diff options
| author | V3n3RiX <venerix@redcorelinux.org> | 2021-04-28 20:21:43 +0100 |
|---|---|---|
| committer | V3n3RiX <venerix@redcorelinux.org> | 2021-04-28 20:21:43 +0100 |
| commit | 40aaaa64e86ba6710bbeb31c4615a6ce80e75e11 (patch) | |
| tree | 758c221bad35c9288d0bd6df9c7dfc226728e52c /sci-biology | |
| parent | 8d5dbd847cbc704a6a06405856e94b461011afe3 (diff) | |
gentoo resync : 28.04.2021
Diffstat (limited to 'sci-biology')
53 files changed, 209 insertions, 430 deletions
diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz Binary files differindex 9a4bd8a29d2d..e1f18eec9323 100644 --- a/sci-biology/Manifest.gz +++ b/sci-biology/Manifest.gz diff --git a/sci-biology/bioperl/Manifest b/sci-biology/bioperl/Manifest index d687d9661fee..fbf3e3d16a68 100644 --- a/sci-biology/bioperl/Manifest +++ b/sci-biology/bioperl/Manifest @@ -1,3 +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-1.6.9.ebuild 1542 BLAKE2B 199c44bf5e2b018efa79c387c247adcade5e477199b9ac7c9dcff8fa98db413520d8365c16ebfe2e38afd799cbd3f1f07a49a24272f3afa3bb8a9aa6a326a493 SHA512 f810d4f0290cfffc3efadc3ce597de747e877c02a302de0614b82209b776dc8c631eeabc3331e9ee4cb590255c5aeb75703f48361453f779c477ed7b64ae8c03 MISC metadata.xml 541 BLAKE2B c01f01fae7a659a708d0d3d6520e98f5bb8fd0e848fd82ae11ba7b6806f18c3ce271d76f94123f6a47c33ca88ea665689b1ec5664c114e28ec18443a87cb31de SHA512 0693aba25e02d3ad67f82c2c77f9987ae06cb6545bb58df2c57f076a22d5c2f6d15c7fdc11b0766748680d53c709c7682b53f866a4f45d7d8a875d1311277e5c diff --git a/sci-biology/bioperl/bioperl-1.6.9.ebuild b/sci-biology/bioperl/bioperl-1.6.9.ebuild index d2519a0d30b6..c39c6244592b 100644 --- a/sci-biology/bioperl/bioperl-1.6.9.ebuild +++ b/sci-biology/bioperl/bioperl-1.6.9.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI="5" @@ -9,13 +9,13 @@ MODULE_VERSION=1.6.901 inherit perl-module SUBPROJECTS="+db +network +run" -MIN_PV=$PV +MIN_PV=${PV} DESCRIPTION="Perl tools for bioinformatics - Core modules" HOMEPAGE="http://www.bioperl.org/" SLOT="0" KEYWORDS="amd64 x86" -IUSE="-minimal graphviz sqlite ${SUBPROJECTS}" +IUSE="minimal graphviz sqlite ${SUBPROJECTS}" REQUIRED_USE="minimal? ( !graphviz )" diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest index 0daf7ceeb4a4..9b594b2d88f3 100644 --- a/sci-biology/biopython/Manifest +++ b/sci-biology/biopython/Manifest @@ -1,3 +1,3 @@ DIST biopython-1.77.tar.gz 16837021 BLAKE2B b5586f0ea3e476b11801dcc98039d5eea7b191e11d390192c0cf348018ded005fe2ad5dc9ba71c83aebc9cdde20c97244905dcc3aeb5436a97588da9f8c79c3e SHA512 6f4b03d46c591e1f49dd1e76bcc4ac5c9aaa2bf748c9dd37ffc5de5a613fbeed38f89b418c01601dd99c65b13b2e294bc8d81ffafc42a9ff1b309c84f840d0d5 -EBUILD biopython-1.77.ebuild 1859 BLAKE2B 54bc3046cf27bcbcb8f3caa3392fcc79628e420bb8f6aa8d8934c854f892a6d6f24a0d76f25208b698a8e893ed3228904968810c121056d2763439e0717a0cd6 SHA512 8c16a575722fa8f3cb512f5855438240da741e9f8c95b721b18f7b9e8e16b765c1a303581fb9fd2a11656bf9be9969d1deba1be3c45db86a64321ea5c091c944 +EBUILD biopython-1.77.ebuild 1918 BLAKE2B 61915c04855bfa88044c7f25f36d10ab774768b8ba2df5591ce6ede34dc90a4553c0331ab85fc12139a724e6fa6a0e40e1b584892f903bcd66b038677ffd843a SHA512 13e0bd3a5bb1ef8c76d8df5d6d2d3d659b48870472c7a8a82a14e19cdae484e19bb9a3e7e2870b0e5a75c056816965e7f5e106d1c910131eefb5c206874901d1 MISC metadata.xml 333 BLAKE2B e1ac45b48b17aaea6da7d681ed0e3c0804d9e1f2a99612b8fa6ca663b443233207ada821d48b03ce778f489b5341151aa7e4b91bc600370dff192fcf7de86364 SHA512 7b82299aa25bb2f19f5bb7cb8eb9871210a9b63c7b0b25122ff6befb3070c65e458e83585cc1f7334fd484527f2c48d04dccbcb6891ecfc412f8df577d766967 diff --git a/sci-biology/biopython/biopython-1.77.ebuild b/sci-biology/biopython/biopython-1.77.ebuild index 387404a1aedc..1dcbc2101c45 100644 --- a/sci-biology/biopython/biopython-1.77.ebuild +++ b/sci-biology/biopython/biopython-1.77.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -53,10 +53,9 @@ python_install_all() { } 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_header "For database support you need to install:" + optfeature "MySQL database support" dev-python/mysql-python + optfeature "PostgreSQL database support" dev-python/psycopg + optfeature_header "Some applications need extra packages:" optfeature "EMBOSS (The European Molecular Biology Open Software Suite)" sci-biology/emboss } diff --git a/sci-biology/cutg/Manifest b/sci-biology/cutg/Manifest index 8adcb37009e2..dad1300c3563 100644 --- a/sci-biology/cutg/Manifest +++ b/sci-biology/cutg/Manifest @@ -1,3 +1,3 @@ DIST cutg-160.tar.xz 178015420 BLAKE2B acfc65f4f152b7293cb8ec8e2bfa3c2c33c5da7bcdcae5349d13122e36c4061931195034548963cb78f6350bce88f72e4fc764f119e181f1f6278ee837b65b6e SHA512 9b72283f311fb805b7b22f59f3ca8fed2ab0af72b82247900922999792c1b112dcaca9b29b265a1e0e7b9eaf9ff846a1dc4c196fb95ddbfb3ee5175755ffb8e7 -EBUILD cutg-160-r1.ebuild 1250 BLAKE2B d973e58297166a5200efa01d08cc1053d6932e44e686b57d8135914fe53e23e6a336e4cf1b851f3c587e6a39087ae9bfb6a24e5e539f3a8892d6a8248a85a927 SHA512 4b7e71b255def1ece36d75ac85aa39e82b9e224317631801731fa0621e4841b00f6aa830e1fc43bb7e74fb387a2663c3848d9e0a5f99f550778448ab571ccacf +EBUILD cutg-160-r1.ebuild 1013 BLAKE2B b60896afcc643f6c0d79361839b004e641f648fdbd48ee1e697a4f6a2b4197f7dd3e752561c7e050bbfc4bd0e7577b1af04c1518bf70015e25a4b502845f602f SHA512 38fc329c36da76f23593ab61bb5a0d09d7018044d398cc014462a63e333b8437e447988acbc091afedea50386f70c9b6948deff1090855c7be74bd97c8956dff MISC metadata.xml 601 BLAKE2B 57d7aecf5afa8d6254de9ac825e0792bcefea19b962204c62c98938d60e2aec4045dcf289b0eebfb36d8a97ddbc91f80e3329a4a87edd0659cd6afc3c976318a SHA512 ed9ad9f404db1bf7e0a1550c139f9486135313a21796d52fb468dc00557228de9433eb1bedc363e5e932eb460be696a22e4ac6fbbed0c877094ebebe13b294c0 diff --git a/sci-biology/cutg/cutg-160-r1.ebuild b/sci-biology/cutg/cutg-160-r1.ebuild index 9a8130969019..97abacaab1e4 100644 --- a/sci-biology/cutg/cutg-160-r1.ebuild +++ b/sci-biology/cutg/cutg-160-r1.ebuild @@ -1,49 +1,42 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 DESCRIPTION="Codon usage tables calculated from GenBank" HOMEPAGE="http://www.kazusa.or.jp/codon/" SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" -SLOT="0" LICENSE="public-domain" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" # Minimal build keeps only the indexed files (if applicable) and the # documentation. The non-indexed database is not installed. IUSE="emboss minimal" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" - -DEPEND="emboss? ( sci-biology/emboss )" -RDEPEND="${DEPEND}" - RESTRICT="binchecks strip" +RDEPEND="emboss? ( sci-biology/emboss )" +BDEPEND="${RDEPEND}" + src_compile() { if use emboss; then mkdir CODONS || die ebegin "Indexing CUTG for usage with EMBOSS." - EMBOSS_DATA="." cutgextract -auto -directory "${S}" || die \ - "Indexing CUTG failed." + EMBOSS_DATA="." cutgextract -auto -directory "${S}" || die "Indexing CUTG failed" eend fi } src_install() { - local file dodoc README CODON_LABEL SPSUM_LABEL + if ! use minimal; then - dodir /usr/share/${PN} - mv *.codon *.spsum "${ED}"/usr/share/${PN} || die \ - "Installing raw CUTG database failed." + insinto /usr/share/cutg + doins *.codon *.spsum fi if use emboss; then - dodir /usr/share/EMBOSS/data/CODONS - cd CODONS || die - for file in *; do - mv ${file} "${ED}"/usr/share/EMBOSS/data/CODONS/ || die \ - "Installing the EMBOSS-indexed database failed." - done + insinto /usr/share/EMBOSS/data + doins -r CODONS fi } diff --git a/sci-biology/fasta/Manifest b/sci-biology/fasta/Manifest index 6cdf5074f707..9ad838facfac 100644 --- a/sci-biology/fasta/Manifest +++ b/sci-biology/fasta/Manifest @@ -1,4 +1,4 @@ AUX fasta-36.3.5e-ldflags.patch 2781 BLAKE2B e6d4e0984b4dadfc9d38504ab215d769084edc6c79cfe641b6b3fba8264a40add1665027295ec4afa19d26277036bfe1a5103ecdf72ef91a1139542ac8272954 SHA512 5424bb8385def72ff75701c2da153f697520cbec82f36cbed8de0e98f93d399de660e79da7700ab0ff688fd5388cf9f42a30ccc4359335ae02042bf8cbb3aae7 DIST fasta-36.3.5e.tar.gz 943763 BLAKE2B 6234d0aee76af6614e6d25ebcfbdfae080db5bc5adf611aeb6edc53ed7c6cb6cef257bf852ed39bc286527cec4175c251765ce23ea5ff39d12ff8947dba97ac6 SHA512 ddfcae36dadd7e2ed5c8c8c0bda2eed077e9f6cd55e4ebf507690671af156358e9da4e7cb1406d2b8713c326c54a9d829fc25e668b16dfa6df48d18e3a009812 -EBUILD fasta-36.3.5e.ebuild 1632 BLAKE2B 847d914602ffd07f31f4d02a592fb3a8ccfe5b0f3601bc5f7ba05cb5c0ca475834e1b84e0710ae8dcc967e12fa246be9301cde0e148c73a8c754399ae11ec445 SHA512 43cea919f46d031c4a56729e57236bde05eff8f1b869fb40ddad60386a38357cd605a57b02de76adc858f5476c6d06b3d37312cb5fc99e53408744848b476bff +EBUILD fasta-36.3.5e.ebuild 1632 BLAKE2B 6165b7f1fc3440d94b337c13c0d520e5848d14b95720a27d941594355d70233af1c9db75e30603e4ae817ba2d2f3b1f5f7711dbcf37a2881effaade2608bc175 SHA512 f4c5cf2cb35e653d14c6afc8fd56743c8f7afb6302dd6227aec04bd8cb3efa9846fe32b6078b1b3dda94359857a214ec1580a2905aacb4ea9ed5234e2667b51c MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/fasta/fasta-36.3.5e.ebuild b/sci-biology/fasta/fasta-36.3.5e.ebuild index 6ac8d96b424f..c4c94d0e7f21 100644 --- a/sci-biology/fasta/fasta-36.3.5e.ebuild +++ b/sci-biology/fasta/fasta-36.3.5e.ebuild @@ -3,7 +3,7 @@ EAPI=5 -inherit eutils flag-o-matic toolchain-funcs +inherit epatch flag-o-matic toolchain-funcs DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package" HOMEPAGE="https://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml" diff --git a/sci-biology/gatk/Manifest b/sci-biology/gatk/Manifest index b616ea3de733..df7ae7e85fe8 100644 --- a/sci-biology/gatk/Manifest +++ b/sci-biology/gatk/Manifest @@ -1,3 +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-2.4.ebuild 845 BLAKE2B 49efa9285196e9028f6b25976c019d93b48013ab2a049faa8173d6c0204033c1247eb12303bd08bff8393c50b9b6aee49997546c49a37e2970b41aa529961b68 SHA512 2eacd0d6c4351071e42b87a35e5930502d85dff08c7a67dd5403690ab99d402fc9755464ce7055c5ed69752c27d0304cbd1fc3747a80e73d115e034ceccde2a9 MISC metadata.xml 349 BLAKE2B 277c979d19162d54c5a762e24fcc90d6fc043e5ddd315824b1ccc2376354db4169690933e9d9ebedaf8589636066bf5b32a646ca28892615e8626d7a8d3c43ac SHA512 1605fb041826c7197edcd3658343ed3ac50aea7dfa53262700b9f9e1a45ee81df501e55bf1e8417201f0f2709b6b6e29bb6e5036b7c187846b4dec5e89903f54 diff --git a/sci-biology/gatk/gatk-2.4.ebuild b/sci-biology/gatk/gatk-2.4.ebuild index 1a885b922b87..bab228e77f5f 100644 --- a/sci-biology/gatk/gatk-2.4.ebuild +++ b/sci-biology/gatk/gatk-2.4.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2013 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 EANT_BUILD_TARGET="dist" EANT_NEEDS_TOOLS="true" @@ -15,20 +15,14 @@ SRC_URI="https://github.com/broadgsa/gatk/archive/${PV}.tar.gz -> ${P}.tar.gz" LICENSE="MIT" SLOT="0" -IUSE="" KEYWORDS="~amd64" -COMMON_DEPS="" -DEPEND=" - >=virtual/jdk-1.6 - ${COMMON_DEPS}" -RDEPEND=" - >=virtual/jre-1.6 - ${COMMON_DEPS}" +RDEPEND=">=virtual/jre-1.6" +DEPEND="${RDEPEND}" src_prepare() { - sed -i '/property name="ivy.home"/ s|${user.home}|'${WORKDIR}'|' build.xml || die java-pkg-2_src_prepare + sed -i '/property name="ivy.home"/ s|${user.home}|'${WORKDIR}'|' build.xml || die } src_install() { diff --git a/sci-biology/glimmer/Manifest b/sci-biology/glimmer/Manifest index 6455e2a011b1..ff6038c01462 100644 --- a/sci-biology/glimmer/Manifest +++ b/sci-biology/glimmer/Manifest @@ -1,11 +1,6 @@ -AUX glimmer-3.02-glibc210.patch 799 BLAKE2B e9c09d46982314f5780d5e958ec27f7b71955a1fa462f8c8086ed1ef36cd940742af897c0e0528101ec86d337ba30dfec3df463410748a3488b9a1f2b76c3f4a SHA512 7a6b05a9b626dbefdabf4535026077b6259747cd2603847e6aa7fed991d456d87bc658ca923959fbdd2ceb4e43e096d46925946ffc135277794a1a6399433a1b -AUX glimmer-3.02-jobserver-fix.patch 433 BLAKE2B c337abe08b47e9cdc3ea600e0ebea9b168ba0d6dfc087f1a3c1865583df148a126178acb9418fc330cda48152b5ee56e827efcaaa8b1c0d7c2810854c2738e2f SHA512 51bb9c5223a034b4d5d76df33528172d8f642d8fac0d51a1c4ad1be74c253a4859ed87ccad219bf5cdbcd1b5d4684061ebd91751c7b213767e1c950af13a430d -AUX glimmer-3.02-ldflags.patch 2057 BLAKE2B 1333aa5d94d218dfd7f986cdea3f7e5c4485e1ed3a3e0ff970b113b686035c3f3da3a3b7c2b747502ea772413f19cdbb15bc5988a26240eab7b380b7a8426ee1 SHA512 aeeac4ee64e358c932a91c4b660c83f8afbfb3ef1b292c9cf8598c56d8645f0d820f4bbc545319e91fe2e65efa5d3aec22f381f75e12aa1574bb7a3b854df6a8 AUX glimmer-3.02b-jobserver-fix.patch 433 BLAKE2B c337abe08b47e9cdc3ea600e0ebea9b168ba0d6dfc087f1a3c1865583df148a126178acb9418fc330cda48152b5ee56e827efcaaa8b1c0d7c2810854c2738e2f SHA512 51bb9c5223a034b4d5d76df33528172d8f642d8fac0d51a1c4ad1be74c253a4859ed87ccad219bf5cdbcd1b5d4684061ebd91751c7b213767e1c950af13a430d -AUX glimmer-3.02b-ldflags.patch 2057 BLAKE2B 1333aa5d94d218dfd7f986cdea3f7e5c4485e1ed3a3e0ff970b113b686035c3f3da3a3b7c2b747502ea772413f19cdbb15bc5988a26240eab7b380b7a8426ee1 SHA512 aeeac4ee64e358c932a91c4b660c83f8afbfb3ef1b292c9cf8598c56d8645f0d820f4bbc545319e91fe2e65efa5d3aec22f381f75e12aa1574bb7a3b854df6a8 +AUX glimmer-3.02b-ldflags.patch 2091 BLAKE2B f4ff77a5b16896b349dfc7dd916b350b11afa61661216bea1292d772492eb94a911fcea6ae21fe13879fe0b91f1530ce757cce82c1a98a75569bb95fa6e97aa3 SHA512 4ffd4fdc5ec51c01e74e886814c61cb6d4268452d074168aca56ad36e2b5a15deda5305a7c45820ad00d6895ec9088062c932a28dda3c22f9d0a131f14e73c0a AUX glimmer-3.02b-rename_extract.patch 9286 BLAKE2B ce955f8f721f8043fe2beed82b7676e6503da20bd9a4cc556e1e29fcfcd9ffdfab1a430a98ece99f13a03241771f7b393d7c7290bf1d5c6652e67bdc5905950c SHA512 b5c08ba7ac973e723aeb8bc8808f69eded90b1e59c9d14804519d1d689e820193bf71860026642b3aed049881289c651f9cfd45bc05d53d73a2e9ab891f9b342 -DIST glimmer302.tar.gz 5637075 BLAKE2B 07fc22a9192644c42291bd305a24bd7c40881cf5e8b668885ffdd5695100a2370b9cdbb275956e36df9007b1cb7bbfba84ab84863f26b70e68638fdf35e608d0 SHA512 c28e5902bffab00566560fa0bcf61909921932935f8298f098361aeb58eb67a40403c23709cf5075fb47dc87bcf54e25572840f110bb15cd21325a072050407c DIST glimmer302b.tar.gz 5637975 BLAKE2B 76c0b19fe08e9ece3e930fe3e53444a2b620e565ac3c83db484294627403e34c3ab77165e4b82176282df340fe47672bf28e5694edbcea9e17a57b61a502ae11 SHA512 00d44a02a8099ceac4b4d2a1cd5d69cc2b787942bb87f612cd63edacf7e502bc9a65cdf9b9270ad789981a84c940cc01e187882d21d2c9de4dcc12b492b041a6 -EBUILD glimmer-3.02-r3.ebuild 1361 BLAKE2B e493ff1e9f6237b23f3d2a010385d955b1dcc1fc4668a16be7325711ed03d7444388b67a3e187bc7f18930dee933d770dc86eb3cd47dcf068a96e7f1170fd3a8 SHA512 0fd7e98d14981ea15c9b19d1a8a3af7ee316c9038d82956f232c9842ef476f2a5636ff87339dbcf1eb935448788fb3fd45caaefd90ce73d00c1bef05b17f0ad5 -EBUILD glimmer-3.02b.ebuild 1714 BLAKE2B d737bc73c36fd390c5b9235323f738a740c008571d37b87c74372a9ec7f1492bbbeb6a4c16b9a6cabee70a06ea76f2607406453307e98068e463cbde5656646b SHA512 df03f729fa5b0dd6b1e0121701e58d0c6a60b4e8d70d02bdebf6bd7ddd10523a7429c3e13ff4267e4835220cac3a15970565fbcac7979b400ff87707cbaca29c +EBUILD glimmer-3.02b.ebuild 1676 BLAKE2B 3e81fee625fb53db07ddb9c782e0d6a73878592b276a51f741f7f46f15f0213cfccb2592a9e82b5735a4ef9a83a791d0a268de197cf9c1760d1b6f04b6bfbafe SHA512 880de5402658689993b818391a769b1f592febf98e5ba84be9fc9fc97c286287afbbae29133bb2e6c3badaac7874a0fca8f666be49f3a2e874cdf4c93c4fde05 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch b/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch deleted file mode 100644 index f6051ec82054..000000000000 --- a/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch +++ /dev/null @@ -1,24 +0,0 @@ -diff -durr glimmer3.02-orig/src/Common/gene.cc glimmer3.02/src/Common/gene.cc ---- glimmer3.02-orig/src/Common/gene.cc 2009-12-28 13:34:21.577437056 +0000 -+++ glimmer3.02/src/Common/gene.cc 2009-12-28 13:36:06.914974685 +0000 -@@ -443,7 +443,7 @@ - // Return a subscript corresponding to character ch . - - { -- char * p; -+ const char * p; - - p = strchr (CONVERSION_STRING, tolower (ch)); - if (p == NULL) -diff -durr glimmer3.02-orig/src/ICM/icm.cc glimmer3.02/src/ICM/icm.cc ---- glimmer3.02-orig/src/ICM/icm.cc 2009-12-28 13:34:21.577437056 +0000 -+++ glimmer3.02/src/ICM/icm.cc 2009-12-28 13:36:44.649451803 +0000 -@@ -1981,7 +1981,7 @@ - // model) for character ch . - - { -- char * p; -+ const char * p; - - p = strchr (ALPHA_STRING, tolower (Filter (ch))); - if (p == NULL) diff --git a/sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch b/sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch deleted file mode 100644 index 91498b116d12..000000000000 --- a/sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch +++ /dev/null @@ -1,22 +0,0 @@ -diff -ru glimmer3.02-orig/src/Makefile glimmer3.02/src/Makefile ---- glimmer3.02-orig/src/Makefile 2006-06-12 21:40:14.000000000 +0200 -+++ glimmer3.02/src/Makefile 2010-03-18 14:30:15.000000000 +0100 -@@ -2,12 +2,12 @@ - - - all: -- @ TGT=objs -- @ $(dosubdirs) -- @ TGT=libs -- @ $(dosubdirs) -- @ TGT=progs -- @ $(dosubdirs) -+ @+ TGT=objs -+ @+ $(dosubdirs) -+ @+ TGT=libs -+ @+ $(dosubdirs) -+ @+ TGT=progs -+ @+ $(dosubdirs) - - - install: all diff --git a/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch b/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch deleted file mode 100644 index 0a04fbef1dcc..000000000000 --- a/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch +++ /dev/null @@ -1,88 +0,0 @@ -diff --git a/src/c_make.gen b/src/c_make.gen -index 414dead..84c3030 100644 ---- a/src/c_make.gen -+++ b/src/c_make.gen -@@ -200,45 +200,12 @@ LOCAL_SYS_INC=$(SEP_PATH)/../SYS/inc - #### Do not redefine if (a) passed in on command line, or (b) - #### defined in an environment variable. - --ifneq "$(origin CC)" "environment" --CC = cc --endif -- --ifneq "$(origin CPPFLAGS)" "environment" --CPPFLAGS= --endif -- --ifneq "$(origin CFLAGS)" "environment" --CFLAGS = --endif -- --ifneq "$(origin CDEFS)" "environment" --CDEFS = --endif -- --ifneq "$(origin CXX)" "environment" --CXX = g++ --endif -- --ifneq "$(origin CXXFLAGS)" "environment" --CXXFLAGS= --endif -- --ifneq "$(origin CXXDEFS)" "environment" --CXXDEFS= -D__cplusplus --endif -- --ifneq "$(origin AR)" "environment" --AR = ar --endif -- --ifneq "$(origin ARFLAGS)" "environment" --ARFLAGS = rvs --endif -- --ifneq "$(origin LDFLAGS)" "environment" --LDFLAGS = --endif -+CC ?= cc -+CXX ?= g++ -+CXXFLAGS ?= -+CXXDEFS = -D__cplusplus -+AR ?= ar -+ARFLAGS ?= rvs - - #### Delete default suffix rules - .SUFFIXES: -@@ -359,13 +326,13 @@ $(PROGS): - cd $(LOCAL_OBJ); \ - if $(CC) -o $(LOCAL_BIN)/$(notdir $@) $(LDFLAGS) \ - $(LD_DIRS) $(filter-out lib%.a, $+) \ -- $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) ; then \ -+ $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LIBS) ; then \ - true; else rm -f $(LOCAL_BIN)/$(notdir $@); fi; \ - else \ - cd $(LOCAL_OBJ); \ - if $(CXX) -o $(LOCAL_BIN)/$(notdir $@) $(LDFLAGS) \ - $(LD_DIRS) $(filter-out lib%.a, $+) \ -- $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) ; then \ -+ $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LIBS) ; then \ - true; else rm -f $(LOCAL_BIN)/$(notdir $@); fi; \ - fi ; - -diff --git a/src/c_make.glm b/src/c_make.glm -index 0decc17..b82131c 100644 ---- a/src/c_make.glm -+++ b/src/c_make.glm -@@ -8,10 +8,7 @@ include $(LOCAL_WORK)/src/c_make.gen - - SUBDIRS = Common ICM Glimmer Util - --CFLAGS = -g -Wall --CXXFLAGS = -g -Wall -- --LDFLAGS = -g -lm -+LIBS = -lm - - - #AS_BUILD_DIR =$(LOCAL_WORK) diff --git a/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch b/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch index 0a04fbef1dcc..dc41ef00de7e 100644 --- a/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch +++ b/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch @@ -1,8 +1,6 @@ -diff --git a/src/c_make.gen b/src/c_make.gen -index 414dead..84c3030 100644 --- a/src/c_make.gen +++ b/src/c_make.gen -@@ -200,45 +200,12 @@ LOCAL_SYS_INC=$(SEP_PATH)/../SYS/inc +@@ -200,45 +200,11 @@ #### Do not redefine if (a) passed in on command line, or (b) #### defined in an environment variable. @@ -48,13 +46,12 @@ index 414dead..84c3030 100644 +CC ?= cc +CXX ?= g++ +CXXFLAGS ?= -+CXXDEFS = -D__cplusplus +AR ?= ar +ARFLAGS ?= rvs #### Delete default suffix rules .SUFFIXES: -@@ -359,13 +326,13 @@ $(PROGS): +@@ -359,13 +325,13 @@ cd $(LOCAL_OBJ); \ if $(CC) -o $(LOCAL_BIN)/$(notdir $@) $(LDFLAGS) \ $(LD_DIRS) $(filter-out lib%.a, $+) \ @@ -70,11 +67,9 @@ index 414dead..84c3030 100644 true; else rm -f $(LOCAL_BIN)/$(notdir $@); fi; \ fi ; -diff --git a/src/c_make.glm b/src/c_make.glm -index 0decc17..b82131c 100644 --- a/src/c_make.glm +++ b/src/c_make.glm -@@ -8,10 +8,7 @@ include $(LOCAL_WORK)/src/c_make.gen +@@ -8,18 +8,14 @@ SUBDIRS = Common ICM Glimmer Util @@ -86,3 +81,12 @@ index 0decc17..b82131c 100644 #AS_BUILD_DIR =$(LOCAL_WORK) + INC_IMPORT_DIRS += \ + $(patsubst %, $(LOCAL_WORK)/src/%, $(strip $(SUBDIRS))) \ + $(LOCAL_WORK)/inc +-LIB_IMPORT_DIRS += $(LOCAL_WORK)/lib /usr/lib /usr/shlib /usr/X11R6/lib \ +- $(SYBASE)/lib ++LIB_IMPORT_DIRS += $(LOCAL_WORK)/lib + + OBJ_SEARCH_PATH = $(LOCAL_WORK)/obj + diff --git a/sci-biology/glimmer/glimmer-3.02-r3.ebuild b/sci-biology/glimmer/glimmer-3.02-r3.ebuild deleted file mode 100644 index 9a32e3dbf895..000000000000 --- a/sci-biology/glimmer/glimmer-3.02-r3.ebuild +++ /dev/null @@ -1,60 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI="5" - -inherit eutils toolchain-funcs - -MY_PV=${PV//./} - -DESCRIPTION="An HMM-based microbial gene finding system from TIGR" -HOMEPAGE="https://ccb.jhu.edu/software/glimmer/index.shtml" -SRC_URI="http://www.cbcb.umd.edu/software/${PN}/${PN}${MY_PV}.tar.gz" - -LICENSE="Artistic" -SLOT="0" -IUSE="" -KEYWORDS="amd64 x86" - -DEPEND="" -RDEPEND="app-shells/tcsh" - -S="${WORKDIR}/${PN}${PV}" - -PATCHES=( - "${FILESDIR}"/${P}-glibc210.patch - "${FILESDIR}"/${P}-jobserver-fix.patch - "${FILESDIR}"/${P}-ldflags.patch - "${FILESDIR}"/${PN}-3.02b-rename_extract.patch -) - -src_prepare() { - sed -i -e 's|\(set awkpath =\).*|\1 /usr/share/'${PN}'/scripts|' \ - -e 's|\(set glimmerpath =\).*|\1 /usr/bin|' scripts/* || die "failed to rewrite paths" - # Fix Makefile to die on failure - sed -i 's/$(MAKE) $(TGT)/$(MAKE) $(TGT) || exit 1/' src/c_make.gen || die - # GCC 4.3 include fix - sed -i 's/include <string>/include <string.h>/' src/Common/delcher.hh || die - epatch "${PATCHES[@]}" -} - -src_compile() { - emake \ - -C src \ - CC=$(tc-getCC) \ - CXX=$(tc-getCXX) \ - AR=$(tc-getAR) \ - CXXFLAGS="${CXXFLAGS}" \ - CFLAGS="${CFLAGS}" \ - LDFLAGS="${LDFLAGS}" -} - -src_install() { - rm bin/test || die - dobin bin/* - - insinto /usr/share/${PN} - doins -r scripts - - dodoc glim302notes.pdf -} diff --git a/sci-biology/glimmer/glimmer-3.02b.ebuild b/sci-biology/glimmer/glimmer-3.02b.ebuild index 4318b60ff949..c9332c5143a1 100644 --- a/sci-biology/glimmer/glimmer-3.02b.ebuild +++ b/sci-biology/glimmer/glimmer-3.02b.ebuild @@ -1,28 +1,25 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI="5" +EAPI=7 -inherit eutils toolchain-funcs +inherit toolchain-funcs MY_PV=${PV//./} DESCRIPTION="An HMM-based microbial gene finding system from TIGR" HOMEPAGE="https://ccb.jhu.edu/software/glimmer/index.shtml" SRC_URI="https://ccb.jhu.edu/software/${PN}/${PN}${MY_PV}.tar.gz" +S="${WORKDIR}/${PN}3.02" LICENSE="Artistic" SLOT="0" -IUSE="" KEYWORDS="~amd64 ~x86" -DEPEND="" -RDEPEND="app-shells/tcsh +RDEPEND=" + app-shells/tcsh sci-biology/elph" -#S="${WORKDIR}/${PN}${PV}" -S="${WORKDIR}/${PN}3.02" - PATCHES=( "${FILESDIR}"/${P}-jobserver-fix.patch "${FILESDIR}"/${P}-ldflags.patch @@ -37,12 +34,13 @@ src_prepare() { # GCC 4.3 include fix sed -i 's/include <string>/include <string.h>/' src/Common/delcher.hh || die # - sed -i "s+/fs/szgenefinding/Glimmer3/bin+%${D}/bin/glimmer3+" scripts/g3-* || die - sed -i "s+/fs/szgenefinding/Glimmer3/scripts+%${D}/share/glimmer/scripts+" scripts/g3-* || die - sed -i "s+/nfshomes/adelcher/bin/elph+%${D}/bin/elph+" scripts/g3-* || die + sed -i "s:/fs/szgenefinding/Glimmer3/bin:%${EPREFIX}/usr/bin/glimmer3:" scripts/g3-* || die + sed -i "s:/fs/szgenefinding/Glimmer3/scripts:%${EPREFIX}/usr/share/glimmer/scripts:" scripts/g3-* || die + sed -i "s:/nfshomes/adelcher/bin/elph:%${EPREFIX}/usr/bin/elph:" scripts/g3-* || die sed -i "s/@ if/if/" src/c_make.gen || die + # avoid file collision on /usr/bin/extract #247394 - epatch "${PATCHES[@]}" + default } src_compile() { @@ -60,7 +58,7 @@ src_install() { rm bin/test || die dobin bin/* - insinto /usr/share/${PN} + insinto /usr/share/glimmer doins -r scripts dodoc glim302notes.pdf diff --git a/sci-biology/mira/Manifest b/sci-biology/mira/Manifest index bd2f1f6ab348..ca5165677704 100644 --- a/sci-biology/mira/Manifest +++ b/sci-biology/mira/Manifest @@ -3,5 +3,5 @@ AUX mira-4.0.2-cmath.patch 295 BLAKE2B 30892b3a519682db7e04b1a0169c4018d7f4dd4e3 AUX mira-4.0.2-cout.patch 735 BLAKE2B d386a704829b7f3264ee69d55d7451a5479a9d121e49cbd8d9322c9a27a065073076608569d169982784fcc6cc4ae4423712d15d1c4d642a6b8fd0dd7d5fe3a3 SHA512 9d1aa493d20481d0a7e3eaefba36dc29d7903f70c9a445b6e0ea478d04124e8a81de37c437f0fb28c0a395562db7e78217cf09e500fd4a1f2a1f929c1d4d2a5a DIST mira-4.0.2.tar.bz2 10368046 BLAKE2B cc84c6c13c8024409634ccafd103be8a4f2a9e27fa7f19d2ef401393db9e8063a6fac2f21cd25dfe58e90aee8cf38983369d928241f9bc65e78da0e95fa41d3b SHA512 a7f9845de207cefb87ffa652f4f6b9b85735ef22eeb29b456e4d946ba1675e7dd2c78abb2da56f11fddcb699f5c0700a08ce298196ce1a8e586a758a8d3bdc7e DIST mira_3rdparty_06-07-2012.tar.bz2 31656 BLAKE2B 7e952d96e9073acd8ab1d1fc7c51c37f6526287d31698c5090500d421147285b535e8cab7e49f4e51a5634c901d1cd969206b1727e683d3fcebdc195399e3589 SHA512 4d4dbdf7ab5126f9d47160bee8bc127b6a225de8087f6b9914c754324a74d966333207c86a3f38cf0ea9f91408707e2a24086dbe1318fdfa2870b0c39bc5033b -EBUILD mira-4.0.2.ebuild 2565 BLAKE2B 63493cce65380db11e2dca8371894780095e56d5cea1d23891664925e3587ac4ee8ee828309f126d442078d186bafde88edec2d0fa0f8b14c4f8f6858c34f533 SHA512 0c0eee188139c72c816fd50634e3d3bc48d5737e081929d5c154468bb0250c382ca4c4499cb1ee8740f7f5f78ccc8e9eeaed8c379205aeb10afc22d0abe8435e +EBUILD mira-4.0.2.ebuild 2558 BLAKE2B de1f15bf2fc98b4f7487d2a354a319a335357f0decd483ea01584c7de9a4fbddb0717415e4cdd7552865768decb52763d6bbd869c39f8a9461c9349eb8299846 SHA512 65f3ae83abe4f97cb21b16157dbbd172b7c4780eb414acbf1c337bad2890899bd0cc35d0d1e7f51d4e328563f2cdbe0314f8883216c6ccfc6fdb40a4664ba8d0 MISC metadata.xml 355 BLAKE2B 2557fbd5c3427ccced7fc6d233954a3e9d4297c0bec17158997f4f7fb490b525235ae27fff1ed19113b596de77a23518505e20531c7e40020e3f54932f5d9e6f SHA512 9d9037805b94622cb468553fa27c948de2849ac4c6dc1eafae8c3261554b5e97b631fe77e4e589eff613822d316b2843bcab0c47547b202651c8a804a516554e diff --git a/sci-biology/mira/mira-4.0.2.ebuild b/sci-biology/mira/mira-4.0.2.ebuild index ddd64d3cd5e9..c37fa2333129 100644 --- a/sci-biology/mira/mira-4.0.2.ebuild +++ b/sci-biology/mira/mira-4.0.2.ebuild @@ -6,7 +6,7 @@ EAPI=6 MIRA_3RDPARTY_PV="06-07-2012" MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to mira-4.0rc2 (upstream fromat) -inherit autotools eutils multilib +inherit autotools multilib DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Illumina" HOMEPAGE="http://www.chevreux.org/projects_mira.html" diff --git a/sci-biology/mothur/Manifest b/sci-biology/mothur/Manifest index a28de67ee118..e673f0859e3c 100644 --- a/sci-biology/mothur/Manifest +++ b/sci-biology/mothur/Manifest @@ -1,5 +1,5 @@ AUX mothur-1.27.0-makefile.patch 1196 BLAKE2B dbe053a5f5629eadae57bd09545ef46106741204050d0c888532388fe0b7f8f2fe4d5f311163e95812d0d828aae2228a2f72b7f0c861f5a3d42a41e17b6ba4f3 SHA512 8a78ddbc926d4e116deed440fda8431ccbca3299ac182fc84850259187dc130cc43fb6f23845d055d998293fa43f94cbe35930242c5f6aa049f8275ad3e42adf AUX mothur-1.27.0-overflows.patch 4894 BLAKE2B a9de0276a9ccbb5e86d6cf208f86414ea8c0befdf80807e05b40bee0c6f685cb40a608005e69eb3f77b85990424a36cde14971044cb6a1136a50d85078eb9f1f SHA512 aa392b2060cecc38006a7ac50aaa8e4249a020029234ac2abdc33441b12a09faabb0335144ff4d888e55a1da1838a45347981f49f6658f3546a54a30b5e2133a DIST mothur-1.27.0.zip 7095054 BLAKE2B 96a6410d36f64ff50591955aa22bfddf6217c7568022c8c7f70ab70c65d57af2217477de56b6f9ceaf11237cdc5380bd354cf6564002357546539585d0f58221 SHA512 81821ca95d4ce3f0d1e6aa920c4fe3fddd70f716157312ed0590c1c4ad728e6786bfe79f6badddcfb060ed5d1996cc1b5062c320a59209fef35f68e687ba3dd5 -EBUILD mothur-1.27.0-r1.ebuild 883 BLAKE2B dbdda281b6c7a79e4c3202add586f038011502e1c5bf7cc386a4a5c5f90b1926fb16fa3202d6266db77ef5350bad0f56722adb69f1ac7faa50a73a1ae0f5f558 SHA512 c0d22ad5dbe6290f6aed0d055f2ad57b8b25bb33fcb1166c154e604d7337a367beb23f9acc61487ed969e6698ca6f115f8c8d36dc14863a36d08e3f8dd08cf1d +EBUILD mothur-1.27.0-r1.ebuild 845 BLAKE2B 52cc28dcfd3df857f51b9c430c1ec5f658562e922f1394f0d79cba4fd6cd33161cb5639e0d7ca95c6b5daeffebe376baa5c2df0c5db6e8c6382fda40a215060d SHA512 6fa585f94e0caf8cbe40a2673d4e5eb49c6c8c9e5cbc279deef1b525d1674ce986068a08a994fecc079b5cee2301cd92fb395d884c4e23c98afe7587a49cabeb MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/mothur/mothur-1.27.0-r1.ebuild b/sci-biology/mothur/mothur-1.27.0-r1.ebuild index 9e9bf2160310..12b628475aac 100644 --- a/sci-biology/mothur/mothur-1.27.0-r1.ebuild +++ b/sci-biology/mothur/mothur-1.27.0-r1.ebuild @@ -1,43 +1,42 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 -inherit eutils flag-o-matic fortran-2 toolchain-funcs +inherit flag-o-matic fortran-2 toolchain-funcs DESCRIPTION="A suite of algorithms for ecological bioinformatics" HOMEPAGE="https://www.mothur.org/" SRC_URI="https://www.mothur.org/w/images/c/cb/Mothur.${PV}.zip -> ${P}.zip" +S="${WORKDIR}/${PN^}.source" LICENSE="GPL-3" SLOT="0" -IUSE="mpi +readline" KEYWORDS="amd64 x86" +IUSE="mpi +readline" RDEPEND=" sci-biology/uchime mpi? ( virtual/mpi )" -DEPEND="${RDEPEND} - app-arch/unzip" +DEPEND="${RDEPEND}" +BDEPEND="app-arch/unzip" -S=${WORKDIR}/Mothur.source +PATCHES=( + "${FILESDIR}"/${P}-makefile.patch + "${FILESDIR}"/${P}-overflows.patch +) -pkg_setup() { - fortran-2_pkg_setup - use mpi && export CXX=mpicxx || export CXX=$(tc-getCXX) +src_configure() { + use mpi && export CXX=mpicxx || tc-export CXX use amd64 && append-cppflags -DBIT_VERSION } -src_prepare() { - epatch \ - "${FILESDIR}"/${P}-makefile.patch \ - "${FILESDIR}"/${P}-overflows.patch -} - src_compile() { - emake USEMPI=$(usex mpi) USEREADLINE=$(usex readline) + emake \ + USEMPI=$(usex mpi) \ + USEREADLINE=$(usex readline) } src_install() { - dobin ${PN} + dobin mothur } diff --git a/sci-biology/mrbayes/Manifest b/sci-biology/mrbayes/Manifest index 89c72da46a5b..faf3dab4cfed 100644 --- a/sci-biology/mrbayes/Manifest +++ b/sci-biology/mrbayes/Manifest @@ -1,4 +1,4 @@ AUX mb_readline_312.patch 1108 BLAKE2B 4413b4193ee7c0c51a1ad7a422474f137682151f932b28fc6ee98390a228a4e5bbabcf30f3d78fc56a79a665ffc40bf05376fbbf14b68ff43bc10a9001ec8e6e SHA512 0a169b8560853dbff87c983bf8220384dcf22f53106ce5711bf3b1fc76d8a9adbf1860618176dde65a8657abe3ad888521bf5485fc00d4014adf1acb7ba3f114 DIST mrbayes-3.1.2.tar.gz 545968 BLAKE2B f4c5bbdde765fb9e596c17d5fd890b168c22cefb0d24b67c1c68623e1dcfa4df716a896fe120f7a1cac4234125b6ed524973506e47492ba3ec26e389783d618a SHA512 2fb0ee7224cbb69c1acf2ffb0c6c8974f63002cda4f39a626eadf80fad9cfc23861f8c03f5545970f3a81e02093d62b6a0549ab7d7f7080557e91e21b2c3ee14 -EBUILD mrbayes-3.1.2-r2.ebuild 1347 BLAKE2B 6587af6372eff67641954301a26fd6b9bcb9bb5b1ba04fb4217da6a6686e71c166409a514c348c93334a5a191bcfdb96afe915f1edd93e5985380c314dce853c SHA512 c8655ecaf9933a963b072a242e44c156f89c635fae00fa135262911e2588beb623764a92634c27a16dcdac4fb70c16b88a428aa154a56ea816fd9b9ff2418037 +EBUILD mrbayes-3.1.2-r2.ebuild 1344 BLAKE2B f0b52d8b615dabe59d1d1e2dedbeb3f86513127fd3b2112783e64c38b812a3a998f5b33c397b7d9f1b333ed58bcc8ecdce8d5d5c4f73d2abe29ba631c3929d48 SHA512 d64b835015f70b4c28c3bfe37438be5e27c42b4546e24f8f4c40089f9ca98d5b29b7340fa88efa7fb9f764cb46c4396ced213ca9d35c3d64f33454b6a4854f9b MISC metadata.xml 916 BLAKE2B 511d932eff0de935a1c8634cc6398bfe6cceb7f2766534e5486f5ff2aa4c900b8d48d7dabc5cee2506061c36421f0ef336f43b5df5d23a03ab5911a1fef87b1b SHA512 ab6be2e4111088bc13e6da5f65d11437dc05dbcdeab83e5d3899b913ff9ad3dc1f22ec81f2fe73f60bf991d01f0a8691eaa124ba24bd7ebb17d995fdd271bfef diff --git a/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild b/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild index ebe9926212c9..ecc44fe43454 100644 --- a/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild +++ b/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 -inherit eutils toolchain-funcs +inherit epatch toolchain-funcs DESCRIPTION="Bayesian Inference of Phylogeny" HOMEPAGE="http://mrbayes.csit.fsu.edu/" diff --git a/sci-biology/ncbi-tools/Manifest b/sci-biology/ncbi-tools/Manifest index 45adecacdcf8..7bbabc7adc05 100644 --- a/sci-biology/ncbi-tools/Manifest +++ b/sci-biology/ncbi-tools/Manifest @@ -6,5 +6,5 @@ AUX ncbi-tools-extra_vib.patch 1393 BLAKE2B 3c9e0ffa614e7baccf87beea601561a8f6e1 AUX ncbi-tools-lop.patch 701 BLAKE2B 9df2fd3ba86bc9a4f52d3c1809b4d795392666c601aa607d2377129c42562a99087387eaa69d9e9ae07545ea91808902db65718ccf3d671ca88f7255119b1028 SHA512 706dfb29f9b1eff1fcc7dc1df1d533563d9d12ead5b930930121ad92a3e8c159d1d7cf30acd9f4462772e8f27e6dcf45cd6125f2fa077b3902145f6faf1c8352 AUX ncbirc 57 BLAKE2B 140c208cf1c7dbb6a204e58632c576e4edf0cd71d151b69f70839f1b06ae19db0d74d49179d2f0bc1320a40fabad49bed18a98a8bd2a75f6ecf068e647382c60 SHA512 0b9b68116b362ccc625623abf4e959abfb8555c31117216eefe3093fe2dd122c3ce508fe389c07a069d6f4322d889718e455de65dd3ab7d55a16d947ecb07cfd DIST ncbi-tools-2.2.26.tar.gz 68691452 BLAKE2B 21444227c6896c387f46a5490db1e4cf3ac437f94029c68f11ee3c5438bf2c34584d4b1b0ab18d3996f9c4e423a7e17fece510a96a1aa8be5dea6c5a2688f24c SHA512 da167216b56386b8c91a660e8ea0f3ac39b991d4519af9e02fc26aa16ed602eb3d9d874446f69a8f6840ae31a4d5a29da170e04e8a72b56f8c3ca038d1437014 -EBUILD ncbi-tools-2.2.26-r2.ebuild 4612 BLAKE2B 817bb5d68cfda66ba62011a0e0cd627a1722942e748fc8e9d6fb93ae28a4088f7dfb95e291ff02e46251fa0732d82e6873b865cca29f9198f568b01a6ba9b81f SHA512 e9ee979f8a1daa5fdf2618235da187f666dfc04a20d7be61705df7d7f853190fbcd368878c5b5a7721af64535cba09d9a782b947652a86d69f758490af4ee9b9 +EBUILD ncbi-tools-2.2.26-r2.ebuild 4631 BLAKE2B 0a31d2096d49f16b8a5c4a2220fe55aa40557cc33b6a7fa5d4136f86fa0008d24e089b725fa6a12609475c3cbd58c7f379c65a77eab6c957fc811110d60f64f5 SHA512 7d9a4e2dfd3edaa28e36f8caf223b794fb37306270177bfa383f952b96799b177fd68f2688cd79fb81d85801d17d5f9e01faf3d7c8978d77372260b81d95d992 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild b/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild index 2c59e13b5a97..2a3668a82a53 100644 --- a/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild +++ b/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 -inherit eutils flag-o-matic prefix toolchain-funcs +inherit epatch flag-o-matic prefix toolchain-funcs DESCRIPTION="Development toolkit and applications for computational biology, including BLAST" HOMEPAGE="https://www.ncbi.nlm.nih.gov/" @@ -27,7 +27,10 @@ RDEPEND=" x11-libs/libXmu x11-libs/libXt )" -DEPEND="${RDEPEND}" +DEPEND=" + ${RDEPEND} + virtual/pkgconfig +" S="${WORKDIR}/ncbi" diff --git a/sci-biology/plink/Manifest b/sci-biology/plink/Manifest index 8922b631e9c0..f7bc93be9327 100644 --- a/sci-biology/plink/Manifest +++ b/sci-biology/plink/Manifest @@ -1,3 +1,3 @@ DIST plink-1.90_pre140514.zip 822157 BLAKE2B 3c29670862de99c9715bc37d8cffc2b02c0cb25ad746975f253ca1e8094b24668cc6739943c68bfa407471f30835a74c6ad027eaa56a92f13445e0a02854cad3 SHA512 679f1e136b11f35f1d49636bc44ffd17e72e4e38edc5daa270cd963ca39f7b8a80f31905a94de517059e5b3ea7a6bf518ae34a5c2af8a05c530bd6df771606c4 -EBUILD plink-1.90_pre140514.ebuild 1129 BLAKE2B ded7a69c8a040d4b4e2bcb2bb931adf6eeeccd6168d78dc7285322490f1744f7b4ae6c7e112e62a00ab0663227896cb3088c607a5a4a1d3903a080806618d6d7 SHA512 152653b04caa40c548108bb9cade22c968475faef8fd4af2627462928a6b2b364a8831bba569d467ff4a435e6fe76ce5d9862cb19da9565db1e9b974305fd0e4 +EBUILD plink-1.90_pre140514.ebuild 1119 BLAKE2B 71e5c5abf54d97212a1c21b722f12326052f4f01b0892e7aef288aa22ccc57075ab806268fd5d99b4d638e6ffba01ebeb86855596c038a9a84d72960cc98cf43 SHA512 2867a0d71b034886afef5adc81fe6e48b41b4f9a3dadd72b5286769388bcc7977688dc19eb27b52b6cfa9a952e249d7e876dd0547f455824dd972ce2011b6952 MISC metadata.xml 261 BLAKE2B 3768c926bca545090342a947ba83e706a8954c51b99a5e7b3476ba5198cd326fe1c3b8efb51dfd6be1800682556b8ceea065e388981463ab32f3d687951872f3 SHA512 537da0d3aa2741ebe4442d5dd9b53409decfc9d12ca8e5af8e737c4deb2910c884207e2d441025d19469816100889f04c11038bdffd6a1a15c6217495445090a diff --git a/sci-biology/plink/plink-1.90_pre140514.ebuild b/sci-biology/plink/plink-1.90_pre140514.ebuild index 9abd1604abc4..ab931553b923 100644 --- a/sci-biology/plink/plink-1.90_pre140514.ebuild +++ b/sci-biology/plink/plink-1.90_pre140514.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 -inherit eutils toolchain-funcs +inherit toolchain-funcs DESCRIPTION="Whole genome association analysis toolset" HOMEPAGE="http://pngu.mgh.harvard.edu/~purcell/plink/" diff --git a/sci-biology/probcons/Manifest b/sci-biology/probcons/Manifest index 8b648a04fa39..0e374b576c6c 100644 --- a/sci-biology/probcons/Manifest +++ b/sci-biology/probcons/Manifest @@ -2,5 +2,5 @@ AUX gcc-4.3.patch 1300 BLAKE2B fd74d2cb3311ef89cb012276a55025e4430b452cd603d2386 AUX probcons-1.12-cxxflags.patch 1957 BLAKE2B 5308ee19d8bec42bc23ba8bf6ee38b4d559be0bbffdae032138f32a5890e6524d3025124f48188f4b580035b398e4957ba246a9305d05577b58909259a73f396 SHA512 033e92e414d3e2d1db867aec980d82759a662cf46692e3cc908bb7b3428d5eca105fb81cbdd8764c54dd3d759d29e713ef085fc48aac183426d26fe68a48a38e AUX probcons-1.12-gcc-4.6.patch 306 BLAKE2B 0b0dcba7749192be0361fcf2a0778e8a4ef168a1d867e9d1ccaa097fb75c8b580a255dacf25d1312e648bb623e5796370d695afd742304a06e2d18547ceac4c4 SHA512 f8a393cce2a860ea54aa18add7ba236aa43e21893925e4484b272190e29aa2dc27bf20b11edc5694446f027c6d8d6ff3c3f92383f0b0c8958b1b1d5b7564f828 DIST probcons_v1_12.tar.gz 43200 BLAKE2B db59a4472e5ea4ce1801ca74807aa1b1bdb2861a9e52f9b3a4297b37d048ecd6e34298cfd181523093f8fb1cd9a81285e58098bcdec6ffa32caa9cc1117b8b8f SHA512 ce061ea5cca4204d6e66beb893c1ba508f094b7ea3ee08196dc75a5443ebd0afca14dc8d7cd6c8da4ce1578b8750ea1981e5815408c0b122e8f97ec27b3bf008 -EBUILD probcons-1.12-r1.ebuild 1184 BLAKE2B 9ceede9555c3fd4e978036a8f97ddd16c042d812273dea733b0e6ce1a835c8e309b28061011d8a2df754de50c4588f2965ae3242b950629fc9746674c0718d48 SHA512 da6c987d200faa0aa9a8a243eb8ac9a6ebe7381e9b1488477dbc659106df88aaeca8bb6005c25bbfad0757c5178e15b346a2872562705f76a921cccd68f8a466 +EBUILD probcons-1.12-r1.ebuild 1132 BLAKE2B 1ed9f556e3d393ba41611b505cf6a8d682d747d7f0b93001793989d56c710564c77326cc704a50f80e3c9ca338f529f02bdd56536ef6f2083d51439de792640c SHA512 2a506f516adc4190e74d3d756a5a11779f1d06473e4daf132a34829cc9f07cdafa50bb1d3b908df984037ecef885698734c7c964fcd013b3af29e20e71158618 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/probcons/probcons-1.12-r1.ebuild b/sci-biology/probcons/probcons-1.12-r1.ebuild index 01973b88cab9..15960982abff 100644 --- a/sci-biology/probcons/probcons-1.12-r1.ebuild +++ b/sci-biology/probcons/probcons-1.12-r1.ebuild @@ -1,35 +1,31 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 -inherit eutils toolchain-funcs +inherit toolchain-funcs MY_P="${PN}_v${PV/./_}" DESCRIPTION="Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences" HOMEPAGE="http://probcons.stanford.edu/" SRC_URI="http://probcons.stanford.edu/${MY_P}.tar.gz" +S="${WORKDIR}/${PN}" LICENSE="public-domain" SLOT="0" KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" -IUSE="" # Gnuplot is explicitly runtime-only, it's run using system() RDEPEND=" !sci-geosciences/gmt sci-visualization/gnuplot" -DEPEND="" - -S="${WORKDIR}/${PN}" -src_prepare() { - epatch \ - "${FILESDIR}"/${P}-cxxflags.patch \ - "${FILESDIR}"/gcc-4.3.patch \ - "${FILESDIR}"/${P}-gcc-4.6.patch -} +PATCHES=( + "${FILESDIR}"/${P}-cxxflags.patch + "${FILESDIR}"/gcc-4.3.patch + "${FILESDIR}"/${P}-gcc-4.6.patch +) src_compile() { emake \ diff --git a/sci-biology/psipred/Manifest b/sci-biology/psipred/Manifest index f55dab11c9d8..ae2d7f82a568 100644 --- a/sci-biology/psipred/Manifest +++ b/sci-biology/psipred/Manifest @@ -3,5 +3,5 @@ AUX 3.1-path.patch 1128 BLAKE2B ea445427fe2ff574028b3d82ae353da5a1dfe3f5c7fade41 AUX 3.2-fgets.patch 427 BLAKE2B dba911ef9d28c230e38d326336fa7adfae31ffafd225d525968f58b1013df2f5812b0c678f37576714c7bfa396c7378b2e1201f8c6b2bea844c2e042eea7c0ec SHA512 a8a59a765057e20b9c606b8e4d76b5657a9a06150247b426d939805547148ddc8a1cb4282e04bcdcd756bfa6df7bebffcc77b84f62c86be2f643069d2ff913bb DIST psipred3.5.tar.gz 1101579 BLAKE2B 2fd86841cbc4bb86045b51f8283550832df8356ee88a6ef2c85281b5810debb23ac53652ddc5ffc9bd6f8e9e7248ce39ccee23400ff8fb49cd05b877d730b553 SHA512 a7b3f7d149f6a29cf0b48bdb900f6983d42af01132d8b54a7be88994d09fcf27dbe57115d41ec9654da6daf6898d5986d08fbdcefa3a4c81af0d358500cd40c2 DIST tdbdata.tar.gz 40241247 BLAKE2B c85a2fde9b29a14e1da27be1a7ea5fe1704f72b66cd79514dd50a3a0d2d8aab9341f7d5075f6d1896cefa54ca83948387b902b38780181777dc505a9a15b4aab SHA512 f96d7ffbb77e129251e27f62b7f099d944bacd14935e03fc52c9f0b262cce1ad477ad43520a93b407951fb8f5dd3ba2e27ff6b5ae8a637ec03bc02f8c7c3990c -EBUILD psipred-3.5.ebuild 1215 BLAKE2B da6e40d6c96916d638aec4343a06be76705d0b0b729ab4332613e998539044780b76b94bdde12ebb01059ba1f5763c070dea0d13f2f1d934e1c3db1aaa4d2dab SHA512 8299f0b758e7192418794fcfaae2d81cc6b4f95dc0507b75b5aeac31c60318c9bfd7d0e9a307f23f163887ebe3af986b2c654d19e27bbf7d4111e56e46a1b649 +EBUILD psipred-3.5.ebuild 1215 BLAKE2B b51ae7660ff58dd8d8c738b0019cf935afa8e4049af536065348a5afdf4ac8bba3e8d49fbd456de633a6ab471a3a4c4dee126e213c3b76a8ca75401dbbc0be2c SHA512 dc506a260d7cefb6b632dae25410860c9efc2561581735eabdbf321c635b4347f1a8ba911abb326c7bf80d85b3ae945b483d538e12f21ef3255c5b3edc8a4e17 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/psipred/psipred-3.5.ebuild b/sci-biology/psipred/psipred-3.5.ebuild index 1fe4c6dced52..f5619ef4b544 100644 --- a/sci-biology/psipred/psipred-3.5.ebuild +++ b/sci-biology/psipred/psipred-3.5.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 -inherit eutils prefix toolchain-funcs versionator +inherit epatch prefix toolchain-funcs versionator #MY_P="${PN}$(delete_all_version_separators)" MY_P="${PN}${PV}" diff --git a/sci-biology/raxml/Manifest b/sci-biology/raxml/Manifest index 224df3f6ebf7..3b965935e19e 100644 --- a/sci-biology/raxml/Manifest +++ b/sci-biology/raxml/Manifest @@ -1,4 +1,4 @@ -AUX raxml-7.2.6-makefile.patch 777 BLAKE2B 294eff4ddc4046a4e29974c6f4850d040c9a7c4907415913da209b7f71eee336dfa439d446f67284b4eaabb413905012c867e38a2b44653e7f8b618537108a13 SHA512 0cc326e8fed0882c56193fef9d1c98577f2252acc4dc25e650e0806d89ded0e2911e6967272a6d101cf830cfe63a190a8f5220fd7573864f5fa60106069ad74f +AUX raxml-7.2.6-makefile.patch 786 BLAKE2B d6fc28b20fc3b00b33cefd93fa90f0db255eec642a3fd760baa5489ab90dbb31d9896fe7a595e9f2e4e47b53ab24e1ef2a80486dbe77062f835fce17687a50ae SHA512 955c1403dbae7d5308f10808c3689d04cd4bc6166647fd5d7c6a5eafca45b42f409a22642a57dc19a8f3ce4e00e2e554988ed5a02954ee85ab805759e60beeea DIST RAxML-7.2.6.tar.bz2 202803 BLAKE2B 579676ff9fad1563eabb9507015acff010977a89ae087df9b828b80bc9352ed44c98faeaf4c8d884ffa14176bfa28772dc9872ad8b5d401aff8b834c728e5f65 SHA512 b0027a7e583e6471a774d9e784a0be1ff63b3824a8cfbebca68bf9e414adab297206ea2d43c9b97456e6acc0a6a15f55ca33983381dd6150f9e7ea71ddecdcd3 -EBUILD raxml-7.2.6.ebuild 962 BLAKE2B d9ab298e6e8ac66ed9f2274fed8ed2b1f87d66a5532af63402bc7d4b14e8b50e558697ddb3a5654451c19f20a588962140d7cd073825794df6fed4cc5bf9179b SHA512 dd75e9c82ef3a3d2c3c2813690af6ac95548842e727c7819b63054d7e982b4ea7ebfd9020c4ee7b9f80bd0b38162c5559e25a19bf5a60efd2d63e3798fae243b +EBUILD raxml-7.2.6.ebuild 902 BLAKE2B 23d2b1a93bf50587d5bcacbaf261ad98eecd4e6d6d86bce62bad4459286bdb678c60ad5699cd22c5d6e03df4fb49ccd95c40bbb30f6ec7990e8f81518709aa66 SHA512 5583a0fcb21f80f1cc1d7fe282f56235b6b0add1699330652f8c6c669cbbb1975eb8e088f566252b897a94e5bb80f2738de538d570951bd7508b5a607324c34f MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/raxml/files/raxml-7.2.6-makefile.patch b/sci-biology/raxml/files/raxml-7.2.6-makefile.patch index ae83e2eef4e7..6b82ed65b770 100644 --- a/sci-biology/raxml/files/raxml-7.2.6-makefile.patch +++ b/sci-biology/raxml/files/raxml-7.2.6-makefile.patch @@ -14,7 +14,7 @@ index 716b6c6..f0c1de2 100644 -CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -msse -+CFLAGS += -D_GNU_SOURCE ++CPPFLAGS += -D_GNU_SOURCE @@ -23,7 +23,7 @@ index 716b6c6..f0c1de2 100644 raxmlHPC : $(objs) - $(CC) -o raxmlHPC $(objs) $(LIBRARIES) -+ $(CC) $(LDFLAGS) -o raxmlHPC $(objs) $(LIBRARIES) ++ $(CC) $(LDFLAGS) -o raxmlHPC $(objs) $(LIBRARIES) $(LIBS) classify.o : classify.c $(GLOBAL_DEPS) evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS) diff --git a/sci-biology/raxml/raxml-7.2.6.ebuild b/sci-biology/raxml/raxml-7.2.6.ebuild index 50fffc34accb..adb044426381 100644 --- a/sci-biology/raxml/raxml-7.2.6.ebuild +++ b/sci-biology/raxml/raxml-7.2.6.ebuild @@ -1,34 +1,29 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 -inherit eutils flag-o-matic toolchain-funcs +inherit flag-o-matic toolchain-funcs DESCRIPTION="Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees" HOMEPAGE="http://wwwkramer.in.tum.de/exelixis/software.html" SRC_URI="http://wwwkramer.in.tum.de/exelixis/software/RAxML-${PV}.tar.bz2" +S="${WORKDIR}/RAxML-${PV}" -SLOT="0" LICENSE="GPL-2" +SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="cpu_flags_x86_sse3 +threads" - REQUIRED_USE="cpu_flags_x86_sse3" # mpi is not supported in version 7.2.2. mpi is enabled by adding -DPARALLEL to CFLAGS -DEPEND="" # mpi? ( virtual/mpi )" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/RAxML-${PV}" - -src_prepare() { - epatch "${FILESDIR}"/${P}-makefile.patch +PATCHES=( "${FILESDIR}"/${P}-makefile.patch ) - use cpu_flags_x86_sse3 && append-cflags -D__SIM_SSE3 +src_configure() { + use cpu_flags_x86_sse3 && append-cppflags -D__SIM_SSE3 use threads && \ - append-cflags -D_USE_PTHREADS && \ - append-ldflags -pthread + append-cppflags -D_USE_PTHREADS && \ + append-libs -pthread tc-export CC } diff --git a/sci-biology/repeatmasker-libraries/Manifest b/sci-biology/repeatmasker-libraries/Manifest index a11add8140fa..682ae744e75b 100644 --- a/sci-biology/repeatmasker-libraries/Manifest +++ b/sci-biology/repeatmasker-libraries/Manifest @@ -1,3 +1,3 @@ DIST repeatmaskerlibraries-20120418.tar.gz 28059668 BLAKE2B 0683305f0d3045ff1bcb9f1c952d3c12e92a3003f79ba18a16334805049a64e0b307fac2cf7fad236c9b0cab80e3317ebb1d93bf6487bafd9d45de2455565879 SHA512 254d47faeee72ee62e6854ebc389578691d66e99d9d5e2a0c2462bf752ac5b4d2171c9e6b45d4f87f548a96b62753bb9c37c2d2c00e06544e91dd09fe2bbfe32 -EBUILD repeatmasker-libraries-20120418.ebuild 772 BLAKE2B e862447ecb7252ff0c0d7c034413a72ea245684f29e97d79092a56ced93fc4fe4fd7e40b28c021771dae3dd0173c86f9be4e3b3bdc6d0b87799b819f2830e4b4 SHA512 08ac03023c4384fb1f1eacdb34db3bd07563bbbeeb2d2e7df30f6567095a655b56bbf43946a25f2d3747f57566d1521d948804c24d2edcad739d084ad1cae9d9 +EBUILD repeatmasker-libraries-20120418.ebuild 741 BLAKE2B 5226277bfa19b7642ab426572f799318e54e823728297371b580038b60c3d9c6226156e889e8562c546fd06e1fb443811354062344d78a80addf84a7ff322dba SHA512 e72c9eb08d6cbf11199e3aaeb9b847afcc764857f9624a2c8d5e228160a5a058bf6d0e1521ddfb82c43104084a397f10a5164009598a25f06ae54d121908e7a2 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20120418.ebuild b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20120418.ebuild index aefecb784ba2..9445ce8e5278 100644 --- a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20120418.ebuild +++ b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20120418.ebuild @@ -1,22 +1,16 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 DESCRIPTION="A special version of RepBase used by RepeatMasker" HOMEPAGE="http://repeatmasker.org/" SRC_URI="repeatmaskerlibraries-${PV}.tar.gz" +S="${WORKDIR}/Libraries" LICENSE="all-rights-reserved" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND="" - -S="${WORKDIR}/Libraries" - RESTRICT="fetch" pkg_nofetch() { @@ -27,8 +21,9 @@ pkg_nofetch() { } src_install() { + HTML_DOCS=( README.html ) + einstalldocs + insinto /usr/share/repeatmasker/Libraries - doins "${S}"/RepeatMaskerLib.embl - dodoc README - dohtml README.html + doins RepeatMaskerLib.embl } diff --git a/sci-biology/rmblast/Manifest b/sci-biology/rmblast/Manifest index 10b761c8a307..aeebda0dc150 100644 --- a/sci-biology/rmblast/Manifest +++ b/sci-biology/rmblast/Manifest @@ -1,4 +1,4 @@ DIST rmblast-1.2-gcc47.patch.bz2 7803 BLAKE2B cd3bb1aa2b6eb9e188f28589d42ce91f027866d91013f2a6123ee61e7ce28f980b858e775bc15313cf1573f0bc827f9e663d46c1bd0d2fe218745cfbbc3781a1 SHA512 4cd72dd5c777ad866b9cf674384872de5424404b524ac536e58ab412b98b6601aa5f609d05ea2329b77f16e7aca215bbc6eb3531652e5fe81e48cf997b56d13b DIST rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz 10744076 BLAKE2B 6539ec8fcd345bcc1c3ecede6acec233cdc343c3df18748e195dc525f4a65fefeee8398471a26dc671bfed8612e010c26b7a8a66a3c7198f142c2e068ff72751 SHA512 e7c2ebd114aee045ea3f3f462cf2658440e13a2d1eb777648386e1c5eeda9f8083af383c019f9b5802d935d6eb2367eef20822afc45233ddb44a426b4dd7ddb6 -EBUILD rmblast-1.2-r1.ebuild 1194 BLAKE2B a9a30ea494d819720a50c194d80d8f63141c9f37101dbb8b2bbbaf79938aa2a21910932a1339bc944d4270c050633fa5a81ced90ddf43800710aa38211f5880d SHA512 75821816764975bbc935ff0e2edf4b0b30e9f8b5cad2e236512993da1cada6079876a36c7ee87aa9c1e95c7ce38e720ade531f0e261559571398d80364be0d2a +EBUILD rmblast-1.2-r1.ebuild 1191 BLAKE2B b096fcac217355ebecf8a33b1f145ae6482663e7437b78d1024858959d1653e2424f250d69fb238118751cb4133016fb17cc584f10a299bb6bcbae2a08806d53 SHA512 b2b4cd8e6eed2df9ff4a39783006515e57614dca8a14e38ae4335badb3af81056d4dad7aa377f78aafc659a06eb6cd8f184b60c4581771e2f6c077d3d635304a MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/rmblast/rmblast-1.2-r1.ebuild b/sci-biology/rmblast/rmblast-1.2-r1.ebuild index 72c740fd30e3..20a68f97763c 100644 --- a/sci-biology/rmblast/rmblast-1.2-r1.ebuild +++ b/sci-biology/rmblast/rmblast-1.2-r1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 -inherit eutils flag-o-matic toolchain-funcs +inherit epatch flag-o-matic toolchain-funcs MY_NCBI_BLAST_V=2.2.23+ diff --git a/sci-biology/sibsim4/Manifest b/sci-biology/sibsim4/Manifest index fc049c6f28a9..805e39d3ab00 100644 --- a/sci-biology/sibsim4/Manifest +++ b/sci-biology/sibsim4/Manifest @@ -1,3 +1,4 @@ +AUX sibsim4-0.20-makefile.patch 603 BLAKE2B 1d5bf536aec1c8d6716a2feeefc19d9397c8a8446899d40bdc58abe577ed5b4e7234b21bd428a831fcccd9ed0cdf6da70e9fda0db3070e3d51506b91b4324d01 SHA512 d434cf369ec418e29df7d34b139acf06182d84d1e83a7aaafe2d5df2ee49884ff86ad7fd5b6697108e7d1dea865652c8755459ff4ec0ae6395b1ec8c46126e55 DIST SIBsim4-0.20.tar.gz 32118 BLAKE2B 79b1f080d547732ee6a5996885c26f422f8a1590fa37d525f35cfa3dee353fd36ce9aa4677fe7e570f43e8283c26541c8c9e76ca03788a66d1c356adb3d649d5 SHA512 3802520095e83d3c691804b661696095a4198c4b2a16385c55ccdc8e4e836f82cc9c2251a5d37cb5918c2ee80aeb81737d751e6b065fbfe9c64f1aee3e0ea0c8 -EBUILD sibsim4-0.20.ebuild 639 BLAKE2B fa9d2b944f158ce6fea94566603e796a58f12fbdff8d94057f6e378bbd7e2cc251a7b38047af227284630157e9dd917128c852738f91a5bbfea79b3bad1aa4e3 SHA512 ef670faca5998f05252622a170e9faa3748b55a10af9a0556a49ef912cdd2e1d985100001846033da0708479112321557a34fb20ccb1b3e82149a79b2da92195 +EBUILD sibsim4-0.20.ebuild 518 BLAKE2B 0999e252ed6713e462f04dfa6d1ee0c48982ff614b54aa4126fae1ab4bcb615153abcef38806a193e32bce14daf9d7b22ff71a86d005b7c222b497dd7aff23be SHA512 903d8d9a98e31197a9018cb13d255a7ce7ca2cfc94d40f4fe8ee793ef2f8e7736907a6f37633b900b02430a842fae11e55ad1880e551807dc40e8069c2aff59f MISC metadata.xml 348 BLAKE2B 4765b3098d0a6ac9ac1f5677bc13ab1e767d4beb7d9fd02adedab808382a80ab9ad0acf994783bfbfd66fbb5c580459f569215426d713b8c385054586387012b SHA512 9628452f960b9837192126173a46e916bfa1f16421a470166ce3812d7e8d455a2f8eb5ba78ccb6f52e5d0acbbc009f31f0eabd5619bc864790c258220333aba0 diff --git a/sci-biology/sibsim4/files/sibsim4-0.20-makefile.patch b/sci-biology/sibsim4/files/sibsim4-0.20-makefile.patch new file mode 100644 index 000000000000..6436747e3dd9 --- /dev/null +++ b/sci-biology/sibsim4/files/sibsim4-0.20-makefile.patch @@ -0,0 +1,26 @@ +--- a/Makefile ++++ b/Makefile +@@ -21,13 +21,12 @@ + # to change it to this: + # CFLAGS = -Xc + +-CFLAGS = -std=gnu99 -W -Wall -Wconversion -pedantic $(DEBUG) $(OPT) ++CFLAGS += -std=gnu99 -Wall -Wconversion -pedantic + + + # The default is GCC. On Solaris, you might put: + # CC = /opt/SUNWspro/bin/cc + +-CC = gcc + + + # Depending on the compile flags you use, you might need to explicitly use the +@@ -42,7 +41,7 @@ + OBJS = sim4b1.o align.o misc.o sim4.init.o + + sim4: $(OBJS) +- $(CC) -o SIBsim4 $(CFLAGS) $(OBJS) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o SIBsim4 $(OBJS) $(LIBS) + + clean: + rm -f SIBsim4 *.o diff --git a/sci-biology/sibsim4/sibsim4-0.20.ebuild b/sci-biology/sibsim4/sibsim4-0.20.ebuild index bf431c666920..679cb462e045 100644 --- a/sci-biology/sibsim4/sibsim4-0.20.ebuild +++ b/sci-biology/sibsim4/sibsim4-0.20.ebuild @@ -1,31 +1,22 @@ -# Copyright 1999-2013 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 inherit toolchain-funcs DESCRIPTION="A rewrite and improvement upon sim4, a DNA-mRNA aligner" HOMEPAGE="http://sibsim4.sourceforge.net/" SRC_URI="mirror://sourceforge/${PN}/SIBsim4-${PV}.tar.gz" +S="${WORKDIR}/SIBsim4-${PV}" LICENSE="GPL-2" SLOT="0" -IUSE="" KEYWORDS="amd64 x86" -DEPEND="" -RDEPEND="" - -S="${WORKDIR}/SIBsim4-${PV}" +PATCHES=( "${FILESDIR}"/${P}-makefile.patch ) -src_prepare() { - sed \ - -e 's/CFLAGS = /CFLAGS +=/' \ - -e '/^CC/s:=:?=:' \ - -e '/^OPT/d' \ - -e "s:-o:${LDFLAGS} -o:g" \ - -i "${S}/Makefile" || die +src_configure() { tc-export CC } diff --git a/sci-biology/treeviewx/Manifest b/sci-biology/treeviewx/Manifest index 807e4bf5a789..e7b206537f60 100644 --- a/sci-biology/treeviewx/Manifest +++ b/sci-biology/treeviewx/Manifest @@ -1,11 +1,11 @@ -AUX treeviewx-0.5.1-70_choose_tree.patch 439 BLAKE2B 5730b4f8b20ef4be14fbd4956100571cf9b26ef697834773095a3f11f2510466bc0c85582c31c1e2d0fd113ab4540db394831abb5891e4ff36c6c5a44a8f5a73 SHA512 efe6e903929264359388f88288a95ea28d98efe1eb3dca6248801afa0ab44ee7afdf456f271d088f7b3231b1b9db58c5fde7b147c4ca76b5761d77a1139762bc +AUX treeviewx-0.5.1-70_choose_tree.patch 347 BLAKE2B deb36ebad2fce531b353376d3e115bafad9a21ee7ac62ea7cc9571733e2565903f85e733fc27cef306bb82b038e2bd16c7a69a7666af2aa9c7a04ea04319f244 SHA512 8e83180f7619e61ab6a6cdce7a576820a8e12fc2c0caf73b68c3943a98c7e618fcf0d477276b976039b594d60388a80a24f0502ebbc45ec1be371946f5c0cf1e AUX treeviewx-0.5.1-fix_loading_crash.patch 951 BLAKE2B 7fb391335a57114a9f8ee707ffe908839a064bbe6aeab05fe0b1af8928ccb0504d91ce9e25cc55a7762422f71978e28f1479adae11293249a8a67ce8536f8d05 SHA512 9c205520dce7851520b24532f88348906c4d5a7f0fe392348099ee9f7377b778792170620856d533a275251a024756482bbd4b83d1da8281b84c39cdf2b3a711 AUX treeviewx-0.5.1-gcc4.3.patch 2601 BLAKE2B 740a3efb736389fa0de40b0f2344e2767450809547189ef6cf659b05b6d80954550b5d5688e03a904ce6f8ec45866dff174cda0dbdbee5b0baff8cef86992240 SHA512 4629ad00ca712163fccbdb029dbb42970d432b2bcaf6b6345a7bf3dca2331ab988742a6dfbc8874e2624988c699b4ba1fff8032dda53afcffbd8264df62b480b AUX treeviewx-0.5.1-svg.patch 1181 BLAKE2B b647b33738af0a933d0a946aa15d02f67b87175c4845813e9f01578dad6a3052902cc946b2f13dfe19451595364094094e388d8838c6c67b1448f8a32a832a65 SHA512 d71ee136f4f47792ce98826d8f7bca18320f404937abd90cdacd2685f62ed28f48601a105dd1cfb9717891a8930be339b6a663b11784f305d03af0cba24b4c4f AUX treeviewx-0.5.1-treeview-xpm-not-xbm.patch 519 BLAKE2B 33a73602f4da18a723e292b0903a695add936697fbfd29ef978267f5e2ae1e1aa6dd49754c21900fabaf6259f732d7531f4d571f85ee544bc3d18f99961a31d4 SHA512 324b77dc43a99b55be45e1b561e528c8bb2f56ec4b1c7162987c848d0e6ea034efe262d910ee67fddcf0137b6eaeedfb50f26b8b2106b0459582942f5eccfbd4 -AUX treeviewx-0.5.1-wx30.patch 2211 BLAKE2B a0327c8a4238d0ff3aa0f7e108dc6df85a9e025862e1a72bd80669bb11f692d7b3033f6f9fe8dab5464731658434ecfa56423cdf4c3d8ac2056abffe4298b929 SHA512 0f1c05495badabba586d88a6fd0e3610b28dc5779c036d3da4956de6c5e02aabf1ef59e9aceffe85cc78ea582329965f6e228774ad6a944d91542e8bacb5daa6 +AUX treeviewx-0.5.1-wx30.patch 1722 BLAKE2B bc7d24b8b3953316ea4f8cb9eb26ab78fb7aee2adfce63f1ad6a758eb7d061badbcaf305d913c23fbf84773ead36242ec6995b476a1b795eb4110bc67ed4d135 SHA512 3efeea31429d623c65c958fc0ec859918e8e8b52d83973f7c7a131e47894093a2cbaafbb69c9a962ba12c0cf1ad733f2bf6d605888800d42a784d7bf3535c071 AUX treeviewx-0.5.1-wxstring-maxlen.patch 1438 BLAKE2B a2dc6fe39c0312559628b61d86975a21db846e4c7cc3a0bb5739dd971417abd3ab9187ea56ef44d37c0394b28d4017981073eb4d890622d0d929f7a4d428950f SHA512 6e02ac59e8a28da8e94d5d6fdea71b3db9bc4501d9becf2d7aa6472d3f9f9b571fe68730390fd4cf6e1e422d618c21c40d86442d6b710e8395db107fc3445392 -AUX treeviewx-wxt.patch 1854 BLAKE2B 2b11d2395d6a2f8cde176feb04bcadca3c8fbd9ee3bc48fdb8f3d20c5d2f268fcf20f1f2f7bb9fe6263be2518610f2b87e2cdcf86d254185f81ada5484ef5248 SHA512 35f9682bd8f17a2d2436ae6c0b729bcb766fd848b9b24e3f17577e4cef0cd6fd820a8686818feaf6e1414c0f10891bac0befa818a9befc337fd5e87f5120e520 +AUX treeviewx-wxt.patch 1716 BLAKE2B f869d1d90dd23a7f0e242d9c1d0b0b97e0e053b5b2f00b283073f6e7f2d714cd2bf23656e65af1f3496bef0bf681ebb0618024f259b7f4d6dea777b048a438e4 SHA512 97d074e9501000099d0c5b3e3f56a796b1526499d4ccb44ef6f0b851bde1c27fc78bbc64f439ba5ecd3afa531b752c69148d7cd3b1e5a08a01566ad6155ce25c DIST tv-0.5.1.tar.gz 426745 BLAKE2B 080c4e09f441fd83da3406990bbe97f9e29fa531f47a65533ca887580f8a3ec561bb4766e66e2ef4764f68eee86fdabf48481cece56ddda90f9ffdc3c80b3a1a SHA512 45a7ac6dff5b22771e4428d6b1ee528c0039956a462658d28d4f588b6df32620d8f69b3bcf5ca23643e2bdd5361da00625fcb1495bcf4f74d44ee22022c63143 -EBUILD treeviewx-0.5.1-r3.ebuild 894 BLAKE2B 57111a7a18629dcfb207b2acd256db107324b4308240d55e656ca2eb9dea762b950109cf03e938ef09ef9d91ba2b101631871cfbdd4e72ee9ff0ce9bdac46614 SHA512 316d9b8359813322cf77338aae8b7f687d4a40ca52cd70d739fbf76b28a188e45ac97d430b90fdec2b2c0e081de868cc3c842d0a94a56c8f3d0124eac058ffa9 +EBUILD treeviewx-0.5.1-r3.ebuild 908 BLAKE2B 5d52ec68fa05f79848314599bb9b4a22378de9e26a5d958327f948780634a2de1a6155449968cc330f459525fb50ef28a5158e37bff9ae0e658174a2e92162a5 SHA512 92012299b8ca8dc97529c308e989258fd842e6c76bde1c267891afed198aa8c6ffd3b1f301b18c356613ecca47c32e61f60e2491d04a54d54f2eebfba874eb0d MISC metadata.xml 530 BLAKE2B e28ef45f05b4ade77b26155b743afe8e72989065c4dba57b7a645e738366afff1d99c827dc1ea1f5cdb192ae2ef790be6de9a6905eeebd58e792e5d4e02b0dcb SHA512 28c429150fb8df5db3205b352f077fe431f3e2ca530195468a340909a3b37882fae67e05452a7810ac34ffb8a02979625b48c28285a7d3abf31004238fce1463 diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-70_choose_tree.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-70_choose_tree.patch index ed5aa43e23c3..7a614edff72e 100644 --- a/sci-biology/treeviewx/files/treeviewx-0.5.1-70_choose_tree.patch +++ b/sci-biology/treeviewx/files/treeviewx-0.5.1-70_choose_tree.patch @@ -1,9 +1,8 @@ -## 70_choose_tree.dpatch by William Alexander Grant <william.grant@ubuntu.com.au> ---- tv-0.5.orig/tview.cpp -+++ tv-0.5/tview.cpp -@@ -209,7 +209,7 @@ - wxT("SVG vector picture files (*.svg)|*.svg"), - wxSAVE|wxOVERWRITE_PROMPT); +--- a/tview.cpp ++++ b/tview.cpp +@@ -208,7 +208,7 @@ + pictureFileName, wxT("SVG vector picture files (*.svg)|*.svg"), + wxSAVE|wxOVERWRITE_PROMPT); - if (dialog.ShowModal() == wxID_OK) + if ((dialog.ShowModal() == wxID_OK) && (p.GetNumTrees() != 0)) diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-wx30.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-wx30.patch index b1db5749990c..a1cfd906f176 100644 --- a/sci-biology/treeviewx/files/treeviewx-0.5.1-wx30.patch +++ b/sci-biology/treeviewx/files/treeviewx-0.5.1-wx30.patch @@ -1,14 +1,6 @@ - tv.cpp | 4 ++-- - tview.cpp | 12 ++++++++---- - 2 files changed, 10 insertions(+), 6 deletions(-) - -diff --git a/tv.cpp b/tv.cpp -old mode 100755 -new mode 100644 -index 1abe90b..0df45a8 --- a/tv.cpp +++ b/tv.cpp -@@ -163,9 +163,9 @@ bool MyApp::OnInit(void) +@@ -163,9 +163,9 @@ { // Optional command line argument is name of file to open #if wxUSE_UNICODE @@ -20,10 +12,6 @@ index 1abe90b..0df45a8 #endif // Read input/output files if (argc > 1) -diff --git a/tview.cpp b/tview.cpp -old mode 100755 -new mode 100644 -index 93972c3..4b2d593 --- a/tview.cpp +++ b/tview.cpp @@ -62,9 +62,13 @@ @@ -40,7 +28,7 @@ index 93972c3..4b2d593 // GUI interface #include "tv.h" -@@ -186,7 +190,7 @@ void TView::OnSavePicture (wxCommandEvent& WXUNUSED(event)) +@@ -186,7 +190,7 @@ wxFrame *f = GetMainFrame(); wxFileDialog dialog((wxWindow *)f, wxT("Save Picture as"), wxT(""), pictureFileName, wxT("Enhanced metafile (*.emf)|*.emf"), @@ -49,16 +37,16 @@ index 93972c3..4b2d593 if (dialog.ShowModal() == wxID_OK) { -@@ -206,7 +210,7 @@ void TView::OnSavePicture (wxCommandEvent& WXUNUSED(event)) +@@ -206,7 +210,7 @@ #endif wxFileDialog dialog((wxWindow *)f, wxT("Save Picture as"), wxT(""), pictureFileName, wxT("SVG vector picture files (*.svg)|*.svg"), - wxSAVE|wxOVERWRITE_PROMPT); + wxFD_SAVE|wxFD_OVERWRITE_PROMPT); - if (dialog.ShowModal() == wxID_OK) + if ((dialog.ShowModal() == wxID_OK) && (p.GetNumTrees() != 0)) { -@@ -361,7 +365,7 @@ bool TView::OnClose(bool deleteWindow) +@@ -361,7 +365,7 @@ // Clear the canvas in case we're in single-window mode, // and the canvas stays. @@ -67,7 +55,7 @@ index 93972c3..4b2d593 canvas->ClearBackground(); #else canvas->Clear(); -@@ -686,7 +690,7 @@ void TView::OnLeafFont (wxCommandEvent& WXUNUSED(event)) +@@ -686,7 +690,7 @@ wxFontData data; data.SetInitialFont (LeafFont); diff --git a/sci-biology/treeviewx/files/treeviewx-wxt.patch b/sci-biology/treeviewx/files/treeviewx-wxt.patch index b1c03bbb39f9..a971e1a85074 100644 --- a/sci-biology/treeviewx/files/treeviewx-wxt.patch +++ b/sci-biology/treeviewx/files/treeviewx-wxt.patch @@ -1,5 +1,5 @@ ---- tv.cpp~ 2005-10-01 16:47:35.000000000 -0400 -+++ tv.cpp 2005-10-01 16:52:30.000000000 -0400 +--- a/tv.cpp ++++ b/tv.cpp @@ -312,11 +312,15 @@ { #ifdef __WXMSW__ @@ -18,8 +18,8 @@ #endif #endif file_menu->AppendSeparator(); ---- tview.cpp~ 2005-10-01 16:47:45.000000000 -0400 -+++ tview.cpp 2005-10-01 16:50:42.000000000 -0400 +--- a/tview.cpp ++++ b/tview.cpp @@ -184,10 +184,10 @@ wxString pictureFileName = GetFrame()->GetTitle(); pictureFileName += wxT(".emf"); diff --git a/sci-biology/treeviewx/treeviewx-0.5.1-r3.ebuild b/sci-biology/treeviewx/treeviewx-0.5.1-r3.ebuild index 7d1fe1c773e0..6ef3961e4df8 100644 --- a/sci-biology/treeviewx/treeviewx-0.5.1-r3.ebuild +++ b/sci-biology/treeviewx/treeviewx-0.5.1-r3.ebuild @@ -1,25 +1,22 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 -WX_GTK_VER=3.0 - -inherit autotools eutils wxwidgets +WX_GTK_VER="3.0" +inherit autotools wxwidgets DESCRIPTION="A phylogenetic tree viewer" HOMEPAGE="http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/" SRC_URI="http://darwin.zoology.gla.ac.uk/~rpage/${PN}/download/0.5/tv-${PV}.tar.gz" -LICENSE="GPL-2" +S="${WORKDIR}/tv-${PV}" -KEYWORDS="amd64 x86" +LICENSE="GPL-2" SLOT="0" -IUSE="" - -DEPEND="x11-libs/wxGTK:${WX_GTK_VER}[X]" -RDEPEND="${DEPEND}" +KEYWORDS="amd64 x86" -S="${WORKDIR}/tv-${PV}" +RDEPEND="x11-libs/wxGTK:${WX_GTK_VER}[X]" +DEPEND="${RDEPEND}" PATCHES=( "${FILESDIR}"/${PN}-wxt.patch @@ -30,10 +27,15 @@ PATCHES=( "${FILESDIR}"/${P}-svg.patch "${FILESDIR}"/${P}-treeview-xpm-not-xbm.patch "${FILESDIR}"/${P}-wxstring-maxlen.patch - ) +) src_prepare() { - epatch "${PATCHES[@]}" + default mv configure.{in,ac} || die eautoreconf } + +src_configure() { + setup-wxwidgets + default +} diff --git a/sci-biology/update-blastdb/Manifest b/sci-biology/update-blastdb/Manifest index 06c56e8f3e33..8c4972f793b2 100644 --- a/sci-biology/update-blastdb/Manifest +++ b/sci-biology/update-blastdb/Manifest @@ -1,3 +1,3 @@ DIST ncbi_cxx--12_0_0.tar.gz 37925914 BLAKE2B 45490961293d8b3ace24c21602f4039041003f9b45d9f1763957c97ba1e55d6d336c33b6116262b2e774cc26b9366cc3d61bead0c0c7fbd4c461cad2921d80d4 SHA512 1a79f2d95960efde6263289814102499460ec235dad36337dd398d668665e44015e06e40fd0e66a8fb16f526d326949adcaadcb667debeba5d8570b1a92e30ed -EBUILD update-blastdb-12.0.0.ebuild 654 BLAKE2B 4a41a73d1047ae8cc8fdcb8f7eab348dc56ff8213b32fa4c55eeb4751496d342ceb8f1ca153b953abd3769290887afe65f60f1a9cf4525fa87218ddae533a588 SHA512 3d83521ff73cb97d9f816b61e0aa30ceb690b4720d3486d1c377c9d4da7bb168d22e43d40ce3edd85dd1d7a8a133084734895223a0eb3ea5b7bf420d093ddb92 +EBUILD update-blastdb-12.0.0.ebuild 590 BLAKE2B cdce0586b4f0f74dc8e541830cd36b6e75098a9c741337ed9b07697c3d32d7637bf8d2da02d300540526affb25d34876738008fb732ff0fc59db3ba2e89c3429 SHA512 641587a3b01422516add65044172b56c0825e4b26b32171c9bc728b4e7fcac5a8de4bdb89fad1cc11e4e84ffea90b02bd704110086ce34a26cb4bc698be6d0e0 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/update-blastdb/update-blastdb-12.0.0.ebuild b/sci-biology/update-blastdb/update-blastdb-12.0.0.ebuild index e1524b487a03..293055ff1633 100644 --- a/sci-biology/update-blastdb/update-blastdb-12.0.0.ebuild +++ b/sci-biology/update-blastdb/update-blastdb-12.0.0.ebuild @@ -1,27 +1,22 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 -inherit versionator - -MY_PV="$(replace_all_version_separators _)" +MY_PV="$(ver_rs 1- _)" DESCRIPTION="update_blastdb.pl for local blast db maintainance" HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit" SRC_URI="ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/${MY_PV}/ncbi_cxx--${MY_PV}.tar.gz" +S="${WORKDIR}" -SLOT="0" LICENSE="public-domain" +SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" RDEPEND=" dev-lang/perl !sci-biology/ncbi-tools++" -DEPEND="" - -S="${WORKDIR}" src_install() { dobin ncbi_cxx--${MY_PV}/src/app/blast/update_blastdb.pl diff --git a/sci-biology/velvet/Manifest b/sci-biology/velvet/Manifest index 40f51b903d70..c1f07d33f7b9 100644 --- a/sci-biology/velvet/Manifest +++ b/sci-biology/velvet/Manifest @@ -1,3 +1,3 @@ DIST velvet_1.2.10.tgz 18818559 BLAKE2B 5723c9c040e570cd88b774e5b0044dd04def88778fe2b137ec7c007ab83fc98e5423ad1d9d0499780cf6d3152347ca1a4e4e6b6c1900ce4adfc4930f1f6d3c34 SHA512 a6f3e35cebceb22cc10e83088b8cd9758492da78866237cae63d8826d6f5cfb44d82dd8bfcb1185d37cd434d4c7a0f2ac7135bb80a51db86e754afd6156ea874 -EBUILD velvet-1.2.10.ebuild 2106 BLAKE2B d7ea6a576303cffaf8785fc125b6848d3dde0775756867c952d196f0f1e55959e5d7a3b29c0096108208db043658d5f7e382e3ef701b20c4c6a383cc3f561934 SHA512 6c02607cd77b12cd2a64a92cc2a469994aba906823b3acf5c36537749a6268e8766bbc4e319d057430204af1ae36c9351f68ff579d4065048851fac9e12ccc3b +EBUILD velvet-1.2.10.ebuild 2096 BLAKE2B 3a85f8e1a24af2e9794be70bfe691f7df2e2321619af96b5fcac5b8b0d445b96d258b2b9cd6d4474e05fb60559fc1e3015229d1fc933378974ec795129f15aed SHA512 96bc66027211a3700bcac197fc7c2de3bec34b44f5a39bee4ef7d25f2247617351fca293ebfde1c64f4b7931b41cc5bda87515a3b05d1fe5d308d3879fabe89d MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/velvet/velvet-1.2.10.ebuild b/sci-biology/velvet/velvet-1.2.10.ebuild index 3de28bdb7481..b4d8ae8641b2 100644 --- a/sci-biology/velvet/velvet-1.2.10.ebuild +++ b/sci-biology/velvet/velvet-1.2.10.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 -inherit eutils flag-o-matic toolchain-funcs +inherit flag-o-matic toolchain-funcs MY_P=${PN}_${PV} diff --git a/sci-biology/wise/Manifest b/sci-biology/wise/Manifest index ba7c4502f898..36db61e514cd 100644 --- a/sci-biology/wise/Manifest +++ b/sci-biology/wise/Manifest @@ -1,4 +1,4 @@ DIST wise-2.4.0_alpha-patchset.tar.bz2 7244 BLAKE2B 3c921b61e6a30515d790abd8168b5fbc4f8add44f1133cf7d163a98a6935a74ae7c9f79b72874a509bb743aa5b340c92a049ad091380f9cd33b0b9154cca5974 SHA512 ca73f1b03e14cef44d84484c64d06c4856d6ef33b7434de5ac58725cea1d071d875a7b073fc181da33a7490c4f086f674a9a52db4d36e78f4f5b75b28b855cfe DIST wise2.4.0alpha.tar.gz 3296399 BLAKE2B a7fbac022c62606ce865250f4091497e9c86331d2d2050fc4f69614aa5e95313eac3a0fcd49451c724c9b50bc6ac63700cd44828736b7a4d15eff2bc21fc29ec SHA512 a2288d7304e7768328689514a986aeff62a0ca6538ee61177a434fb08065f83ab5db39e0cb9101dd8ae9a91f7d95d05528d7ad23df0c394587717c584bf2341c -EBUILD wise-2.4.0_alpha.ebuild 1740 BLAKE2B bc82688af330de9693862d767503e0c96e17483fd1631be4d60ff7952de8af77cf3ceacdcb35ff081faa39f024fbc11202a92e7992c8fae080650ea51b35596b SHA512 345ff496a93020ad0b219b83b53ee8c21eb287384559573cc7101e976022c78c42322a2f05a1f89acce6af4252e2d544719f2072cf80003beb70a3dc00d0c02d +EBUILD wise-2.4.0_alpha.ebuild 1737 BLAKE2B 29ae17532ef9a4919db09b4f6b71b92f3b89d1a03b75b1ce90a1defe49ea9d572d9e902620a6d267ad8fc77506a25fda84ede0804f4f0676ba8a0eb41df049c9 SHA512 b73b8fd3a78cdcdda2c39326bbd4dfd99c2828c38ae78537b33c8ea50291323841d0d348eb2b6965cfe1986d808f26ef83e115715fa7c14e31cb7a7e337d867c MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/wise/wise-2.4.0_alpha.ebuild b/sci-biology/wise/wise-2.4.0_alpha.ebuild index aa971e0c6932..c37a8972e84e 100644 --- a/sci-biology/wise/wise-2.4.0_alpha.ebuild +++ b/sci-biology/wise/wise-2.4.0_alpha.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 -inherit eutils toolchain-funcs versionator +inherit epatch toolchain-funcs versionator DESCRIPTION="Intelligent algorithms for DNA searches" HOMEPAGE="http://www.ebi.ac.uk/Wise2/" |