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-rw-r--r--sci-biology/last/Manifest1
-rw-r--r--sci-biology/last/files/last-852-fix-build-system.patch54
-rw-r--r--sci-biology/last/files/last-852-portable-shebangs.patch56
-rw-r--r--sci-biology/last/last-852.ebuild42
-rw-r--r--sci-biology/last/metadata.xml8
5 files changed, 0 insertions, 161 deletions
diff --git a/sci-biology/last/Manifest b/sci-biology/last/Manifest
deleted file mode 100644
index eadb2539b..000000000
--- a/sci-biology/last/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST last-852.zip 721683 BLAKE2B e2a8d1c59d369f580e46723c2153ffc406f781502c7d7fa60dbc50556ac14703122d76c1a2ec8d938c6dcf0954d02347ee3d4beef60515839c248fa7e6467e18 SHA512 9945967efb5025b72507dfeb28531e1595d9691096dc2d074711fd1f5cce92714341a387577b7c6054f3b2605084528817381ed6f39bd32e828341f4a06380b9
diff --git a/sci-biology/last/files/last-852-fix-build-system.patch b/sci-biology/last/files/last-852-fix-build-system.patch
deleted file mode 100644
index 6ee4f5a67..000000000
--- a/sci-biology/last/files/last-852-fix-build-system.patch
+++ /dev/null
@@ -1,54 +0,0 @@
---- last-852/makefile.ori 2016-12-13 07:22:11.000000000 +0100
-+++ last-852/makefile 2017-05-10 11:04:14.610665834 +0200
-@@ -1,6 +1,7 @@
--CXXFLAGS = -O3 -std=c++11 -pthread -DHAS_CXX_THREADS
-+CXXFLAGS ?= -O3
-+CXXFLAGS += -std=c++11 -pthread -DHAS_CXX_THREADS
- all:
-- @cd src && $(MAKE) CXXFLAGS="$(CXXFLAGS)"
-+ $(MAKE) -C src
-
- progs = src/lastdb src/lastal src/last-split src/last-merge-batches \
- src/last-pair-probs src/lastdb8 src/lastal8 src/last-split8
-@@ -13,17 +14,17 @@
- cp $(progs) scripts/* $(bindir)
-
- clean:
-- @cd src && $(MAKE) clean
-+ $(MAKE) -C src clean
-
- html:
-- @cd doc && $(MAKE)
-+ $(MAKE) -C doc
-
- distdir = last-`hg id -n`
-
- RSYNCFLAGS = -aC --exclude '*8' --exclude 'last??' --exclude last-split --exclude last-merge-batches --exclude last-pair-probs
-
- dist: log html
-- @cd src && $(MAKE) version.hh CyclicSubsetSeedData.hh ScoreMatrixData.hh
-+ $(MAKE) -C src version.hh CyclicSubsetSeedData.hh ScoreMatrixData.hh
- rsync $(RSYNCFLAGS) build doc examples makefile scripts src data *.txt $(distdir)
- zip -qrm $(distdir) $(distdir)
-
---- last-852/src/makefile.ori 2016-12-13 06:53:24.000000000 +0100
-+++ last-852/src/makefile 2017-05-10 11:05:22.792501835 +0200
-@@ -1,12 +1,13 @@
--CXX = g++
--CC = gcc
-+CXX ?= g++
-+CC ?= gcc
-
--CXXFLAGS = -O3 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef \
---Wcast-align -pedantic -g -std=c++11 -pthread -DHAS_CXX_THREADS
-+CXXFLAGS ?= -O3 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef \
-+-Wcast-align -pedantic -g
-+CXXFLAGS += -std=c++11 -pthread -DHAS_CXX_THREADS
- # -Wconversion
- # -fomit-frame-pointer ?
-
--CFLAGS = -Wall -O2
-+CFLAGS ?= -Wall -O2
-
- alpObj = alp/sls_alignment_evaluer.o alp/sls_pvalues.o \
- alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o \
diff --git a/sci-biology/last/files/last-852-portable-shebangs.patch b/sci-biology/last/files/last-852-portable-shebangs.patch
deleted file mode 100644
index c2131da63..000000000
--- a/sci-biology/last/files/last-852-portable-shebangs.patch
+++ /dev/null
@@ -1,56 +0,0 @@
---- last-852/scripts/last-dotplot.ori 2017-05-10 11:14:05.206748593 +0200
-+++ last-852/scripts/last-dotplot 2017-05-10 11:15:31.009058957 +0200
-@@ -1,4 +1,4 @@
--#! /usr/bin/env python
-+#! /usr/bin/env python2
-
- # Read pair-wise alignments in MAF or LAST tabular format: write an
- # "Oxford grid", a.k.a. dotplot.
---- last-852/scripts/last-map-probs.ori 2017-05-10 11:14:11.856927669 +0200
-+++ last-852/scripts/last-map-probs 2017-05-10 11:15:35.139288498 +0200
-@@ -1,4 +1,4 @@
--#! /usr/bin/env python
-+#! /usr/bin/env python2
-
- # Copyright 2010, 2011, 2012, 2014 Martin C. Frith
-
---- last-852/scripts/last-postmask.ori 2017-05-10 11:14:19.817142021 +0200
-+++ last-852/scripts/last-postmask 2017-05-10 11:15:44.939556158 +0200
-@@ -1,4 +1,4 @@
--#! /usr/bin/env python
-+#! /usr/bin/env python2
-
- # Copyright 2014 Martin C. Frith
-
---- last-852/scripts/last-train.ori 2017-05-10 11:14:27.687353953 +0200
-+++ last-852/scripts/last-train 2017-05-10 11:15:48.679658384 +0200
-@@ -1,4 +1,4 @@
--#! /usr/bin/env python
-+#! /usr/bin/env python2
- # Copyright 2015 Martin C. Frith
-
- import math, optparse, os, random, signal, subprocess, sys, tempfile
---- last-852/scripts/maf-convert.ori 2017-05-10 11:14:34.267531142 +0200
-+++ last-852/scripts/maf-convert 2017-05-10 11:15:52.439761157 +0200
-@@ -1,4 +1,4 @@
--#! /usr/bin/env python
-+#! /usr/bin/env python2
- # Copyright 2010, 2011, 2013, 2014 Martin C. Frith
- # Read MAF-format alignments: write them in other formats.
- # Seems to work with Python 2.x, x>=6
---- last-852/scripts/maf-join.ori 2017-05-10 11:14:41.407723414 +0200
-+++ last-852/scripts/maf-join 2017-05-10 11:15:56.699877600 +0200
-@@ -1,4 +1,4 @@
--#! /usr/bin/env python
-+#! /usr/bin/env python2
-
- # Copyright 2009, 2010, 2011 Martin C. Frith
-
---- last-852/scripts/maf-swap.ori 2017-05-10 11:14:48.417912185 +0200
-+++ last-852/scripts/maf-swap 2017-05-10 11:16:02.300030669 +0200
-@@ -1,4 +1,4 @@
--#! /usr/bin/env python
-+#! /usr/bin/env python2
-
- # Read MAF-format alignments, and write them, after moving the Nth
- # sequence to the top in each alignment.
diff --git a/sci-biology/last/last-852.ebuild b/sci-biology/last/last-852.ebuild
deleted file mode 100644
index b063550b3..000000000
--- a/sci-biology/last/last-852.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit toolchain-funcs python-single-r1
-
-DESCRIPTION="Genome-scale comparison of biological sequences"
-HOMEPAGE="http://last.cbrc.jp/"
-SRC_URI="http://last.cbrc.jp/${P}.zip"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}"
-DEPEND="app-arch/unzip"
-
-PATCHES=(
- "${FILESDIR}"/${PN}-${PV}-fix-build-system.patch
- "${FILESDIR}"/${PN}-${PV}-portable-shebangs.patch
-)
-
-src_configure() {
- tc-export CC CXX
-}
-
-src_install() {
- local DOCS=( doc/*.txt ChangeLog.txt README.txt )
- local HTML_DOCS=( doc/*html )
- einstalldocs
-
- dobin src/lastdb src/lastal src/last-split src/last-merge-batches \
- src/last-pair-probs src/lastdb8 src/lastal8 src/last-split8
-
- cd scripts || die
- dobin *
-}
diff --git a/sci-biology/last/metadata.xml b/sci-biology/last/metadata.xml
deleted file mode 100644
index 8417d1580..000000000
--- a/sci-biology/last/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>