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# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=5
PERL_EXPORT_PHASE_FUNCTIONS=no
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-"${PV}".tgz"
RESTRICT="fetch"
# for academia: GPL-v2 or Artistic-2
# for commercial: ask
LICENSE="|| ( GPL-2 Artistic-2 )"
SLOT="0"
KEYWORDS=""
IUSE="mpi"
# http://search.cpan.org/~rybskej/forks-0.36/lib/forks.pm # bug #566360
# http://search.cpan.org/~rybskej/forks-0.36/lib/forks/shared.pm
DEPEND="
mpi? ( sys-cluster/mpich2 || ( sys-cluster/openmpi ) )
dev-perl/DBI
dev-perl/DBD-SQLite
dev-perl/File-Which
dev-perl/Bit-Vector
dev-perl/Inline-C
dev-perl/IO-All
dev-perl/libwww-perl
dev-perl/DBD-Pg
dev-perl/Module-Build
dev-perl/Want
dev-perl/IO-Prompt
dev-perl/Perl-Unsafe-Signals
dev-perl/forks
>=sci-biology/GAL-0.2.1
>=sci-biology/bioperl-1.6
sci-biology/ncbi-tools || ( sci-biology/ncbi-tools++ )
sci-biology/snap
sci-biology/exonerate
>=sci-biology/augustus-2.0
sci-biology/repeatmasker"
#sci-biology/GeneMark_ES-bin
#sci-biology/GeneMark_S-bin
#>=sci-biology/FGENESH-bin-2.4 (not in gentoo yet)
RDEPEND="${DEPEND}"
# dev-perl/forks-shared ?
# ==============================================================================
# STATUS MAKER v2.31.8
# ==============================================================================
# PERL Dependencies: MISSING
# ! Perl::Unsafe::Signals
# ! Want
# ! forks
# ! forks::shared
#
# External Programs: MISSING
# ! RepeatMasker
#
# External C Libraries: VERIFIED
# MPI SUPPORT: DISABLED
# MWAS Web Interface: DISABLED
# MAKER PACKAGE: MISSING PREREQUISITES
#
#
# Important Commands:
# ./Build installdeps #installs missing PERL dependencies
# ./Build installexes #installs all missing external programs
# ./Build install #installs MAKER
# ./Build status #Shows this status menu
#
# Other Commands:
# ./Build repeatmasker #installs RepeatMasker (asks for RepBase)
# ./Build blast #installs BLAST (NCBI BLAST+)
# ./Build exonerate #installs Exonerate (v2 on UNIX / v1 on Mac OSX)
# ./Build snap #installs SNAP
# ./Build augustus #installs Augustus
# ./Build apollo #installs Apollo
# ./Build gbrowse #installs GBrowse (must be root)
# ./Build jbrowse #installs JBrowse (MAKER copy, not web accecible)
# ./Build webapollo #installs WebApollo (use maker2wap to create DBs)
# ./Build mpich2 #installs MPICH2 (but manual install recommended)
# Building MAKER
#
# * MISSING MAKER PREREQUISITES - CANNOT CONTINUE!!
S="${WORKDIR}"/maker/src
pkg_nofetch() {
einfo "Please visit ${HOMEPAGE} and obtain the file"
einfo "maker-"${PV}".tgz and place it into ${DISTDIR}"
einfo "You must also install sci-biology/repeatmasker otherwise"
einfo "MAKER install process will stop."
einfo "That in turn requires you to register at http://www.girinst.org/server/RepBase"
einfo "to obtain sci-biology/repeatmasker-libraries data file"
einfo "For execution through openmpi or mpich please read INSTALL file"
einfo "Customization typically go into maker_opts.ctl file"
}
src_compile(){
perl Build.PL || die
./Build install || die
}
# If you move it, then the executables won’t be able to locate dependencies in the …/maker/data,
# …/maker/lib, and …/maker/perl directories. You should really either add the location of
# …/maker/bin to you PATH environmental variable or at most soft link the executables somewhere
# else using the ‘ln -s’ command.
src_install(){
cd "${WORKDIR}"/maker || die
rm -f bin/fasta_tool # is part of sci-biology/GAL
# drop development related accessory script requiring Parallel/MPIcar.pm
find . -name mpi_evaluator | xargs rm || die
mv bin/compare bin/compare_gff3_to_chado # rename as agreed by upstream, will be in maker-3 as well
dobin bin/*
perl_set_version
insinto "${VENDOR_LIB}"/MAKER # uppercase, not "${PN}"
doins perl/lib/MAKER/*.pm
doman perl/man/*.3pm
insinto "${VENDOR_LIB}"/Parallel/Application
doins perl/lib/Parallel/Application/*.pm
insinto /usr/share/"${PN}"/data
doins data/*
# FIXME: find equivalent perl packages for lib/* contents, for example lib/GI.pm
dodoc README INSTALL
insinto /usr/share/"${PN}"/GMOD/Apollo
doins GMOD/Apollo/gff3.tiers
insinto /usr/share/"${PN}"/GMOD/JBrowse
doins GMOD/JBrowse/maker.css
}
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