[gentoo-commits] proj/sci:master commit in: sci-biology/transdecoder/

[Martin Mokrejs]

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 <mmokrejs@×××××××××××××××.cz>
+  -transdecoder-20140704.ebuild, transdecoder-2.0.1.ebuild:
+  sci-biology/transdecoder: drop old
+
   17 Apr 2015; Martin Mokrejs <mmokrejs@×××××××××××××××.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"
-}