commit: 27400967c2a16c819a1a57f687b4fbb3bdb18b7d Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Fri Apr 17 22:20:44 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Fri Apr 17 22:20:44 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=27400967
sci-biology/transdecoder: fixed installation of perl-related files Package-Manager: portage-2.2.18 sci-biology/transdecoder/ChangeLog | 4 ++++ sci-biology/transdecoder/transdecoder-2.0.1.ebuild | 14 +++++--------- .../transdecoder/transdecoder-20140704.ebuild | 21 ++++++++++++--------- 3 files changed, 21 insertions(+), 18 deletions(-) diff --git a/sci-biology/transdecoder/ChangeLog b/sci-biology/transdecoder/ChangeLog index 7e276d1..f69ae4d 100644 --- a/sci-biology/transdecoder/ChangeLog +++ b/sci-biology/transdecoder/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 17 Apr 2015; Martin Mokrejs <mmokr...@fold.natur.cuni.cz> + transdecoder-2.0.1.ebuild, transdecoder-20140704.ebuild: + sci-biology/transdecoder: fixed installation of perl-related files + 19 Mar 2015; Martin Mokrejs <mmokr...@fold.natur.cuni.cz> transdecoder-2.0.1.ebuild: dropped hmmer dependency altogether, added pkg_postinst() with diff --git a/sci-biology/transdecoder/transdecoder-2.0.1.ebuild b/sci-biology/transdecoder/transdecoder-2.0.1.ebuild index 43edbbb..b4476f7 100644 --- a/sci-biology/transdecoder/transdecoder-2.0.1.ebuild +++ b/sci-biology/transdecoder/transdecoder-2.0.1.ebuild @@ -4,7 +4,8 @@ EAPI=5 -inherit perl-module +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module eutils toolchain-funcs DESCRIPTION="Extract ORF/CDS regions from FASTA sequences" HOMEPAGE="http://sourceforge.net/projects/transdecoder/"; @@ -36,14 +37,9 @@ S="${WORKDIR}"/TransDecoder-2.0.1 src_install(){ dobin TransDecoder *.pl util/*.pl util/*.sh - eval `perl '-V:installvendorlib'` - vendor_lib_install_dir="${installvendorlib}" - dodir ${vendor_lib_install_dir}/TransDecoder - insinto ${vendor_lib_install_dir}/TransDecoder - doins PerlLib/*.pm - echo "PERL5LIB="${vendor_lib_install_dir}"/TransDecoder" > ${S}"/99TransDecoder" - doenvd ${S}"/99TransDecoder" || die - + perl_set_version + insinto ${VENDOR_LIB}/TransDecoder + dobin PerlLib/*.pm einfo "Fetch on your own:" einfo "wget --mirror -nH -nd http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin"; einfo "hmmpress Pfam-AB.hmm.bin" diff --git a/sci-biology/transdecoder/transdecoder-20140704.ebuild b/sci-biology/transdecoder/transdecoder-20140704.ebuild index ed060b3..db7c9a8 100644 --- a/sci-biology/transdecoder/transdecoder-20140704.ebuild +++ b/sci-biology/transdecoder/transdecoder-20140704.ebuild @@ -4,7 +4,8 @@ EAPI=5 -inherit perl-module +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module eutils toolchain-funcs DESCRIPTION="Extract ORF/CDS regions from FASTA sequences" HOMEPAGE="http://sourceforge.net/projects/transdecoder/"; @@ -37,15 +38,17 @@ src_prepare(){ src_install(){ dobin TransDecoder *.pl util/*.pl util/*.sh - eval `perl '-V:installvendorlib'` - vendor_lib_install_dir="${installvendorlib}" - dodir ${vendor_lib_install_dir}/TransDecoder - insinto ${vendor_lib_install_dir}/TransDecoder - doins PerlLib/*.pm - echo "PERL5LIB="${vendor_lib_install_dir}"/TransDecoder" > ${S}"/99TransDecoder" - doenvd ${S}"/99TransDecoder" || die - + perl_set_version + insinto ${VENDOR_LIB}/TransDecoder + dobin PerlLib/*.pm einfo "Fetch on your own:" einfo "wget --mirror -nH -nd http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin"; einfo "hmmpress Pfam-AB.hmm.bin" } + +pkg_postinst(){ + einfo "It is recommended to use TransDecoder with hmmer-3 or at least NCBI blast" + einfo "from either sci-biology/ncbi-blast+ (released more often) or" + einfo "from sci-biology/ncbi-toolkit++ (huge bundle with releases and less frequent bugfixes)" + einfo "Author says the minimum requirement is sci-biology/cd-hit" +}
