reinit the tree, so we can have metadata

7 files changed, 202 insertions, 0 deletions

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 cec0331b56114bd36085c1a64b048979579984b769102358365e4c719b03b1fb6b52919f4397b97c424613811e4e1ef572f3e6fb595aa5340e25d6881bc46e97
+AUX fasttree-2.1.8-format-security.patch 783 SHA256 cd838048ce9b99adb462f75cdb56ec65274e0c96340685c736858580b38c2579 SHA512 9bbf66cddca2b6c202fdeeab4092036852cb1ebe132ebf4d96cba1bea75bb5668dd6ee97d4d020a4b7cf7111bee6d0c3004b0bd74ee4685ef98eeeb5e9a23eb3 WHIRLPOOL d20139d2ba391ed11924b70495d16fdf706171953f712214b5d0a83395cd97a0395c7dc8a6e586c3ee87579c1124c7599cc89e933ba684940909daa7eda11f2d
+DIST FastTree-2.1.7.c 383551 SHA256 da148297bb64711e43e38481186228496d418bb4ec0166e09df62a72248085a0 SHA512 e88916e6586885e095948e78e6654081f966c78fbf637cfdac01970f5337bfe5616efcd165fb5f9718af0831ff45047b165944f5da9c5931d9725ea6f49cb59e WHIRLPOOL c4b267d8c3d92f0e76110eed31fcbdb4c142a967c3df31ca30ef816716231e1a9867094d183173af28fc3e7cb9acba81a55d455fcb8833539b2cad0667683775
+DIST FastTree-2.1.8.c 385231 SHA256 b172d160f1b12b764d21a6937c3ce01ba42fa8743d95e083e031c6947762f837 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 538b44382137e6055452c901c76007b1c388a541c193c37f7baff26e59eb477450ce8acf7466d5debe0bc973fecc645d1f88d54f6f871670826bb151fd5b7496
+DIST MOTreeComparison-2.1.7.tar.gz 13523 SHA256 aea482d47aca528026cdf86fc96dc59b7a9f66ea33b9e974f5c007b46335d174 SHA512 24d2247650d7728942bd1d987b548cefd65a16b433a3810876613e9fd1cff223d4349ee720b3d8d10a73af220c2c9f59a24d77ad34ff009325fe9f22aa35c72b WHIRLPOOL 7ed1009d622ce77c59cf79078a08a08dafb281e87a6ae99be7b7fba9451f2748bfd7a51036c041e3667ea8e29f7545276b799d708aabb7ea1988ea443f73f475
+DIST MOTreeComparison-2.1.8.tar.gz 13523 SHA256 aea482d47aca528026cdf86fc96dc59b7a9f66ea33b9e974f5c007b46335d174 SHA512 24d2247650d7728942bd1d987b548cefd65a16b433a3810876613e9fd1cff223d4349ee720b3d8d10a73af220c2c9f59a24d77ad34ff009325fe9f22aa35c72b WHIRLPOOL 7ed1009d622ce77c59cf79078a08a08dafb281e87a6ae99be7b7fba9451f2748bfd7a51036c041e3667ea8e29f7545276b799d708aabb7ea1988ea443f73f475
+EBUILD fasttree-2.1.7.ebuild 1191 SHA256 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 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+  <use>
+    <flag name="double-precision">
+	use double precision instead of single-precision floating point 
+	(2x memroy required)
+	</flag>
+  </use>
+</pkgmetadata>