[gentoo-commits] proj/sci:master commit in: sci-biology/maker/

[Andrew Ammerlaan]

commit:     9aab83a69bedd08a4acf16d01347b3851ab73da4
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Aug 31 09:22:41 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Aug 31 09:22:41 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9aab83a6

sci-biology/maker: remove last-rited pack

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 sci-biology/maker/maker-3.01.02_beta.ebuild | 135 ----------------------------
 sci-biology/maker/metadata.xml              |  12 ---
 2 files changed, 147 deletions(-)

diff --git a/sci-biology/maker/maker-3.01.02_beta.ebuild b/sci-biology/maker/maker-3.01.02_beta.ebuild
deleted file mode 100644
index 975a83c14..000000000
--- a/sci-biology/maker/maker-3.01.02_beta.ebuild
+++ /dev/null
@@ -1,135 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit perl-functions
-
-DESCRIPTION="A genome annotation viewer and pipeline for small eukaryota and prokaryota"
-HOMEPAGE="http://www.yandell-lab.org/software/maker.html"
-SRC_URI="maker-"${PV}".tgz"
-
-RESTRICT="fetch"
-
-# for academia: GPL-v2 or Artistic-2
-# for commercial: ask
-LICENSE="|| ( GPL-2 Artistic-2 )"
-SLOT="0"
-KEYWORDS=""
-IUSE="mpi"
-
-# http://search.cpan.org/~rybskej/forks-0.36/lib/forks.pm             # bug #566360
-# http://search.cpan.org/~rybskej/forks-0.36/lib/forks/shared.pm
-#
-# MAKER does not work with MVAPICH2.
-# It can work with Intel MPI and OpenMPI with some command line modification.
-# It always works with MPICH, but MPICH may not be able to scale to more than ~100 CPUs.
-DEPEND="
-	mpi? ( sys-cluster/mpich2 || ( sys-cluster/openmpi ) )
-	dev-perl/DBI
-	dev-perl/DBD-SQLite
-	dev-perl/File-Which
-	dev-perl/Bit-Vector
-	dev-perl/Inline-C
-	dev-perl/IO-All
-	dev-perl/libwww-perl
-	dev-perl/DBD-Pg
-	dev-perl/Module-Build
-	dev-perl/Want
-	dev-perl/IO-Prompt
-	dev-perl/Perl-Unsafe-Signals
-	dev-perl/forks
-	>=sci-biology/GAL-0.2.1
-	>=sci-biology/bioperl-1.6
-	sci-biology/ncbi-tools || ( sci-biology/ncbi-tools++ )
-	sci-biology/snap
-	sci-biology/exonerate
-	>=sci-biology/augustus-2.0
-	sci-biology/repeatmasker"
-	#sci-biology/GeneMark_ES-bin
-	#sci-biology/GeneMark_S-bin
-	#>=sci-biology/FGENESH-bin-2.4 (not in gentoo yet)
-RDEPEND="${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 your DISTDIR folder"
-	einfo "If it is '-beta' rename it to '_beta'"
-	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 able to locate dependencies
-# in the /maker/data, /maker/lib, /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 "${WORKDIR}"/maker || die
-	rm -f bin/fasta_tool # is part of sci-biology/GAL
-	mv bin/compare bin/compare_gff3_to_chado # rename as agreed by upstream, will be in maker-3 as well
-	dobin bin/*
-	perl_set_version
-	perl_domodule perl/lib/MAKER/*.pm
-	doman perl/man/*.3pm
-	perl_domodule perl/lib/Parallel/Application/*.pm
-	insinto /usr/share/"${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
-}

diff --git a/sci-biology/maker/metadata.xml b/sci-biology/maker/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/maker/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@×××××××××××××××.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@g.o</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>