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commit: 8e3157e581a2503912b86bb5e48fb73e82c26cc9 |
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Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Tue Mar 31 20:18:38 2015 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Tue Mar 31 20:18:38 2015 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8e3157e5 |
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|
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sci-biology/amos: fix installation process and dependencies |
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|
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Package-Manager: portage-2.2.18 |
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|
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sci-biology/amos/ChangeLog | 9 ++- |
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sci-biology/amos/amos-3.1.0-r2.ebuild | 66 ++++++++++++++++++++++ |
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sci-biology/amos/amos-9999.ebuild | 27 ++++++++- |
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sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch | 15 +++++ |
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...mos-3.1.0-goBambus2.py-indent-and-cleanup.patch | 25 ++++++++ |
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5 files changed, 138 insertions(+), 4 deletions(-) |
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|
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diff --git a/sci-biology/amos/ChangeLog b/sci-biology/amos/ChangeLog |
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index 7d1df6d..9bdce77 100644 |
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--- a/sci-biology/amos/ChangeLog |
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+++ b/sci-biology/amos/ChangeLog |
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@@ -1,7 +1,14 @@ |
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# ChangeLog for sci-biology/amos |
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-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 |
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+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 |
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# $Header: $ |
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|
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+*amos-3.1.0-r2 (31 Mar 2015) |
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+ |
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+ 31 Mar 2015; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> |
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+ +amos-3.1.0-r2.ebuild, +files/amos-3.1.0-gcc-4.7.patch, |
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+ +files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch, amos-9999.ebuild: |
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+ sci-biology/amos: fix installation process and dependencies |
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+ |
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29 Dec 2013; Justin Lecher <jlec@g.o> -amos-3.1.0-r1.ebuild, |
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amos-9999.ebuild, -files/amos-3.1.0-gcc-4.7.patch, |
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-files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch, |
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|
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diff --git a/sci-biology/amos/amos-3.1.0-r2.ebuild b/sci-biology/amos/amos-3.1.0-r2.ebuild |
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new file mode 100644 |
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index 0000000..b814791 |
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--- /dev/null |
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+++ b/sci-biology/amos/amos-3.1.0-r2.ebuild |
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@@ -0,0 +1,66 @@ |
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+# Copyright 1999-2015 Gentoo Foundation |
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+# Distributed under the terms of the GNU General Public License v2 |
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+# $Header: /var/cvsroot/gentoo-x86/sci-biology/amos/amos-3.1.0-r1.ebuild,v 1.1 2013/12/29 00:24:16 jlec Exp $ |
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+ |
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+EAPI=5 |
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+ |
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+PYTHON_COMPAT=( python{2_6,2_7} ) |
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+ |
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+inherit eutils python-r1 |
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+ |
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+DESCRIPTION="A Modular, Open-Source whole genome assembler" |
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+HOMEPAGE="http://amos.sourceforge.net/" |
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+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" |
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+ |
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+LICENSE="Artistic" |
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+SLOT="0" |
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+KEYWORDS="~amd64 ~x86" |
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+IUSE="qt4" |
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+ |
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+DEPEND=" |
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+ dev-libs/boost |
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+ qt4? ( dev-qt/qtcore:4 )" |
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+RDEPEND="${DEPEND} |
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+ dev-lang/perl |
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+ dev-perl/DBI |
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+ dev-perl/Statistics-Descriptive |
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+ sci-biology/blat |
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+ sci-biology/mummer" |
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+ |
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+MAKEOPTS+=" -j1" |
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+ |
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+src_prepare() { |
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+ epatch \ |
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+ "${FILESDIR}"/${P}-gcc-4.7.patch \ |
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+ "${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch |
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+} |
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+ |
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+# amos-3.1.0-r2/work/amos-3.1.0/src/Bambus/Untangler/DotLib.pm |
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+# amos-3.1.0-r2/work/amos-3.1.0/src/Bambus/Untangler/AsmLib.pm |
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+# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTAreader.pm |
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+# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/AmosFoundation.pm |
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+# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/Foundation.pm |
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+# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/AmosLib.pm |
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+# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTArecord.pm |
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+# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/ParseFasta.pm |
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+# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/xfig.pm |
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+# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTAwriter.pm |
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+# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTAgrammar.pm |
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+# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTAiterator.pm |
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+ |
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+# --with-jellyfish location of Jellyfish headers |
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+ |
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+src_install() { |
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+ default |
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+ python_replicate_script "${ED}"/usr/bin/goBambus2 |
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+ # bambus needs TIGR::FASTAreader.pm and others |
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+ # configure --libdir sadly copies both *.a files and *.pm into /usr/lib64/AMOS/ and /usr/lib64/TIGR/, work around it |
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+ mkdir -p "${D}"/usr/share/"${PN}"/perl/AMOS || die |
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+ mv "${D}"/usr/lib64/AMOS/*.pm "${D}"/usr/share/"${PN}"/perl/AMOS || die |
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+ mkdir -p "${D}"/usr/share/"${PN}"/perl/TIGR || die |
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+ mv "${D}"/usr/lib64/TIGR/*.pm "${D}"/usr/share/"${PN}"/perl/TIGR || die |
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+ echo "PERL5LIB=/usr/share/${PN}/perl" > "${S}/99${PN}" |
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+ doenvd "${S}/99${PN}" || die |
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+ # move also /usr/lib64/AMOS/AMOS.py to /usr/bin |
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+ mv "${D}"/usr/lib64/AMOS/*.py "${D}"/usr/bin || die |
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+} |
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|
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diff --git a/sci-biology/amos/amos-9999.ebuild b/sci-biology/amos/amos-9999.ebuild |
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index baecc2f..610c3d6 100644 |
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--- a/sci-biology/amos/amos-9999.ebuild |
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+++ b/sci-biology/amos/amos-9999.ebuild |
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@@ -1,4 +1,4 @@ |
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-# Copyright 1999-2014 Gentoo Foundation |
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+# Copyright 1999-2015 Gentoo Foundation |
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# Distributed under the terms of the GNU General Public License v2 |
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# $Header: $ |
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|
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@@ -16,11 +16,32 @@ EGIT_REPO_URI="git://amos.git.sourceforge.net/gitroot/amos/amos" |
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LICENSE="Artistic" |
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SLOT="0" |
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KEYWORDS="" |
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-IUSE="" |
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+IUSE="mpi qt4" |
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|
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DEPEND=" |
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+ mpi? ( virtual/mpi ) |
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dev-libs/boost |
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- dev-qt/qtcore:4" |
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+ qt4? ( dev-qt/qtcore:4 ) |
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+ sci-biology/blat |
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+ sci-biology/jellyfish" |
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RDEPEND="${DEPEND} |
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dev-perl/DBI |
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+ dev-perl/Statistics-Descriptive |
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sci-biology/mummer" |
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+ |
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+# --with-jellyfish location of Jellyfish headers |
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+ |
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+src_install() { |
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+ default |
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+ python_replicate_script "${ED}"/usr/bin/goBambus2 |
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+ # bambus needs TIGR::FASTAreader.pm and others |
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+ # configure --libdir sadly copies both *.a files and *.pm into /usr/lib64/AMOS/ and /usr/lib64/TIGR/, work around it |
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+ mkdir -p "${D}/usr/share/${PN}/perl/AMOS" || die |
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+ mv "${D}"/usr/lib64/AMOS/*.pm "${D}/usr/share/${PN}/perl/AMOS" || die |
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+ mkdir -p "${D}"/usr/share/"${PN}"/perl/TIGR || die |
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+ mv "${D}"/usr/lib64/TIGR/*.pm "${D}"/usr/share/"${PN}"/perl/TIGR || die |
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+ echo "PERL5LIB=/usr/share/${PN}/perl" > "${S}/99${PN}" |
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+ doenvd "${S}/99${PN}" || die |
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+ # move also /usr/lib64/AMOS/AMOS.py to /usr/bin |
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+ mv "${D}"/usr/lib64/AMOS/*.py "${D}"/usr/bin || die |
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+} |
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|
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diff --git a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch |
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new file mode 100644 |
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index 0000000..de2a411 |
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--- /dev/null |
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+++ b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch |
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@@ -0,0 +1,15 @@ |
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+ src/Align/find-tandem.cc | 1 + |
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+ 1 files changed, 1 insertions(+), 0 deletions(-) |
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+ |
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+diff --git a/src/Align/find-tandem.cc b/src/Align/find-tandem.cc |
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+index ddf1cab..a29e21e 100644 |
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+--- a/src/Align/find-tandem.cc |
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++++ b/src/Align/find-tandem.cc |
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+@@ -7,6 +7,7 @@ |
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+ #include <vector> |
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+ #include <ctime> |
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+ #include <sys/time.h> |
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++#include <unistd.h> |
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+ using namespace std; |
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+ |
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+ const int OFFSET_TABLE_SIZE = 100; |
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|
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diff --git a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch |
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new file mode 100644 |
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index 0000000..97a8f59 |
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--- /dev/null |
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+++ b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch |
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@@ -0,0 +1,25 @@ |
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+--- amos-3.1.0/src/Pipeline/goBambus2.py.orig 2013-09-11 01:05:29.850090457 +0200 |
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++++ amos-3.1.0/src/Pipeline/goBambus2.py 2013-09-11 01:07:03.250090701 +0200 |
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+@@ -1,7 +1,7 @@ |
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+ #pipeline script for assembly + Bambus 2 |
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+ #contributed by Todd J Treangen |
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+ |
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+-import string, sys, os, subprocess#, spincursor |
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++import sys, os, subprocess#, spincursor |
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+ |
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+ RED = "\033[0;31m" |
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+ GREEN = "\033[0;32m" |
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+@@ -360,7 +360,7 @@ |
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+ print "\t\t%s...failed%s"%(RED,NONE) |
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+ sys.exit(1) |
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+ |
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+- p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) |
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++ p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) |
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+ |
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+ if xopt_dict["verbose"] == 1: |
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+ print "10) running OutputResults" |
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+@@ -388,4 +388,3 @@ |
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+ else: |
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+ print "\t\t%s...failed%s"%(RED,NONE) |
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+ sys.exit(1) |
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+-) |