff342060a5ee2c78f92bd9a6bbccb895eeef462891f78e08d49bcd553 SHA512 3836e21a22a375a4b58fc32b29bdf0481f7bd175b44a131069f6b68ee04d5b507732cc8cc8429afd47f4b26b853c54dd244cd1535a6209708b65989f11d7aa2e MISC metadata.xml 347 BLAKE2B 2368d452e759747738601ae0e5e5e7181167badeaa28ed89aa8e07b55ebc9d2f1dbcd351cd5569a4548c307cfaa23b26756d88778c078685848db72dd9b094e7 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e diff --git a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild index 69834a313b8f..3ac088ed6ef9 100644 --- a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild +++ b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2019 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -9,7 +9,7 @@ EBO_EAUTORECONF=1 inherit emboss-r2 -LICENSE+=" freedist" +LICENSE+=" free-noncomm" KEYWORDS="~amd64 ~x86 ~x86-linux" diff --git a/sci-biology/embassy/Manifest b/sci-biology/embassy/Manifest index edf9827cd22e..634ffefa74ec 100644 --- a/sci-biology/embassy/Manifest +++ b/sci-biology/embassy/Manifest @@ -1,2 +1,2 @@ -EBUILD embassy-6.6.0-r1.ebuild 967 BLAKE2B 796a69696e855b0749e4f85b1ab3e5379584ffdcaf4c9cf8c529a65ca1df2fa1cc051d4fcfb9489877fd094ff1491dcebabb0c0351503a3c8bcf3d4518065619 SHA512 028181280e723f6926b9a9ad2fba67f10fb2ce3e78ee9b9dfb5e07948d9b4c1db41c12ee4349794de6b99d2bac8021f856883d01466a5a6421a801eca58f74de +EBUILD embassy-6.6.0-r1.ebuild 965 BLAKE2B 736fb94d1774dfa22a0b7b9ea4809389cb65ed1e79ac44b908eb76c0fc348f1ebed4a41dd7c9d19f7b4118509055309f0e0351b8067872c1a461029d96249c10 SHA512 8dd638ed450b83656c3848bd014f2429a9e269f3e3dea5c16e370becbdb1473f2eec261fbfe2b4bc5675262ac6d9ce871fc287045f777a5d0f85a3f05bbf795b MISC metadata.xml 347 BLAKE2B 2368d452e759747738601ae0e5e5e7181167badeaa28ed89aa8e07b55ebc9d2f1dbcd351cd5569a4548c307cfaa23b26756d88778c078685848db72dd9b094e7 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e diff --git a/sci-biology/embassy/embassy-6.6.0-r1.ebuild b/sci-biology/embassy/embassy-6.6.0-r1.ebuild index 27edbc3fd4f6..b30223eda805 100644 --- a/sci-biology/embassy/embassy-6.6.0-r1.ebuild +++ b/sci-biology/embassy/embassy-6.6.0-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2019 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -6,7 +6,7 @@ EAPI=6 DESCRIPTION="A meta-package for installing all EMBASSY packages (EMBOSS add-ons)" HOMEPAGE="http://emboss.sourceforge.net/embassy/" -LICENSE+=" freedist" +LICENSE="metapackage" SLOT="0" KEYWORDS="~amd64 ~x86 ~x86-linux" diff --git a/sci-biology/gatk/Manifest b/sci-biology/gatk/Manifest index 42b57038dfc3..b616ea3de733 100644 --- a/sci-biology/gatk/Manifest +++ b/sci-biology/gatk/Manifest @@ -1,4 +1,3 @@ DIST gatk-2.4.tar.gz 9106774 BLAKE2B a9ac1602091a2f0902c2841942f8dd739562ef6ebbd35894fa445e6a28d748f3c645936914acbdafc8fa59330149ee5ef0738657d8e78d5cf4af5bd26e37ab6b SHA512 9050fc2024d0b3c9a6b5617787831c0496276bcd7318a872f6c1128c31fc31c6f59429a1b189e5c2cc740909b42d846b5e041f8626b03af3a80442294db34ace EBUILD gatk-2.4.ebuild 914 BLAKE2B a289d4f4ed48d1b522ae6928dd0535991a18f9d3396d15856bf231923fb8b596e95e662d7a719195563f6caed0c014c96a800dd4f3cebf88a18122cd9d67e6f6 SHA512 a1a6fc27407bbc13247e866ed2dbc34428009091bf85e73776b5a47a95f8daca976060ecf092c4a68fee8afc1068f10aebc743e879b837b8ce0cf8ee461f6b6d -EBUILD gatk-9999.ebuild 899 BLAKE2B aaafb718d986716b9e9e27175da83869bcad23c0443c258d3109d82b2c171e658c481347c1362c52f97713da959e8eeb36b6ccd6316e1bbff7fd102810c40db5 SHA512 1bffd684f48d50a84d4c0c55f6ed8ac10bfe7ca93d35ec32d282922ad8f1bdcee5aee284c4202cb547b9a332c3aaf32b4ebf5f4488b83856a9ac11f67f8b36a2 MISC metadata.xml 349 BLAKE2B 277c979d19162d54c5a762e24fcc90d6fc043e5ddd315824b1ccc2376354db4169690933e9d9ebedaf8589636066bf5b32a646ca28892615e8626d7a8d3c43ac SHA512 1605fb041826c7197edcd3658343ed3ac50aea7dfa53262700b9f9e1a45ee81df501e55bf1e8417201f0f2709b6b6e29bb6e5036b7c187846b4dec5e89903f54 diff --git a/sci-biology/gatk/gatk-9999.ebuild b/sci-biology/gatk/gatk-9999.ebuild deleted file mode 100644 index fee2670ad219..000000000000 --- a/sci-biology/gatk/gatk-9999.ebuild +++ /dev/null @@ -1,40 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -EANT_BUILD_TARGET="dist" -EANT_NEEDS_TOOLS="true" -JAVA_ANT_REWRITE_CLASSPATH="true" - -inherit git-2 java-pkg-2 java-ant-2 - -DESCRIPTION="The Genome Analysis Toolkit" -HOMEPAGE="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit" -SRC_URI="" -EGIT_REPO_URI="https://github.com/broadgsa/gatk.git" - -LICENSE="MIT" -SLOT="0" -IUSE="" -KEYWORDS="" - -COMMON_DEPS="" -DEPEND=" - >=virtual/jdk-1.6 - dev-vcs/git - ${COMMON_DEPS}" -RDEPEND=" - >=virtual/jre-1.6 - ${COMMON_DEPS}" - -src_prepare() { - sed -i '/property name="ivy.home"/ s|${user.home}|'${WORKDIR}'|' build.xml || die - java-pkg-2_src_prepare -} - -src_install() { - java-pkg_dojar dist/*.jar - java-pkg_dolauncher GenomeAnalysisTK --jar GenomeAnalysisTK.jar - java-pkg_dolauncher AnalyzeCovariates --jar AnalyzeCovariates.jar -} diff --git a/sci-biology/phylip/Manifest b/sci-biology/phylip/Manifest index 74a149ca13f1..4a74a1a8a1f8 100644 --- a/sci-biology/phylip/Manifest +++ b/sci-biology/phylip/Manifest @@ -1,7 +1,7 @@ AUX README.Gentoo 643 BLAKE2B 95193d4c9c8fc8fb5796bb0a8ca470f440ac66eb1da9b9ed4784494a6a4c9bb12a451223c0ff81ae3ba80da81f4d8d3a00a21cad557f575a81325a180a819c0e SHA512 63ec15ce2788171e5351977bae21e11a7c8609eeed4893849fabc909f0c6713033e253768ea3f485245456a9083ad4aa613e2503ebb4eb71f7b670f1af593f2a DIST phylip-3.69.tar.gz 1511935 BLAKE2B 76aa5a79d2553c6f269c011f633d1101ee4d85ac398a36dd463e5605d90833ecb1e5f6c21edba3e142e2d4ab5ef034fa739e52e0ab3f941a7987915ae352be0b SHA512 e36d12bfe597896b4298c1d0e3b0b7bd783573dc03e861b9472d8284391b2339cb3fb58eb6580298724bbd516127b68925815455514f939da9272fcfed7e229d DIST phylip-3.696.tar.gz 3955721 BLAKE2B dc75fc442eb63e44bc2e68e5dc97b3ff8f741bfa53740ed57ca114b53dcb71db9baeb9a96c3e693f7fae92afbaa71c7b5acfb39e7770bacb6aafa8c33b355be6 SHA512 711a9a34be72b0f63c746733cd1384f091b7cc597dbd9a40c130e074efbf0a0ecc30e5a6b3452bb73dc69cddbdae2fc07d1c0a68f0be207471eab73ab876c6be -EBUILD phylip-3.69-r1.ebuild 1145 BLAKE2B 55565e21aa748ede76c7c37fbc4cef8849707c1f7500ef283485f461ffc99282fca1316af634bf24abdb1ee33005d26e6dce1f2fe30d52c224882dbf3313ae8e SHA512 2f591f9616ab7ba831ea63eb02b8a83ab3ae0ed63221c02a59ad63f5d05475e2b51a4adccb47532740c809ee832cb0dd02e3389208d095c930e68070974e3fb3 +EBUILD phylip-3.69-r1.ebuild 1146 BLAKE2B 690bd802cb7ed4dce34de3c272357df93c528881efe5b40c8b4e3f6c281791eb6809559a5f1680da55d5c9466cac666d290722a513eb3364245bf5f6bcd9204e SHA512 7e7eada3c9c1b6ae479360749d40943ec977505986871ffe8f5972604e2834aaddfd015f49b9e60f3f3292f8e98f410fdeecd240f34a47b86046972f067111c5 EBUILD phylip-3.696-r1.ebuild 1130 BLAKE2B 94c4b4213d24b46fe60f3d180a1d8a742f9c173f5482e18e1521b0f3e61ac2738038c5a558fdbdeaece2f9887e08796d6981bc3ff54bec2e60dfb0ebffa7d156 SHA512 02e33c7a34910a006fb0e63d9cac40b9e71446b5b64185b968d46fdcb78217c4f2bdfe02b96ae2eefe10839e892c2c533581e9d149cfc63f1d64b2b87b1416a9 EBUILD phylip-3.696-r2.ebuild 1204 BLAKE2B d6fcbe08f0528d657bc30da9c61c67571ee403c7f15caec8a86d2ed9a75958e471f8b2582d39c86f1ddb675636bf9d211665d398593651c968b9d87b9fac4a2a SHA512 2827584e9293a5bc95087c0d3f19b4d0ac1a7ecac6b5b81738abb16ee007d65ab91e14baf0885578afc4c369841456583d88ee51bf0738b3d04d4924eb086e5c MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/phylip/phylip-3.69-r1.ebuild b/sci-biology/phylip/phylip-3.69-r1.ebuild index 12f007810806..e54c75d9b356 100644 --- a/sci-biology/phylip/phylip-3.69-r1.ebuild +++ b/sci-biology/phylip/phylip-3.69-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2019 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -10,7 +10,7 @@ HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html" SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.tar.gz" SLOT="0" -LICENSE="freedist" +LICENSE="free-noncomm" IUSE="" KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos" diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest index 5f340369c755..a6062676eabc 100644 --- a/sci-biology/pysam/Manifest +++ b/sci-biology/pysam/Manifest @@ -1,4 +1,4 @@ AUX pysam-0.12-fix-buildsystem.patch 2356 BLAKE2B 95542f99b411a00eeaa24836cb7489bf2bbf690d804669f69f6f1a8c07f66d9c6ef34624eb511036cd36b1268b49959d38db497cb557e9cc40f3a35b2d349f4d SHA512 24c5c521ddd2e8a88a713c2cab2aedb0cd9a589e2ae87696a60815f9714e2b222a5e0824c5ac293f9023f6f772a599256a5c07228b5a2df40b62a1bf7616c84a DIST pysam-0.12.0.1.tar.gz 2672020 BLAKE2B 4bc6330405724f7b1126da91ba3338687f4dd17f015895f42b971f22ffbb6c32eda65e2667035a4cc830c0370b34d95d3aa6ae0f026b2b3276af1fd6841eed28 SHA512 31460ca98ad2ac5489905ffce76bfbb5bf4a295159f3cc8e088c78dcfbfc34b30d6f7871fd1454de01da98f82b7438ac2aca678a771d7b97ae0029a418f29f1d -EBUILD pysam-0.12.0.1.ebuild 1196 BLAKE2B 7223e799c6deb2396c19bf218c9cdc6b1b19a15a9368798fa91dbca4e314b804da6b742bc5953fb72334e4256e69779d2a44f55c6b7dadd5ba5deff4ce3e5324 SHA512 826a36fc59ede855efdea8e8b5069c86f66db99ed0bbeb2c29d196bee8efa9ae8ccd831e89befdce0a9806689ff0f0a513646c07dca91ac59c35a985bce3893b +EBUILD pysam-0.12.0.1.ebuild 1192 BLAKE2B d5ef892543371571dfbee120d3dd07687fce35abfaa302996ffcbd6de1f0cf38b24ff53b96aba8bc545bc1ecf742e4d56701250101db00d87a04ca3b1bd4ef15 SHA512 3e596b01add1f58d9ed4fbb0c44dd4fdba5a3ef899b8941b0c6f2546e83ba098f548e53b814d7bf0eeee18fbb8ea41e154d0285d372698ad1f68393cf7d7daee MISC metadata.xml 410 BLAKE2B ed86e3ffe38a306e581762625b37cf6596dc2a2ba404406ab12f681d5b48529764e281d40411bedbdf6016bc57d02adb705e8c8703b8120cf89b4961f75bed67 SHA512 38bcd511561b2466ef5d39473a6d1a838af0aff6eeb520307331fe0fc3177be3062fa0be39f48a333bb8e31841115cafd9dfb80a5985c316c9b8df1609f00810 diff --git a/sci-biology/pysam/pysam-0.12.0.1.ebuild b/sci-biology/pysam/pysam-0.12.0.1.ebuild index d4f7a7430501..e6500903f847 100644 --- a/sci-biology/pysam/pysam-0.12.0.1.ebuild +++ b/sci-biology/pysam/pysam-0.12.0.1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 -PYTHON_COMPAT=( python2_7 python3_{5,6} ) +PYTHON_COMPAT=( python2_7 python3_6 ) inherit distutils-r1 |