commit: e32ec5ec672fcded9199d4943aaa12cf9f1b9224 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Fri Nov 20 21:26:51 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Fri Nov 20 21:26:51 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e32ec5ec
sci-biology/maker: depend on mpich2 when USE=mpi, add back hard DEPENDency on repeatmasker because install process does not continue without it, document additional perl modules not available in portage Package-Manager: portage-2.2.18 sci-biology/maker/ChangeLog | 5 ++++ sci-biology/maker/maker-2.31.8.ebuild | 56 +++++++++++++++++++++++++++++------ 2 files changed, 52 insertions(+), 9 deletions(-) diff --git a/sci-biology/maker/ChangeLog b/sci-biology/maker/ChangeLog index 62f6717..bf295cf 100644 --- a/sci-biology/maker/ChangeLog +++ b/sci-biology/maker/ChangeLog @@ -3,6 +3,11 @@ # $Id$ 20 Nov 2015; Martin Mokrejs <[email protected]> maker-2.31.8.ebuild: + sci-biology/maker: depend on mpich2 when USE=mpi, add back hard DEPENDency on + repeatmasker because install process does not continue without it, document + additional perl modules not available in portage + + 20 Nov 2015; Martin Mokrejs <[email protected]> maker-2.31.8.ebuild: sci-biology/maker: respect USE=mpi, remove hard DEPENDency on repeatmasker- libraries which are fetch restricted diff --git a/sci-biology/maker/maker-2.31.8.ebuild b/sci-biology/maker/maker-2.31.8.ebuild index d005e19..00a88da 100644 --- a/sci-biology/maker/maker-2.31.8.ebuild +++ b/sci-biology/maker/maker-2.31.8.ebuild @@ -24,7 +24,7 @@ IUSE="mpi" # 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=" - mpi? ( virtual/mpi ) + mpi? ( sys-cluster/mpich2 ) dev-perl/DBI dev-perl/DBD-SQLite dev-perl/File-Which @@ -33,29 +33,67 @@ DEPEND=" dev-perl/IO-All dev-perl/libwww-perl dev-perl/DBD-Pg + dev-perl/Want virtual/perl-Module-Build >=sci-biology/bioperl-1.6 sci-biology/ncbi-tools || ( sci-biology/ncbi-tools++ ) sci-biology/snap sci-biology/exonerate - sci-biology/augustus" + sci-biology/augustus + sci-biology/repeatmasker" RDEPEND="${DEPEND}" +# ============================================================================== +# STATUS MAKER v2.31.8 +# ============================================================================== +# PERL Dependencies: MISSING +# ! Perl::Unsafe::Signals +# ! Want +# ! forks +# ! forks::shared +# +# External Programs: MISSING +# ! RepeatMasker +# +# External C Libraries: VERIFIED +# MPI SUPPORT: DISABLED +# MWAS Web Interface: DISABLED +# MAKER PACKAGE: MISSING PREREQUISITES +# +# +# Important Commands: +# ./Build installdeps #installs missing PERL dependencies +# ./Build installexes #installs all missing external programs +# ./Build install #installs MAKER +# ./Build status #Shows this status menu +# +# Other Commands: +# ./Build repeatmasker #installs RepeatMasker (asks for RepBase) +# ./Build blast #installs BLAST (NCBI BLAST+) +# ./Build exonerate #installs Exonerate (v2 on UNIX / v1 on Mac OSX) +# ./Build snap #installs SNAP +# ./Build augustus #installs Augustus +# ./Build apollo #installs Apollo +# ./Build gbrowse #installs GBrowse (must be root) +# ./Build jbrowse #installs JBrowse (MAKER copy, not web accecible) +# ./Build webapollo #installs WebApollo (use maker2wap to create DBs) +# ./Build mpich2 #installs MPICH2 (but manual install recommended) +# Building MAKER +# +# * MISSING MAKER PREREQUISITES - CANNOT CONTINUE!! + S="${WORKDIR}"/maker/src pkg_nofetch() { einfo "Please visit ${HOMEPAGE} and obtain the file" einfo "maker-"${PV}".tgz and place it into ${DISTDIR}" - einfo "It is also advisable to install sci-biology/repeatmasker" - einfo "and in turn register for sci-biology/repeatmasker-libraries" + einfo "You must also install sci-biology/repeatmasker otherwise" + einfo "MAKER install will stop." + einfo "That in turn requires you to register at http://www.girinst.org/server/RepBase"; + einfo "to obtain for sci-biology/repeatmasker-libraries" } src_compile(){ perl Build.PL || die ./Build install || die } - -pkg_postinst(){ - einfo "It is also advisable to install sci-biology/repeatmasker" - einfo "and in turn register for sci-biology/repeatmasker-libraries" -}
