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commit: 024e8b388e709b7340cfcb8c620d057fc6bcdef4 |
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Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Mon Mar 30 18:25:09 2015 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Mon Mar 30 18:25:09 2015 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=024e8b38 |
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|
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sci-biology/maker: improving the ebuild, needs some perl packages to be first introduced into portage tree; needs proper install and to avoid bundled 3rd-party binaries, not sure if the perl modules are a copy of bioperl or not |
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|
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Package-Manager: portage-2.2.18 |
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|
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sci-biology/maker/ChangeLog | 12 ++++++++ |
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sci-biology/maker/maker-2.31.8.ebuild | 54 +++++++++++++++++++++++++++++++++++ |
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sci-biology/maker/metadata.xml | 9 ++++++ |
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3 files changed, 75 insertions(+) |
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|
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diff --git a/sci-biology/maker/ChangeLog b/sci-biology/maker/ChangeLog |
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new file mode 100644 |
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index 0000000..d954ed6 |
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--- /dev/null |
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+++ b/sci-biology/maker/ChangeLog |
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@@ -0,0 +1,12 @@ |
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+# ChangeLog for sci-biology/MAKER |
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+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 |
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+# $Header: $ |
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+ |
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+ 16 Sep 2014; Christoph Junghans <ottxor@g.o> MAKER-9999.ebuild: |
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+ added license |
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+ |
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+*MAKER-9999 (23 Mar 2014) |
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+ |
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+ 23 Mar 2014; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> +MAKER-9999.ebuild, |
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+ +metadata.xml: |
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+ a skeleton for a new package |
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|
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diff --git a/sci-biology/maker/maker-2.31.8.ebuild b/sci-biology/maker/maker-2.31.8.ebuild |
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new file mode 100644 |
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index 0000000..6bc8ff5 |
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--- /dev/null |
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+++ b/sci-biology/maker/maker-2.31.8.ebuild |
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@@ -0,0 +1,54 @@ |
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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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+EAPI=5 |
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+ |
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+inherit eutils perl-module |
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+ |
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+DESCRIPTION="A genome annotation viewer and pipeline for small eukaryota and prokaryota" |
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+HOMEPAGE="http://www.yandell-lab.org/software/maker.html" |
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+SRC_URI="maker-"${PV}".tgz" |
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+ |
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+RESTRICT="fetch" |
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+ |
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+# for academia: GPL-v2 or Artistic-2 |
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+# for commercial: ask |
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+LICENSE="|| ( GPL-2 Artistic-2 )" |
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+SLOT="0" |
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+KEYWORDS="" |
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+IUSE="" |
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+ |
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+# http://search.cpan.org/~rgarcia/Perl-Unsafe-Signals-0.02/ |
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+# http://search.cpan.org/~rybskej/forks-0.36/lib/forks.pm |
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+# http://search.cpan.org/~rybskej/forks-0.36/lib/forks/shared.pm |
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+# http://search.cpan.org/~dconway/IO-Prompt-0.997002/lib/IO/Prompt.pm |
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+DEPEND="virtual/mpi |
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+ dev-perl/DBI |
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+ dev-perl/DBD-SQLite |
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+ dev-perl/File-Which |
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+ dev-perl/Bit-Vector |
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+ dev-perl/Inline-C |
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+ dev-perl/IO-All |
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+ dev-perl/libwww-perl |
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+ dev-perl/DBD-Pg |
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+ virtual/perl-Module-Build |
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+ >=sci-biology/bioperl-1.6 |
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+ sci-biology/ncbi-tools || ( sci-biology/ncbi-tools++ ) |
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+ sci-biology/snap |
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+ sci-biology/repeatmasker |
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+ sci-biology/exonerate |
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+ sci-biology/augustus" |
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+RDEPEND="${DEPEND}" |
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+ |
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+S="${WORKDIR}"/maker/src |
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+ |
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+pkg_nofetch() { |
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+ einfo "Please visit ${HOMEPAGE} and obtain the file" |
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+ einfo "maker-"${PV}".tgz and place it into ${DISTDIR}" |
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+} |
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+ |
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+src_compile(){ |
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+ perl Build.PL || die |
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+ ./Build install || die |
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+} |
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|
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diff --git a/sci-biology/maker/metadata.xml b/sci-biology/maker/metadata.xml |
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new file mode 100644 |
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index 0000000..2bc8930 |
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--- /dev/null |
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+++ b/sci-biology/maker/metadata.xml |
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@@ -0,0 +1,9 @@ |
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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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+</pkgmetadata> |