diff options
| author |   Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2015-04-27 14:48:28 +0200 |
|---|---|---|
| committer | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2015-04-27 14:48:28 +0200 |
| commit | 5f4adb868d4fb9b93c3db90ad3aa8354d3d132b9 (patch) | |
| tree | 20d0454c49772603d37a58f147a0a537e301e1ad | |
| parent | sci-biology/BRAKER: new package; somehow RDEPENDs are installed wrongly: Can'... (diff) | |
| download | sci-5f4adb86.tar.gz sci-5f4adb86.tar.bz2 sci-5f4adb86.zip | |
sci-biology/transdecoder: drop old
Package-Manager: portage-2.2.18
| -rw-r--r-- | sci-biology/transdecoder/ChangeLog | 4 | ||||
| -rw-r--r-- | sci-biology/transdecoder/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/transdecoder/transdecoder-2.0.1.ebuild | 5 | ||||
| -rw-r--r-- | sci-biology/transdecoder/transdecoder-20140704.ebuild | 54 |
4 files changed, 7 insertions, 57 deletions
diff --git a/sci-biology/transdecoder/ChangeLog b/sci-biology/transdecoder/ChangeLog index f69ae4d0c..8e5aa085b 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: $ + 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + -transdecoder-20140704.ebuild, transdecoder-2.0.1.ebuild: + sci-biology/transdecoder: drop old + 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> transdecoder-2.0.1.ebuild, transdecoder-20140704.ebuild: sci-biology/transdecoder: fixed installation of perl-related files diff --git a/sci-biology/transdecoder/Manifest b/sci-biology/transdecoder/Manifest index ac955bf3b..0d0169f8b 100644 --- a/sci-biology/transdecoder/Manifest +++ b/sci-biology/transdecoder/Manifest @@ -1,2 +1 @@ -DIST TransDecoder_r20140704.tar.gz 21189681 SHA256 fb53c9601c4ae9b3cd8e937f158ae3f15439115609bc7658effffa24af53517e SHA512 fa70e440c3f8b8d11da780858ff6433adf9065b126b29eb047983b17913e382c677a272881ee78be8e30867bbd447eb9bda71bd11abda5203d6a3abfb5316e90 WHIRLPOOL d603d06c8c1e84f3e721c0f5e43b2519766eaae1fc0456ece07ff43c13971706aecb24473813b7606ca885d2ef526648fc28f874200a53037b4aa6b291c4864d DIST transdecoder-2.0.1.tar.gz 9925281 SHA256 ce069da72c8a04e739f8c057af4f97187bf587d3f0d3db40465dfc2c89393e22 SHA512 fd12aeda089a12036e288e58eb0a3c3b9bb1f104f6821102d84ba6ddaec1a9dd32ec7937cd87129ff9814c7c8e26b6b98d27c6af8edd7ed6b5335c4878f649de WHIRLPOOL 61c6b7fe5684becdb28a3bccb113fea07889a2c4e6627e92cd27c1a90ca53f5a88504e048363a1322f1108dd6ebd5549c52aee9d438fbcfb2023390c79c126ec diff --git a/sci-biology/transdecoder/transdecoder-2.0.1.ebuild b/sci-biology/transdecoder/transdecoder-2.0.1.ebuild index b4476f72e..1774cafb6 100644 --- a/sci-biology/transdecoder/transdecoder-2.0.1.ebuild +++ b/sci-biology/transdecoder/transdecoder-2.0.1.ebuild @@ -16,11 +16,12 @@ SLOT="0" KEYWORDS="" IUSE="" -DEPEND=" +DEPEND="" +RDEPEND="${DEPEND} + sci-biology/hmmer sci-biology/cd-hit sci-biology/parafly sci-biology/ffindex" -RDEPEND="${DEPEND}" S="${WORKDIR}"/TransDecoder-2.0.1 diff --git a/sci-biology/transdecoder/transdecoder-20140704.ebuild b/sci-biology/transdecoder/transdecoder-20140704.ebuild deleted file mode 100644 index db7c9a889..000000000 --- a/sci-biology/transdecoder/transdecoder-20140704.ebuild +++ /dev/null @@ -1,54 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -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/" -SRC_URI="http://downloads.sourceforge.net/project/transdecoder/TransDecoder_r20140704.tar.gz" - -LICENSE="BSD-BroadInstitute" -SLOT="0" -KEYWORDS="" -IUSE="" - -DEPEND="sci-biology/hmmer - sci-biology/cd-hit - sci-biology/parafly - sci-biology/ffindex" -RDEPEND="${DEPEND}" - -S="${WORKDIR}"/TransDecoder_r20140704 - -src_prepare(){ - rm -rf 3rd_party - mv Makefile Makefile.old - epatch "${FILESDIR}"/TransDecoder.patch - epatch "${FILESDIR}"/pfam_runner.pl.patch -} - -# avoid fetching 1.5TB "${S}"/pfam/Pfam-AB.hmm.bin, see -# "Re: [Transdecoder-users] Announcement: Transdecoder release r20140704" thread in archives -# -# you cna get it from http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin - -src_install(){ - dobin TransDecoder *.pl util/*.pl util/*.sh - 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" -} |