commit: 5f4adb868d4fb9b93c3db90ad3aa8354d3d132b9
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Apr 27 12:48:28 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Apr 27 12:48:28 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=5f4adb86
sci-biology/transdecoder: drop old
Package-Manager: portage-2.2.18
sci-biology/transdecoder/ChangeLog | 4 ++
sci-biology/transdecoder/transdecoder-2.0.1.ebuild | 5 +-
.../transdecoder/transdecoder-20140704.ebuild | 54 ----------------------
3 files changed, 7 insertions(+), 56 deletions(-)
diff --git a/sci-biology/transdecoder/ChangeLog
b/sci-biology/transdecoder/ChangeLog
index f69ae4d..8e5aa08 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 <mmokr...@fold.natur.cuni.cz>
+ -transdecoder-20140704.ebuild, transdecoder-2.0.1.ebuild:
+ sci-biology/transdecoder: drop old
+
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
diff --git a/sci-biology/transdecoder/transdecoder-2.0.1.ebuild
b/sci-biology/transdecoder/transdecoder-2.0.1.ebuild
index b4476f7..1774caf 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 db7c9a8..0000000
--- 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"
-}
