From: "Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>
To: gentoo-commits@lists.gentoo.org
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/transdecoder/
Date: Thu, 8 Jan 2015 22:35:43 +0000 (UTC) [thread overview]
Message-ID: <1420756272.7d88d8fde0145c729b2cf3f147370866db7ed14c.mmokrejs@gentoo> (raw)
commit: 7d88d8fde0145c729b2cf3f147370866db7ed14c
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jan 8 22:31:12 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jan 8 22:31:12 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7d88d8fd
sci-biology/transdecoder: new package
Package-Manager: portage-2.2.7
---
sci-biology/transdecoder/ChangeLog | 9 +++++
sci-biology/transdecoder/metadata.xml | 9 +++++
.../transdecoder/transdecoder-20140704.ebuild | 44 ++++++++++++++++++++++
3 files changed, 62 insertions(+)
diff --git a/sci-biology/transdecoder/ChangeLog b/sci-biology/transdecoder/ChangeLog
new file mode 100644
index 0000000..252ef53
--- /dev/null
+++ b/sci-biology/transdecoder/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/transdecoder
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*transdecoder-20140704 (08 Jan 2015)
+
+ 08 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml,
+ +transdecoder-20140704.ebuild:
+ sci-biology/transdecoder: new package
diff --git a/sci-biology/transdecoder/metadata.xml b/sci-biology/transdecoder/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/transdecoder/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/transdecoder/transdecoder-20140704.ebuild b/sci-biology/transdecoder/transdecoder-20140704.ebuild
new file mode 100644
index 0000000..c539231
--- /dev/null
+++ b/sci-biology/transdecoder/transdecoder-20140704.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit perl-module
+
+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="~amd64"
+IUSE=""
+
+DEPEND="sys-cluster/openmpi
+ 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
+}
+
+# avoid fetching 1.5TB "${S}"/pfam/Pfam-AB.hmm.bin, see
+# "Re: [Transdecoder-users] Announcement: Transdecoder release r20140704" thread in archives
+#
+# you cna get it from http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin
+
+src_install(){
+ dobin TransDecoder *.pl util/*.pl util/*.sh
+ eval `perl '-V:installvendorlib'`
+ vendor_lib_install_dir="${installvendorlib}"
+ dodir ${vendor_lib_install_dir}
+ insinto ${vendor_lib_install_dir}
+ doins PerlLib/*.pm
+}
next reply other threads:[~2015-01-08 22:35 UTC|newest]
Thread overview: 15+ messages / expand[flat|nested] mbox.gz Atom feed top
2015-01-08 22:35 Martin Mokrejs [this message]
-- strict thread matches above, loose matches on Subject: below --
2015-01-10 1:18 [gentoo-commits] proj/sci:master commit in: sci-biology/transdecoder/ Martin Mokrejs
2015-02-15 16:57 Martin Mokrejs
2015-03-19 10:37 Martin Mokrejs
2015-03-19 10:47 Martin Mokrejs
2015-04-17 22:21 Martin Mokrejs
2015-04-27 12:48 Martin Mokrejs
2015-04-27 12:49 Martin Mokrejs
2015-04-27 13:04 Martin Mokrejs
2015-06-06 10:23 [gentoo-commits] proj/sci:master commit in: sci-biology/TransDecoder/ Justin Lecher
2015-11-19 20:35 Martin Mokrejs
2015-11-19 20:56 Martin Mokrejs
2015-12-25 21:00 Marius Brehler
2016-07-11 9:11 Martin Mokrejs
2021-01-19 16:26 Andrew Ammerlaan
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