sci-biology/maker: improving the ebuild, needs some perl packages to be first introduced into portage tree; needs proper install and to avoid bundled 3rd-party binaries, not sure if the perl modules are a copy of bioperl or not

Package-Manager: portage-2.2.18

4 files changed, 76 insertions, 0 deletions

diff --git a/sci-biology/maker/ChangeLog b/sci-biology/maker/ChangeLog
new file mode 100644
index 000000000..d954ed6f5
--- /dev/null
+++ b/sci-biology/maker/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for sci-biology/MAKER
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> MAKER-9999.ebuild:
+  added license
+
+*MAKER-9999 (23 Mar 2014)
+
+  23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +MAKER-9999.ebuild,
+  +metadata.xml:
+  a skeleton for a new package
diff --git a/sci-biology/maker/Manifest b/sci-biology/maker/Manifest
new file mode 100644
index 000000000..8b2a8d085
--- /dev/null
+++ b/sci-biology/maker/Manifest
@@ -0,0 +1 @@
+DIST maker-2.31.8.tgz 13607357 SHA256 a99c7e433638979808ea3f4bcd2b6b69f4474bd898807aba4520debd58717420 SHA512 1533888c4960a74395f4bfdd26a4f86ba33d93764b1e40094fcd2d8e7e355495464619820b0c805061f467c20d979ddf17bdb2979a7f17117c1a721032ee538d WHIRLPOOL 2df90ae76891160ed08fc3a703d3d8a982e737fa23c3f65d197bd900816588a2e8d8ec364e1122af4be289f01b5c704414487eb19ece8a8fedd9c9aac11e40e2
diff --git a/sci-biology/maker/maker-2.31.8.ebuild b/sci-biology/maker/maker-2.31.8.ebuild
new file mode 100644
index 000000000..6bc8ff57a
--- /dev/null
+++ b/sci-biology/maker/maker-2.31.8.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit eutils perl-module
+
+DESCRIPTION="A genome annotation viewer and pipeline for small eukaryota and prokaryota"
+HOMEPAGE="http://www.yandell-lab.org/software/maker.html"
+SRC_URI="maker-"${PV}".tgz"
+
+RESTRICT="fetch"
+
+# for academia: GPL-v2 or Artistic-2
+# for commercial: ask
+LICENSE="|| ( GPL-2 Artistic-2 )"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+# http://search.cpan.org/~rgarcia/Perl-Unsafe-Signals-0.02/
+# http://search.cpan.org/~rybskej/forks-0.36/lib/forks.pm
+# http://search.cpan.org/~rybskej/forks-0.36/lib/forks/shared.pm
+# http://search.cpan.org/~dconway/IO-Prompt-0.997002/lib/IO/Prompt.pm
+DEPEND="virtual/mpi
+	dev-perl/DBI
+	dev-perl/DBD-SQLite
+	dev-perl/File-Which
+	dev-perl/Bit-Vector
+	dev-perl/Inline-C
+	dev-perl/IO-All
+	dev-perl/libwww-perl
+	dev-perl/DBD-Pg
+	virtual/perl-Module-Build
+	>=sci-biology/bioperl-1.6
+	sci-biology/ncbi-tools || ( sci-biology/ncbi-tools++ )
+	sci-biology/snap
+	sci-biology/repeatmasker
+	sci-biology/exonerate
+	sci-biology/augustus"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/maker/src
+
+pkg_nofetch() {
+	einfo "Please visit ${HOMEPAGE} and obtain the file"
+	einfo "maker-"${PV}".tgz and place it into ${DISTDIR}"
+}
+
+src_compile(){
+	perl Build.PL || die
+	./Build install || die
+}
diff --git a/sci-biology/maker/metadata.xml b/sci-biology/maker/metadata.xml
new file mode 100644
index 000000000..2bc893037
--- /dev/null
+++ b/sci-biology/maker/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>