sci-biology/fasttree: Version BUmp, #494662

Package-Manager: portage-2.2.7/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

5 files changed, 112 insertions, 9 deletions

diff --git a/sci-biology/fasttree/ChangeLog b/sci-biology/fasttree/ChangeLog
index 52ca7a8ed7f3..f4cc081eadaf 100644
--- a/sci-biology/fasttree/ChangeLog
+++ b/sci-biology/fasttree/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/fasttree
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/fasttree/ChangeLog,v 1.3 2013/03/11 15:11:35 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/fasttree/ChangeLog,v 1.4 2013/12/20 09:20:44 jlec Exp $
+
+*fasttree-2.1.7 (20 Dec 2013)
+
+  20 Dec 2013; Justin Lecher <jlec@gentoo.org> +fasttree-2.1.7.ebuild,
+  +files/CMakeLists.txt, metadata.xml:
+  Version BUmp, #494662
 
   11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
   Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
diff --git a/sci-biology/fasttree/Manifest b/sci-biology/fasttree/Manifest
index 2690026e8339..b3bba794e926 100644
--- a/sci-biology/fasttree/Manifest
+++ b/sci-biology/fasttree/Manifest
@@ -1,15 +1,30 @@
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-Hash: SHA256
+Hash: SHA512
 
+AUX CMakeLists.txt 948 SHA256 60c21f04ea3ef04782dfc0328e317b6d04197a45af4d15c5c43f4f87a1f82c44 SHA512 9858800bfce8d256ccb834a06bad5a5230f90f025a9c9b3c9aafe7244d219d66810530f6688e02889cdb67d6a9459d8e26cd1a9fcf2e8825278b31d0e8d51ff3 WHIRLPOOL edc50a85eaec6161924f38569c33ccd35170f9ac89e17741e4a87ceb350b165fdf6e118c20bfd27a02ec1e01aa76be8665908f39c531a292d3d1b706e6c1b25a
 AUX fasttree-2.0.1-asneeded.patch 455 SHA256 f43ec50d2d4284d60b438e62a407686a5149a31e9c5e389744d894b9e55243eb SHA512 fdd5a0f475d7f00c266a35dfafe7b5131919e345e39b03f51f9ab4ef64ac7bbb5372b437354e5498a242805fb973e4357c1254148abbce64ff71c00b57610ad8 WHIRLPOOL 165ccae141b47231192c091c133a004fdeb3aadbf3539fc6abe7af2df388bedc1c9947e2c335a58aabb918f6baf921a03088d07b0e5c1335be36cfa3765fd371
-DIST fasttree-2.0.1.tar.bz2 149279 SHA256 968a42f126c67f471a21c6ffe621cbedb3ed406838a3d80e799487aedc137fb4
+DIST FastTree-2.1.7.c 383551 SHA256 da148297bb64711e43e38481186228496d418bb4ec0166e09df62a72248085a0 SHA512 e88916e6586885e095948e78e6654081f966c78fbf637cfdac01970f5337bfe5616efcd165fb5f9718af0831ff45047b165944f5da9c5931d9725ea6f49cb59e WHIRLPOOL c4b267d8c3d92f0e76110eed31fcbdb4c142a967c3df31ca30ef816716231e1a9867094d183173af28fc3e7cb9acba81a55d455fcb8833539b2cad0667683775
+DIST FastTreeUPGMA-2.1.7.c 95271 SHA256 199acc84910ca899dae9dd96d2ea133b651e76bbd855363cf620bf1b3cbd3abd SHA512 4d6a8e2cb28b8ee201091172a3baa59d432420839c6d2244b5fb8230ed9daa626b6bed22cb692393ca3d78b8f2d071fe18fbb4f9bdcdc47ef149c31e3f45546c WHIRLPOOL 538b44382137e6055452c901c76007b1c388a541c193c37f7baff26e59eb477450ce8acf7466d5debe0bc973fecc645d1f88d54f6f871670826bb151fd5b7496
+DIST MOTreeComparison-2.1.7.tar.gz 13523 SHA256 aea482d47aca528026cdf86fc96dc59b7a9f66ea33b9e974f5c007b46335d174 SHA512 24d2247650d7728942bd1d987b548cefd65a16b433a3810876613e9fd1cff223d4349ee720b3d8d10a73af220c2c9f59a24d77ad34ff009325fe9f22aa35c72b WHIRLPOOL 7ed1009d622ce77c59cf79078a08a08dafb281e87a6ae99be7b7fba9451f2748bfd7a51036c041e3667ea8e29f7545276b799d708aabb7ea1988ea443f73f475
+DIST fasttree-2.0.1.tar.bz2 149279 SHA256 968a42f126c67f471a21c6ffe621cbedb3ed406838a3d80e799487aedc137fb4 SHA512 b6c7fb9f2eb3ac859164ce459da0a258827550020973e126b984c8f4f87a7f708f46731b6c6bb148cc3fe5cf5ddc19c7c1211b78c19880644fcfb05b65b42367 WHIRLPOOL 1aa3b811afb34b4331f411005fb7e2f9972fcefc022fa3bf68d0156f13be89ec969979c8431d0cd209f6994f8241698b10ef0599c5684e3f943edb61ae59b1bc
 EBUILD fasttree-2.0.1.ebuild 783 SHA256 61f547093efad5df2ca57caa7fa35cf9c2b194c8b677fac5a008aecd3d744548 SHA512 933be57dd573f7fc0dc3f1768fc8c2366fb92a5a8c0a66c3065ee4a2b19e804b62c9ebf7f48fb9ff19a03872d8fe419f16f43325373cd081d59ca9927cd970d9 WHIRLPOOL 78c6cacbefa6525423cd2d302a4ae73df14eca0255c254e689360ff2d68e596251965b642f1fb98d1b3caed7b31323532513536be3128f436ae71b9a4bf2bec4
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+EBUILD fasttree-2.1.7.ebuild 1207 SHA256 ad7aec82fa695d183e48f412038cbd454a369b3a1cb7e4a2dae707262e0b307c SHA512 b413f7e050beba9ab0e2e0f8ed47f394de57a68d17cef71bce9bfaf56bdd95be4f235abcc528a077c42b60368ecc79536029556307cc0c7870d3bdefac96ee97 WHIRLPOOL 49b0d703766f4985b4571b1a184ecce2837cfef11ffe3c549aaa46fd3287915666fa63e5ef6b7edd2acec866346d939616aaea4c1cc58881cde4a080ae737d02
+MISC ChangeLog 881 SHA256 17ac691d005a56d796f7612bafcf9deb17c694e544af3fc1da4403cf56c5ce29 SHA512 b86539962779bf8b21e9c5735a60bbf7e981992780d50b1e8c4da0e318092fe17b398416fb3bad726ea41c7df108ff5fe4eb6815e2f23f4e3877ea6f7b7120a2 WHIRLPOOL 45ae9ce94e460066496c23116ac4368b21c6c863bde5a74654911ce5b062b3d46234695d6f49e0af4947101c27647f9fdf558a7df63232f9b7d7ae5e3cb477ce
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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..80d666677e81
--- /dev/null
+++ b/sci-biology/fasttree/fasttree-2.1.7.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/fasttree/fasttree-2.1.7.ebuild,v 1.1 2013/12/20 09:20:44 jlec Exp $
+
+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-${PV}.tar.gz
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="double-precision openmp sse3"
+
+REQUIRED_USE="?? ( double-precision sse3 )"
+
+DOCS=( README )
+
+src_unpack() {
+	mkdir "${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 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/metadata.xml b/sci-biology/fasttree/metadata.xml
index f17a827e3101..5ee1f51e55df 100644
--- a/sci-biology/fasttree/metadata.xml
+++ b/sci-biology/fasttree/metadata.xml
@@ -2,4 +2,10 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
   <herd>sci-biology</herd>
+  <use>
+    <flag name="double-precision">
+	use double precision instead of single-precision floating point 
+	(2x memroy required)
+	</flag>
+  </use>
 </pkgmetadata>