commit: 92e50f54acd3921fced262210c878f1fdc8bf99a Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Tue Jan 19 16:22:20 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Tue Jan 19 16:22:20 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=92e50f54
sci-biology/maker: drop old Package-Manager: Portage-3.0.13, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> sci-biology/maker/maker-2.31.10.ebuild | 154 --------------------------------- 1 file changed, 154 deletions(-) diff --git a/sci-biology/maker/maker-2.31.10.ebuild b/sci-biology/maker/maker-2.31.10.ebuild deleted file mode 100644 index b7dc780a9..000000000 --- a/sci-biology/maker/maker-2.31.10.ebuild +++ /dev/null @@ -1,154 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -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-"${PV}".tgz" - -RESTRICT="fetch" - -# for academia: GPL-v2 or Artistic-2 -# for commercial: ask -LICENSE="|| ( GPL-2 Artistic-2 )" -SLOT="0" -KEYWORDS="" -IUSE="mpi" - -# http://search.cpan.org/~rybskej/forks-0.36/lib/forks.pm # bug #566360 -# http://search.cpan.org/~rybskej/forks-0.36/lib/forks/shared.pm -# -# MAKER does not work with MVAPICH2. -# It can work with Intel MPI and OpenMPI with some command line modification. -# It always works with MPICH, but MPICH may not be able to scale to more than ~100 CPUs. -DEPEND=" - mpi? ( sys-cluster/mpich2 || ( sys-cluster/openmpi ) ) - dev-perl/DBI - dev-perl/DBD-SQLite - dev-perl/File-Which - dev-perl/Bit-Vector - dev-perl/Inline-C - dev-perl/IO-All - dev-perl/libwww-perl - dev-perl/DBD-Pg - dev-perl/Module-Build - dev-perl/Want - dev-perl/IO-Prompt - dev-perl/Perl-Unsafe-Signals - dev-perl/forks - >=sci-biology/GAL-0.2.1 - >=sci-biology/bioperl-1.6 - sci-biology/ncbi-tools || ( sci-biology/ncbi-tools++ ) - sci-biology/snap - sci-biology/exonerate - >=sci-biology/augustus-2.0 - sci-biology/repeatmasker" - #sci-biology/GeneMark_ES-bin - #sci-biology/GeneMark_S-bin - #>=sci-biology/FGENESH-bin-2.4 (not in gentoo yet) -RDEPEND="${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 ${DISTDIR}" - einfo "You must also install sci-biology/repeatmasker otherwise" - einfo "MAKER install process will stop." - einfo "That in turn requires you to register at http://www.girinst.org/server/RepBase"; - einfo "to obtain sci-biology/repeatmasker-libraries data file" - einfo "For execution through openmpi or mpich please read INSTALL file" - einfo "Customization typically go into maker_opts.ctl file" -} - -src_compile(){ - perl Build.PL || die - ./Build install || die - ./Build installdeps || die -} - -# If you move it, then the executables won't able to locate dependencies -# in the /maker/data, /maker/lib, /maker/perl directories. You should -# really either add the location of /maker/bin to you PATH environmental -# variable or at most soft link the executables somewhere -# else using the 'ln -s' command. -src_install(){ - cd "${WORKDIR}"/maker || die - rm -f bin/fasta_tool # is part of sci-biology/GAL - # 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 - # - # FIXME: find equivalent perl packages for lib/* contents, for example lib/GI.pm - # You do not have write access to install missing Modules. - # I can try and install these locally (i.e. only for MAKER) - # in the .../maker/perl/lib directory, or you can run - # './Build installdeps' as root or using sudo and try again. - # Do want MAKER to try and build a local installation? [N ]N - # - # - # WARNING: You do not appear to have write access to install missing - # Modules. Please run './Build installdeps' as root or using sudo. - # - # Do you want to continue anyway? [N ]N - # - doins -r lib/* - insinto "${VENDOR_LIB}"/Parallel/Application - doins perl/lib/Parallel/Application/*.pm - insinto /usr/share/"${PN}"/data - doins data/* - 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 -}
