reinit the tree, so we can have metadata

5 files changed, 136 insertions, 0 deletions

diff --git a/sci-biology/phylip/Manifest b/sci-biology/phylip/Manifest
new file mode 100644
index 000000000000..5010dafb9cf6
--- /dev/null
+++ b/sci-biology/phylip/Manifest
@@ -0,0 +1,8 @@
+AUX README.Gentoo 643 SHA256 d8a737f2ca6e0366fcebb96fbc9e12200b6402fea4c4f71696f4d9175980dfbd SHA512 63ec15ce2788171e5351977bae21e11a7c8609eeed4893849fabc909f0c6713033e253768ea3f485245456a9083ad4aa613e2503ebb4eb71f7b670f1af593f2a WHIRLPOOL 671a6aa44cae7054d402ac111a572145b705052e6d084687a188fe451c8c6f30fd276f8abb89d40bf150be8d119616f696ccaa59fb3ed9177040eae8b3f8b80e
+DIST phylip-3.69.tar.gz 1511935 SHA256 27947ce8dab4416e4823db38b3d1b0bf17bc545b6907cf09dcf6177df94c1a8f SHA512 e36d12bfe597896b4298c1d0e3b0b7bd783573dc03e861b9472d8284391b2339cb3fb58eb6580298724bbd516127b68925815455514f939da9272fcfed7e229d WHIRLPOOL 25c45ac2a96278eaef9a62aecc367aa32a894df0cd5aff9b626abd013ecbe52f9d4bdaf7805ba5c5d8699f9a74d3d26cfe6e1c1b22960c03061171625d16415f
+DIST phylip-3.696.tar.gz 3955721 SHA256 cd0a452ca51922142ad06d585e2ef98565536a227cbd2bd47a2243af72c84a06 SHA512 711a9a34be72b0f63c746733cd1384f091b7cc597dbd9a40c130e074efbf0a0ecc30e5a6b3452bb73dc69cddbdae2fc07d1c0a68f0be207471eab73ab876c6be WHIRLPOOL 7d4d4bd703ecd84b7570c937484c15f52643221ca178fb494f81b18991149fc2f8d1c8c5b99b57e20ada0bef7e93dcb15c55410f8f1012b1656419fab19b3cab
+EBUILD phylip-3.69-r1.ebuild 1142 SHA256 3d6fa8738b4b032844d45d7bd66e127e22cca1f627f042c46765d706df9e5384 SHA512 b7d6638ddc1a035132507918dd49e82e41e450ca31b8e6afbf646e69ce29690b5be74795a108a03eaf79399bc909031d844f664e072861f4cc656aaa0b8946c7 WHIRLPOOL f0d6237fe45518ca5ec4400889ad1f381c964e4bf5792224c31a9c103f30102d082805dccd7ac95ee20341da94de48c300ac1133d2ff5dee5e1b47ba4bb0b1b0
+EBUILD phylip-3.696-r1.ebuild 1134 SHA256 48032ba78c33af8b36b53aafbf455e5419a556e0e38782fdee5a77887ac43704 SHA512 ef7196f540a1bf981dd1d2489fc2cba31fd0ea3135f060331f8f1ba43ce585ae4c6d33cc76f53d561c1c36059c631303caeaa20c28ada2c02ce218119a202872 WHIRLPOOL 56fb7f7895b25362b7ef60e17be8cca51c931e06de6f4b6f23073652e6ed71cfd87856d2ae3f6252011fa9c87765454a2495f44df32357cd5f4d875eb7f20f89
+MISC ChangeLog 2875 SHA256 795996871597ce5b9b96ecbd7e72fa271b2dceda9d172b42af4ef1583207dde8 SHA512 c62f9a8b3cc0d1a7b5f532c7fffeafa95019d868e9dbb789c53342e326259402aaa85f14fb3b50816e4453652a79cfd7eaa675895e032204383bc0d83f2300a4 WHIRLPOOL 5809f10fde8471e47635ba845f959bcd5544b30d047499ae8656b0108dd686585102552706372bf5b6b70b4b0e6d14899ee15860492766ea97366514b6d382dc
+MISC ChangeLog-2015 7026 SHA256 733a3765122ab15458e701cbf902f9408672e47696b84f971182f968e70129bd SHA512 fa87c1d1959303b6d8e402812c1600cd5868724c93e4e8a6bee14f9ec320f8e967da5f443622c39e476b17b6bbe90006e52a0cfcaab8504a23267af74d79c897 WHIRLPOOL 1fb268aea348f615a17c2bee08c81592ff1ea20934cb5ab0b634adb5f490179efecdd67e446308a84f4e562067971dcc5db5935a755bea995969db65d1e81b50
+MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13
diff --git a/sci-biology/phylip/files/README.Gentoo b/sci-biology/phylip/files/README.Gentoo
new file mode 100644
index 000000000000..3b2062003996
--- /dev/null
+++ b/sci-biology/phylip/files/README.Gentoo
@@ -0,0 +1,15 @@
+Using the PHYlogeny Inference Package on Gentoo systems
+
+Location of the factor program
+
+On Gentoo systems, the PHYLIP program "factor" is named "factor-phylip", in
+order to avoid a file collision with the program of the same name provided by
+the "sys-apps/coreutils" package.
+
+Location of the font files
+
+PHYLIP programs will find font files only if they are in a directory
+referenced by the "PATH" variable or if they are in the current working
+directory. When working with PHYLIP programs that need these files, either
+copy or symlink the fonts you need to your working directory, or add
+"/usr/share/phylip/fonts/" to your "PATH" variable.
diff --git a/sci-biology/phylip/metadata.xml b/sci-biology/phylip/metadata.xml
new file mode 100644
index 000000000000..959160fe46b1
--- /dev/null
+++ b/sci-biology/phylip/metadata.xml
@@ -0,0 +1,8 @@
+<?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>
+</pkgmetadata>
diff --git a/sci-biology/phylip/phylip-3.69-r1.ebuild b/sci-biology/phylip/phylip-3.69-r1.ebuild
new file mode 100644
index 000000000000..658c92e785c2
--- /dev/null
+++ b/sci-biology/phylip/phylip-3.69-r1.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit toolchain-funcs
+
+DESCRIPTION=" The PHYLogeny Inference Package"
+HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html"
+SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="freedist"
+IUSE=""
+KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos"
+
+RDEPEND="x11-libs/libXaw"
+DEPEND="${RDEPEND}
+	x11-proto/xproto"
+
+S="${WORKDIR}/${P}/src"
+
+src_prepare() {
+	sed \
+		-e "s/CFLAGS  = -O3 -fomit-frame-pointer/CFLAGS = ${CFLAGS}/" \
+		-e "s/CC        = cc/CC        = $(tc-getCC)/" \
+		-e "s/DC        = cc/DC        = $(tc-getCC)/" \
+		-e "/ -o /s:\(\$(CC)\):\1 ${LDFLAGS}:g" \
+		-i Makefile || die "Patching Makefile failed."
+	mkdir ../fonts || die
+}
+
+src_compile() {
+	emake -j1 all put
+}
+
+src_install() {
+	cd "${WORKDIR}/${P}" || die
+
+	mv exe/font* fonts || die "Font move failed."
+	mv exe/factor exe/factor-${PN} || die "Renaming factor failed."
+
+	dobin exe/*
+
+	dodoc "${FILESDIR}"/README.Gentoo
+
+	dohtml -r phylip.html doc
+
+	insinto /usr/share/${PN}/
+	doins -r fonts
+}
diff --git a/sci-biology/phylip/phylip-3.696-r1.ebuild b/sci-biology/phylip/phylip-3.696-r1.ebuild
new file mode 100644
index 000000000000..03b33b303805
--- /dev/null
+++ b/sci-biology/phylip/phylip-3.696-r1.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit toolchain-funcs
+
+DESCRIPTION=" The PHYLogeny Inference Package"
+HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html"
+SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD-2"
+IUSE=""
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+
+RDEPEND="x11-libs/libXaw"
+DEPEND="${RDEPEND}
+	x11-proto/xproto"
+
+S="${WORKDIR}/${P}/src"
+
+src_prepare() {
+	mv Makefile.unx Makefile || die
+	sed \
+		-e "/ -o /s:\(\$(CC)\):\1 ${LDFLAGS}:g" \
+		-i Makefile || die "Patching Makefile failed."
+	mkdir ../fonts || die
+}
+
+src_compile() {
+	emake -j1 \
+		CC="$(tc-getCC)" \
+		DC="$(tc-getCC)" \
+		CFLAGS="${CFLAGS} -Wno-unused-result" \
+		all put
+}
+
+src_install() {
+	cd "${WORKDIR}/${P}" || die
+
+	mv exe/font* fonts || die "Font move failed."
+	mv exe/factor exe/factor-${PN} || die "Renaming factor failed."
+
+	dolib.so exe/*so && rm exe/*so || die
+	dobin exe/*
+
+	dodoc "${FILESDIR}"/README.Gentoo
+
+	dohtml -r phylip.html doc
+
+	insinto /usr/share/${PN}/
+	doins -r fonts
+}