[gentoo-commits] proj/sci:master commit in: sci-biology/tigr-assembler/, sci-biology/tigr-assembler/files/

[gentoo-commits] proj/sci:master commit in: sci-biology/tigr-assembler/, sci-biology/tigr-assembler/files/

[Justin Lecher]

commit:     7dda553d5086989dc3507e2d3f86c21652c8aff3
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Sep 21 12:52:58 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Sep 21 12:52:58 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7dda553d

Drop obsolete package  Sources unavailable

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 sci-biology/tigr-assembler/ChangeLog               | 15 --------
 sci-biology/tigr-assembler/files/run_TA            | 32 -----------------
 sci-biology/tigr-assembler/metadata.xml            | 10 ------
 .../tigr-assembler/tigr-assembler-2.0.ebuild       | 40 ----------------------
 4 files changed, 97 deletions(-)

diff --git a/sci-biology/tigr-assembler/ChangeLog b/sci-biology/tigr-assembler/ChangeLog
deleted file mode 100644
index 8163ef1..0000000
--- a/sci-biology/tigr-assembler/ChangeLog
+++ /dev/null
@@ -1,15 +0,0 @@
-# ChangeLog for sci-biology/tigr-assembler
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Id$
-
-  24 Jun 2011; Justin Lecher <jlec@gentoo.org> tigr-assembler-2.0.ebuild:
-  Some ebuild cleaning
-
-  27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx>
-  +tigr-assembler-2.0.ebuild:
-  Mass import from sunrise
-
-  19 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +tigr-assembler-2.0.ebuild,
-  +metadata.xml:
-  new package (bug 175282)
-

diff --git a/sci-biology/tigr-assembler/files/run_TA b/sci-biology/tigr-assembler/files/run_TA
deleted file mode 100644
index 679c81d..0000000
--- a/sci-biology/tigr-assembler/files/run_TA
+++ /dev/null
@@ -1,32 +0,0 @@
-#!/bin/sh
-
-# Copyright @ 2000 The Institute for Genomic Research (TIGR). All rights
-# reserved.
-#
-# This software is provided "AS IS". The Institute for Genomic Research makes
-# no warranties, express or implied, including no representation or warranty
-# with respect to the performance of the software and derivatives or their
-# safety, effectiveness, or commercial viability. TIGR does not warrant the
-# merchantability or fitness of the software and derivatives for any
-# particular purpose, or that they may be exploited without infringing the
-# copyrights, patent rights or property rights of others.
-#
-# This software program may not be sold, leased, transferred, exported or
-# otherwise disclosed to anyone, in whole or in part, without written consent
-# of TIGR.
-
-if [ ! -e "$1" ] 
-then
-	asmg_options=$1
-	shift
-else
-	asmg_options=""
-fi
-
-for file in $*
-do
-	file_tail=`basename $file`
-	file_root=${file_tail%%.*}
-	TIGR_Assembler -n ${file_root} -g 8 -l 40 -e 15 -p 97.5 -a ${file_root}.align -f ${file_root}.fasta ${asmg_options} ${file_root}.scratch < ${file} > ${file_root}.asm 2> ${file_root}.error
-done
-

diff --git a/sci-biology/tigr-assembler/metadata.xml b/sci-biology/tigr-assembler/metadata.xml
deleted file mode 100644
index c07e96e..0000000
--- a/sci-biology/tigr-assembler/metadata.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?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>
-	<longdescription>TIGR assembler</longdescription>
-</pkgmetadata>

diff --git a/sci-biology/tigr-assembler/tigr-assembler-2.0.ebuild b/sci-biology/tigr-assembler/tigr-assembler-2.0.ebuild
deleted file mode 100644
index fafbe68..0000000
--- a/sci-biology/tigr-assembler/tigr-assembler-2.0.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=3
-
-DESCRIPTION="A whole-genome shotgun assembler from TIGR"
-HOMEPAGE="http://www.tigr.org/software/assembler/"
-SRC_URI="ftp://ftp.tigr.org/pub/software/assembler/TIGR_Assembler_v2.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/TIGR_Assembler_v2"
-
-src_prepare() {
-	cd "${S}"/bin || die
-	mv run_TA run_TA.csh || die
-	cp "${FILESDIR}"/run_TA run_TA || die
-}
-src_compile() {
-	sed -i 's/^CC/#CC/' "${S}/src/Makefile" || die "sed failed"
-	sed -i 's/CFLAGS.*= -O/CFLAGS := ${CFLAGS}/' "${S}/src/Makefile" || die "sed failed"
-	cd "${S}/src" || die
-	emake || die "emake failed"
-}
-
-src_install() {
-	dobin bin/{run_TA,run_TA.csh,TIGR_Assembler} || die
-	dodoc README || die
-}
-
-src_test() {
-	cd "${S}"/data/201.pre || die
-	PATH="${D}"/usr/bin:$PATH run_TA '-s -q 201.qual -C 201.contigs' 201.seq || die "Failed to execute run_TA"
-	for f in *; do diff -I "^ed_date" -u -w ../201.post/$f $f; done || die "Found some differences in the output files compared to expected results."
-	for f in 201.align/*; do diff -u -w ../201.post/$f $f; done || die "Found some differences in the output files compared to expected results."
-}