commit: 62fb9efa4877ad36d22202ddd025e5801fae9fb7 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Wed May 10 09:40:54 2017 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Wed May 10 09:40:54 2017 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=62fb9efa
sci-biology/last: version bump The src_install() part does not re-introduce the *.sh and *.py file extensions like previous -299 ebuild. Package-Manager: Portage-2.3.5, Repoman-2.3.2 .../last/files/last-852-fix-build-system.patch | 54 +++++++++++++++++++++ .../last/files/last-852-portable-shebangs.patch | 56 ++++++++++++++++++++++ sci-biology/last/last-852.ebuild | 42 ++++++++++++++++ sci-biology/last/metadata.xml | 8 ++++ 4 files changed, 160 insertions(+) diff --git a/sci-biology/last/files/last-852-fix-build-system.patch b/sci-biology/last/files/last-852-fix-build-system.patch new file mode 100644 index 000000000..6ee4f5a67 --- /dev/null +++ b/sci-biology/last/files/last-852-fix-build-system.patch @@ -0,0 +1,54 @@ +--- 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 new file mode 100644 index 000000000..c2131da63 --- /dev/null +++ b/sci-biology/last/files/last-852-portable-shebangs.patch @@ -0,0 +1,56 @@ +--- 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 new file mode 100644 index 000000000..b063550b3 --- /dev/null +++ b/sci-biology/last/last-852.ebuild @@ -0,0 +1,42 @@ +# 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 new file mode 100644 index 000000000..959160fe4 --- /dev/null +++ b/sci-biology/last/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="project"> + <email>[email protected]</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata>
