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commit: 7dda553d5086989dc3507e2d3f86c21652c8aff3 |
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Author: Justin Lecher <jlec <AT> gentoo <DOT> org> |
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AuthorDate: Mon Sep 21 12:52:58 2015 +0000 |
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Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> |
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CommitDate: Mon Sep 21 12:52:58 2015 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7dda553d |
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|
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Drop obsolete package Sources unavailable |
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|
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Signed-off-by: Justin Lecher <jlec <AT> gentoo.org> |
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|
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sci-biology/tigr-assembler/ChangeLog | 15 -------- |
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sci-biology/tigr-assembler/files/run_TA | 32 ----------------- |
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sci-biology/tigr-assembler/metadata.xml | 10 ------ |
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.../tigr-assembler/tigr-assembler-2.0.ebuild | 40 ---------------------- |
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4 files changed, 97 deletions(-) |
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|
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diff --git a/sci-biology/tigr-assembler/ChangeLog b/sci-biology/tigr-assembler/ChangeLog |
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deleted file mode 100644 |
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index 8163ef1..0000000 |
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--- a/sci-biology/tigr-assembler/ChangeLog |
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+++ /dev/null |
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@@ -1,15 +0,0 @@ |
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-# ChangeLog for sci-biology/tigr-assembler |
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-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 |
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-# $Id$ |
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- |
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- 24 Jun 2011; Justin Lecher <jlec@g.o> tigr-assembler-2.0.ebuild: |
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- Some ebuild cleaning |
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- |
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- 27 Apr 2007; Andrey Kislyuk <weaver@×××××××××××.cx> |
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- +tigr-assembler-2.0.ebuild: |
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- Mass import from sunrise |
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- |
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- 19 Apr 2007; Andrey Kislyuk <weaver@×××××××××××.cx> +tigr-assembler-2.0.ebuild, |
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- +metadata.xml: |
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- new package (bug 175282) |
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- |
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|
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diff --git a/sci-biology/tigr-assembler/files/run_TA b/sci-biology/tigr-assembler/files/run_TA |
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deleted file mode 100644 |
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index 679c81d..0000000 |
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--- a/sci-biology/tigr-assembler/files/run_TA |
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+++ /dev/null |
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@@ -1,32 +0,0 @@ |
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-#!/bin/sh |
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- |
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-# Copyright @ 2000 The Institute for Genomic Research (TIGR). All rights |
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-# reserved. |
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-# |
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-# This software is provided "AS IS". The Institute for Genomic Research makes |
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-# no warranties, express or implied, including no representation or warranty |
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-# with respect to the performance of the software and derivatives or their |
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-# safety, effectiveness, or commercial viability. TIGR does not warrant the |
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-# merchantability or fitness of the software and derivatives for any |
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-# particular purpose, or that they may be exploited without infringing the |
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-# copyrights, patent rights or property rights of others. |
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-# |
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-# This software program may not be sold, leased, transferred, exported or |
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-# otherwise disclosed to anyone, in whole or in part, without written consent |
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-# of TIGR. |
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- |
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-if [ ! -e "$1" ] |
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-then |
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- asmg_options=$1 |
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- shift |
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-else |
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- asmg_options="" |
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-fi |
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- |
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-for file in $* |
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-do |
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- file_tail=`basename $file` |
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- file_root=${file_tail%%.*} |
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- 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 |
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-done |
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- |
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|
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diff --git a/sci-biology/tigr-assembler/metadata.xml b/sci-biology/tigr-assembler/metadata.xml |
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deleted file mode 100644 |
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index c07e96e..0000000 |
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--- a/sci-biology/tigr-assembler/metadata.xml |
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+++ /dev/null |
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@@ -1,10 +0,0 @@ |
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-<?xml version="1.0" encoding="UTF-8"?> |
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-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
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-<pkgmetadata> |
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- <herd>sci-biology</herd> |
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- <maintainer> |
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- <email>mmokrejs@×××××××××××××××.cz</email> |
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- <name>Martin Mokrejs</name> |
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- </maintainer> |
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- <longdescription>TIGR assembler</longdescription> |
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-</pkgmetadata> |
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|
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diff --git a/sci-biology/tigr-assembler/tigr-assembler-2.0.ebuild b/sci-biology/tigr-assembler/tigr-assembler-2.0.ebuild |
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deleted file mode 100644 |
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index fafbe68..0000000 |
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--- a/sci-biology/tigr-assembler/tigr-assembler-2.0.ebuild |
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+++ /dev/null |
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@@ -1,40 +0,0 @@ |
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-# Copyright 1999-2014 Gentoo Foundation |
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-# Distributed under the terms of the GNU General Public License v2 |
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-# $Id$ |
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- |
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-EAPI=3 |
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- |
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-DESCRIPTION="A whole-genome shotgun assembler from TIGR" |
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-HOMEPAGE="http://www.tigr.org/software/assembler/" |
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-SRC_URI="ftp://ftp.tigr.org/pub/software/assembler/TIGR_Assembler_v2.tar.gz" |
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- |
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-LICENSE="Artistic" |
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-SLOT="0" |
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-IUSE="" |
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-KEYWORDS="~amd64 ~x86" |
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- |
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-S="${WORKDIR}/TIGR_Assembler_v2" |
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- |
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-src_prepare() { |
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- cd "${S}"/bin || die |
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- mv run_TA run_TA.csh || die |
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- cp "${FILESDIR}"/run_TA run_TA || die |
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-} |
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-src_compile() { |
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- sed -i 's/^CC/#CC/' "${S}/src/Makefile" || die "sed failed" |
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- sed -i 's/CFLAGS.*= -O/CFLAGS := ${CFLAGS}/' "${S}/src/Makefile" || die "sed failed" |
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- cd "${S}/src" || die |
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- emake || die "emake failed" |
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-} |
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- |
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-src_install() { |
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- dobin bin/{run_TA,run_TA.csh,TIGR_Assembler} || die |
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- dodoc README || die |
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-} |
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- |
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-src_test() { |
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- cd "${S}"/data/201.pre || die |
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- PATH="${D}"/usr/bin:$PATH run_TA '-s -q 201.qual -C 201.contigs' 201.seq || die "Failed to execute run_TA" |
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- for f in *; do diff -I "^ed_date" -u -w ../201.post/$f $f; done || die "Found some differences in the output files compared to expected results." |
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- for f in 201.align/*; do diff -u -w ../201.post/$f $f; done || die "Found some differences in the output files compared to expected results." |
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-} |