reinit the tree, so we can have metadata

3 files changed, 71 insertions, 0 deletions

diff --git a/sci-biology/repeatmasker/Manifest b/sci-biology/repeatmasker/Manifest
new file mode 100644
index 000000000000..fdf427105995
--- /dev/null
+++ b/sci-biology/repeatmasker/Manifest
@@ -0,0 +1,5 @@
+DIST RepeatMasker-open-4-0-1.tar.gz 84077910 SHA256 638ed02d970052ecb7dac6c71d2cb9625b0a0713df88d46ae78865aa4fd3fc92 SHA512 6b710a02b2964bca6acb25cc918bd56f7caba7b80b3b683972f0584180bf0fd3704f657d7ee341187a4ac86d9883e62eb4f09da237fa8ef1b481137d1a89963e WHIRLPOOL f2d67ea6e97a0667ac9ce89f8ed8c590b911d9cd4fc4482bdc48c0ea7ca07161a8bec267ed3e2a950f6d8c501f992ceadc62e1211a80b6bc1c90d293cbf45e77
+EBUILD repeatmasker-4.0.1.ebuild 1529 SHA256 ded0d2097778ef62511a10fec641188fd7591271abdf5fbd8a5f1da8219ffc19 SHA512 72c2663f3c614e476f23d880551c6f78fcc239c56905726c90663a467af22ad42cb4518667c2a1301f55230d890b390967a5799bb4460c4d0e9909bc2d5c5bd3 WHIRLPOOL a597c4108a5c1d773ebe0914b13b1d04e0a7e1f0bcc8cf31a1996f8adc64ee0858e5d698eee0adc6f46aa179f9749bf49aedbcbec0496b863f435208e1da6ad0
+MISC ChangeLog 2445 SHA256 88f77fb918a8ae5f0f65d30235ca572fa6fb2e2168aa01c7691073c0ac8ced3c SHA512 e5d989a78a952dc80d8a991f2399c96006aa408d314fa48a3bacbbbd922e7a252d8b825ad06d56e093eb5324350886eb14e911ac36a3ddc14b0ab7184a0768dc WHIRLPOOL c892bcb7d4765b501c11cc61363a39e59670ced8c121c148f84b46118c7608dda4f99eaf891945ed21f454daee7718917aa244edfe32e2aeda2b3253fd17c891
+MISC ChangeLog-2015 1664 SHA256 34f3c51d3517b7dc7cb6482ca766bd2b1cf6f1037b24ccba8fe19f07219e0f60 SHA512 583ea65bfc2ac3b5016af35025b298fbc0a526585beaa5c33730459429b760af13afb3e72313c1902cd00f60f41be3f545dadf1c6a5d38da41bdb23d6096a68e WHIRLPOOL a60e3053b51f4eb83178fbb4b4c494771fa429317296c8d755b8182e22624108fff3a221fc8ee99965d6bd8df8366b0819d7886ea0c3aa3eb5c8138556d6d705
+MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13
diff --git a/sci-biology/repeatmasker/metadata.xml b/sci-biology/repeatmasker/metadata.xml
new file mode 100644
index 000000000000..959160fe46b1
--- /dev/null
+++ b/sci-biology/repeatmasker/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/repeatmasker/repeatmasker-4.0.1.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild
new file mode 100644
index 000000000000..41c28eb17f4e
--- /dev/null
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild
@@ -0,0 +1,58 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+MY_PV=${PV//\./-}
+
+DESCRIPTION="Screen DNA sequences for interspersed repeats and low complexity DNA"
+HOMEPAGE="http://repeatmasker.org/"
+SRC_URI="http://www.repeatmasker.org/RepeatMasker-open-${MY_PV}.tar.gz"
+
+LICENSE="OSL-2.1"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="
+	sci-biology/rmblast
+	sci-biology/trf
+	sci-biology/repeatmasker-libraries"
+
+S="${WORKDIR}/RepeatMasker"
+
+src_configure() {
+	sed -i -e 's/system( "clear" );//' \
+		-e 's|> \($rmLocation/Libraries/RepeatMasker.lib\)|> '${D}'/\1|' "${S}/configure" || die
+	echo "
+env
+/usr/share/${PN}
+/usr/bin
+2
+/opt/rmblast/bin
+Y
+5" | "${S}/configure" || die "configure failed"
+	sed -i -e 's|use lib $FindBin::RealBin;|use lib "/usr/share/'${PN}'/lib";|' \
+		-e 's|".*\(taxonomy.dat\)"|"/usr/share/'${PN}'/\1"|' \
+		-e '/$REPEATMASKER_DIR/ s|$FindBin::RealBin|/usr/share/'${PN}'|' \
+		"${S}"/{DateRepeats,ProcessRepeats,RepeatMasker,DupMasker,RepeatProteinMask,RepeatMaskerConfig.pm,Taxonomy.pm} || die
+}
+
+src_install() {
+	exeinto /usr/share/${PN}
+	for i in DateRepeats ProcessRepeats RepeatMasker DupMasker RepeatProteinMask; do
+		doexe $i || die
+		dosym /usr/share/${PN}/$i /usr/bin/$i || die
+	done
+
+	dodir /usr/share/${PN}/lib
+	insinto /usr/share/${PN}/lib
+	doins "${S}"/*.pm || die
+
+	insinto /usr/share/${PN}
+	doins -r util Matrices Libraries taxonomy.dat *.help || die
+	keepdir /usr/share/${PN}/Libraries
+
+	dodoc README INSTALL *.help
+}