From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-biology/fasttree/Manifest | 14 +++++++ sci-biology/fasttree/fasttree-2.1.7.ebuild | 47 ++++++++++++++++++++++ sci-biology/fasttree/fasttree-2.1.8.ebuild | 47 ++++++++++++++++++++++ sci-biology/fasttree/files/CMakeLists.txt | 30 ++++++++++++++ .../files/fasttree-2.1.7-format-security.patch | 25 ++++++++++++ .../files/fasttree-2.1.8-format-security.patch | 25 ++++++++++++ sci-biology/fasttree/metadata.xml | 14 +++++++ 7 files changed, 202 insertions(+) create mode 100644 sci-biology/fasttree/Manifest create mode 100644 sci-biology/fasttree/fasttree-2.1.7.ebuild create mode 100644 sci-biology/fasttree/fasttree-2.1.8.ebuild create mode 100644 sci-biology/fasttree/files/CMakeLists.txt create mode 100644 sci-biology/fasttree/files/fasttree-2.1.7-format-security.patch create mode 100644 sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch create mode 100644 sci-biology/fasttree/metadata.xml (limited to 'sci-biology/fasttree') diff --git a/sci-biology/fasttree/Manifest b/sci-biology/fasttree/Manifest new file mode 100644 index 000000000000..fcba17331e2a --- /dev/null +++ b/sci-biology/fasttree/Manifest @@ -0,0 +1,14 @@ +AUX CMakeLists.txt 948 SHA256 60c21f04ea3ef04782dfc0328e317b6d04197a45af4d15c5c43f4f87a1f82c44 SHA512 9858800bfce8d256ccb834a06bad5a5230f90f025a9c9b3c9aafe7244d219d66810530f6688e02889cdb67d6a9459d8e26cd1a9fcf2e8825278b31d0e8d51ff3 WHIRLPOOL edc50a85eaec6161924f38569c33ccd35170f9ac89e17741e4a87ceb350b165fdf6e118c20bfd27a02ec1e01aa76be8665908f39c531a292d3d1b706e6c1b25a +AUX fasttree-2.1.7-format-security.patch 783 SHA256 83e4b1b6de9fb5f8875a4d53ed274866bb34bbb36610b0f7bbda22ebea60fd07 SHA512 cabda061de75a1e1b34732946448ee08717f265d7fa8ea413f56eb8bad150ebde9f376a13591167a7786caf17a0d4bb1f8cb7176b74965a47f79b9608d32bcf8 WHIRLPOOL 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SHA512 39a7d284412a602208c2a5df3d0a9a30fe3a584f7f7788d741fb1463b698692017f47bb23f70046d0873e9c8fd27c84ec23f6ca48adb0594193765ac732e6559 WHIRLPOOL 31331c85584c2030f56955e79250c6d6c06147007c6dd10f324c207fdebd4a1b89c87dcce52e5bab6e8d89cc69656d95a51bd808f52b8d61f6d29af40a5d4976 +DIST FastTreeUPGMA-2.1.7.c 95271 SHA256 199acc84910ca899dae9dd96d2ea133b651e76bbd855363cf620bf1b3cbd3abd SHA512 4d6a8e2cb28b8ee201091172a3baa59d432420839c6d2244b5fb8230ed9daa626b6bed22cb692393ca3d78b8f2d071fe18fbb4f9bdcdc47ef149c31e3f45546c WHIRLPOOL 538b44382137e6055452c901c76007b1c388a541c193c37f7baff26e59eb477450ce8acf7466d5debe0bc973fecc645d1f88d54f6f871670826bb151fd5b7496 +DIST FastTreeUPGMA-2.1.8.c 95271 SHA256 199acc84910ca899dae9dd96d2ea133b651e76bbd855363cf620bf1b3cbd3abd SHA512 4d6a8e2cb28b8ee201091172a3baa59d432420839c6d2244b5fb8230ed9daa626b6bed22cb692393ca3d78b8f2d071fe18fbb4f9bdcdc47ef149c31e3f45546c WHIRLPOOL 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3dcf70859370142cfdf2212c76a7bec530b440c7f6eb862688086487f8cbd178 SHA512 0f229a132f237f11ac0fdd15083745e71fbb5072fe58afcc1ed1d41050520d3da030e23f57ed50fc3c2460c123b5a4d5665242caf21408b5c032828e8fe2cc46 WHIRLPOOL 5f3d492775aac0917ca498e217fea3bc3de6eed8c91a55e5bbf4746c8e203a9fbeb21e2ba51ab8d6710620c340e2b25d764873b554dc5cb7404f4f235dbe921d +EBUILD fasttree-2.1.8.ebuild 1193 SHA256 904c1f11c30a54ef6749904cded02ceec9fe0c3259837645e148c6df0e707e51 SHA512 e14223969bdac00b28a2223ce500cf6acf9d2d964f9bb5e55b6ebd22fa453e88a8943d195c655c4f6c246cf1dddac7c6f06aeab7d8f4e35f596192674ca2fa3f WHIRLPOOL ea6b5f089e6cd25a59eb27b56d74287872dc17238089481781da480b76fe63a83a517c1fba3e2b2a21df9cccd20f38b01702a5af64baeffdab3ee18a6aea79dd +MISC ChangeLog 2604 SHA256 9d0e0f54b5b644d8e731a814d8825004c81801636acb4ac83541e766ff19bab1 SHA512 7e045f1d7f3ae8b88b103a3ad7ed2816357c76617d7be6c6b5c735ef4dd736112d385bff14ef75bc4d1570333aacf7c7a641ccc3674cdee455f55c71ae480e01 WHIRLPOOL 8b73fdd334955af4fc9112ed76b36fcc5519369eeac55548a7961e2161de541926c1ed5e923bc865c248579098ccdd8151acad6b2ead9a4fc7e0749135a246c0 +MISC ChangeLog-2015 1505 SHA256 bd24d5bdac6616a54937c42b0492276ebeb20109a33850b2b6076937db1ee53d SHA512 15c646ec4e0f55f8aa572926b7ca87babac5b7aec34a7121ffd0a3fd20c799f81d47e41198d79389f53bf32fe5882070e3d6aa1e75808945cb709a3e987f776f WHIRLPOOL feee169c62e088f5c2c93a03c4a74ebd5889209e056f3a9dea2763dffa71579b47d1067d09c43fbddc4d12575d88d6a8f1c9e9415df57d36d35c5530e78fe5d8 +MISC metadata.xml 416 SHA256 f0bcc143c0fc170b2a4406f972f9166d5b561d1c261575e1e11fae6741c88785 SHA512 35edf392bfe7f9495120b6f156d8a37262029386f262b1e5c4d12e2b0436e78c8ba98db3d13e0f006909e45bcc13aec80e775b38efd7de1ad20b78c74c21b421 WHIRLPOOL 1673750cd290ce87f08e50b824c5073bf4b18c65c8cf52f08aad634590fd3786a875ad39f13a36fd002ffbbda135504c444f5e7927b83621642ce8df592f3c98 diff --git a/sci-biology/fasttree/fasttree-2.1.7.ebuild b/sci-biology/fasttree/fasttree-2.1.7.ebuild new file mode 100644 index 000000000000..aa5979522691 --- /dev/null +++ b/sci-biology/fasttree/fasttree-2.1.7.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit cmake-utils + +DESCRIPTION="Fast inference of approximately-maximum-likelihood phylogenetic trees" +HOMEPAGE="http://www.microbesonline.org/fasttree/" +SRC_URI=" + http://www.microbesonline.org/fasttree/FastTree-${PV}.c + http://www.microbesonline.org/fasttree/FastTreeUPGMA.c -> FastTreeUPGMA-${PV}.c + http://www.microbesonline.org/fasttree/MOTreeComparison.tar.gz -> MOTreeComparison-${PV}.tar.gz +" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="double-precision openmp cpu_flags_x86_sse3" + +REQUIRED_USE="?? ( double-precision cpu_flags_x86_sse3 )" + +DOCS=( README ) + +PATCHES=( "${FILESDIR}"/${P}-format-security.patch ) + +src_unpack() { + mkdir "${S}" || die + cd "${S}" || die + unpack ${A} + cp "${DISTDIR}"/{FastTreeUPGMA-${PV}.c,FastTree-${PV}.c} . || die +} + +src_prepare() { + cp "${FILESDIR}"/CMakeLists.txt . || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DVERSION="${PV}" + $(cmake-utils_use_has cpu_flags_x86_sse3 sse3) + $(cmake-utils_use_use openmp) + $(cmake-utils_use_use double-precision double) + ) + cmake-utils_src_configure +} diff --git a/sci-biology/fasttree/fasttree-2.1.8.ebuild b/sci-biology/fasttree/fasttree-2.1.8.ebuild new file mode 100644 index 000000000000..7df71ee4474d --- /dev/null +++ b/sci-biology/fasttree/fasttree-2.1.8.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit cmake-utils + +DESCRIPTION="Fast inference of approximately-maximum-likelihood phylogenetic trees" +HOMEPAGE="http://www.microbesonline.org/fasttree/" +SRC_URI=" + http://www.microbesonline.org/fasttree/FastTree-${PV}.c + http://www.microbesonline.org/fasttree/FastTreeUPGMA.c -> FastTreeUPGMA-${PV}.c + http://www.microbesonline.org/fasttree/MOTreeComparison.tar.gz -> MOTreeComparison-${PV}.tar.gz +" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="double-precision openmp cpu_flags_x86_sse3" + +REQUIRED_USE="?? ( double-precision cpu_flags_x86_sse3 )" + +DOCS=( README ) + +PATCHES=( "${FILESDIR}"/${P}-format-security.patch ) + +src_unpack() { + mkdir "${S}" || die + cd "${S}" || die + unpack ${A} + cp "${DISTDIR}"/{FastTreeUPGMA-${PV}.c,FastTree-${PV}.c} . || die +} + +src_prepare() { + cp "${FILESDIR}"/CMakeLists.txt . || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DVERSION="${PV}" + $(cmake-utils_use_has cpu_flags_x86_sse3 sse3) + $(cmake-utils_use_use openmp) + $(cmake-utils_use_use double-precision double) + ) + cmake-utils_src_configure +} diff --git a/sci-biology/fasttree/files/CMakeLists.txt b/sci-biology/fasttree/files/CMakeLists.txt new file mode 100644 index 000000000000..e7c53afdaf36 --- /dev/null +++ b/sci-biology/fasttree/files/CMakeLists.txt @@ -0,0 +1,30 @@ +cmake_minimum_required (VERSION 2.6) +project(fasttree C) + +option(USE_OPENMP "Use OpenMP to parallelize many of the steps in computing a tree" ON) +option(USE_DOUBLE "Use double precission" OFF) +option(HAS_SSE3 "Use SSE2/SSE3 instructions to speed up some inner loops" ON) + +if(USE_OPENMP) + SET( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DOPENMP -fopenmp" ) + SET( CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -DOPENMP -fopenmp" ) +endif(USE_OPENMP) + +if(USE_DOUBLE) + SET( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DUSE_DOUBLE" ) +endif(USE_DOUBLE) + +if(NOT HAS_SSE3) + SET( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DNO_SSE" ) +endif(NOT HAS_SSE3) + + +add_executable(FastTree FastTree-${VERSION}.c) +add_executable(FastTreeUPGMA FastTreeUPGMA-${VERSION}.c) + +target_link_libraries(FastTree m) +target_link_libraries(FastTreeUPGMA m) + +install (TARGETS FastTree FastTreeUPGMA DESTINATION bin) + +install(FILES MOTree.pm CompareTree.pl CompareToBootstrap.pl DESTINATION share/fasttree) diff --git a/sci-biology/fasttree/files/fasttree-2.1.7-format-security.patch b/sci-biology/fasttree/files/fasttree-2.1.7-format-security.patch new file mode 100644 index 000000000000..31dafdad46de --- /dev/null +++ b/sci-biology/fasttree/files/fasttree-2.1.7-format-security.patch @@ -0,0 +1,25 @@ + FastTreeUPGMA-2.1.7.c | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/FastTreeUPGMA-2.1.7.c b/FastTreeUPGMA-2.1.7.c +index af76cb1..4065f42 100644 +--- a/FastTreeUPGMA-2.1.7.c ++++ b/FastTreeUPGMA-2.1.7.c +@@ -535,7 +535,7 @@ int main(int argc, char **argv) { + break; + } + if(iArg < argc-1) { +- fprintf(stderr, usage); ++ fprintf(stderr, "%s", usage); + exit(1); + } + +@@ -953,7 +953,7 @@ void PrintUPGMA(FILE *fp, UPGMA_t *UPGMA, char **names, + assert(first >= 0); + /* Print the name, or the subtree of duplicate names */ + if (nameNext[first] == -1) { +- fprintf(fp, names[uniqueFirst[node]]); ++ fprintf(fp, "%s", names[uniqueFirst[node]]); + } else { + fprintf(fp,"(%s:0.0",names[first]); + int iName = nameNext[first]; diff --git a/sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch b/sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch new file mode 100644 index 000000000000..15f5c174ec40 --- /dev/null +++ b/sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch @@ -0,0 +1,25 @@ + FastTreeUPGMA-2.1.8.c | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/FastTreeUPGMA-2.1.8.c b/FastTreeUPGMA-2.1.8.c +index af76cb1..4065f42 100644 +--- a/FastTreeUPGMA-2.1.8.c ++++ b/FastTreeUPGMA-2.1.8.c +@@ -535,7 +535,7 @@ int main(int argc, char **argv) { + break; + } + if(iArg < argc-1) { +- fprintf(stderr, usage); ++ fprintf(stderr, "%s", usage); + exit(1); + } + +@@ -953,7 +953,7 @@ void PrintUPGMA(FILE *fp, UPGMA_t *UPGMA, char **names, + assert(first >= 0); + /* Print the name, or the subtree of duplicate names */ + if (nameNext[first] == -1) { +- fprintf(fp, names[uniqueFirst[node]]); ++ fprintf(fp, "%s", names[uniqueFirst[node]]); + } else { + fprintf(fp,"(%s:0.0",names[first]); + int iName = nameNext[first]; diff --git a/sci-biology/fasttree/metadata.xml b/sci-biology/fasttree/metadata.xml new file mode 100644 index 000000000000..802ef76f0cb9 --- /dev/null +++ b/sci-biology/fasttree/metadata.xml @@ -0,0 +1,14 @@ + + + + + sci-biology@gentoo.org + Gentoo Biology Project + + + + use double precision instead of single-precision floating point + (2x memroy required) + + + -- cgit v1.2.3