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commit: ae7eb86ca691a1713ac4afef719d7baeb376e45f |
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Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Fri Mar 28 14:00:53 2014 +0000 |
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Commit: Nicolas Bock <nicolasbock <AT> gmail <DOT> com> |
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CommitDate: Mon Mar 31 15:27:34 2014 +0000 |
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URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ae7eb86c |
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|
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sci-biology/biopieces: skeleton for a new package; has it's own install.sh script |
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|
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Package-Manager: portage-2.2.7 |
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|
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--- |
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sci-biology/biopieces/ChangeLog | 11 +++++ |
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sci-biology/biopieces/biopieces-0.51.ebuild | 63 +++++++++++++++++++++++++++++ |
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sci-biology/biopieces/biopieces-9999.ebuild | 63 +++++++++++++++++++++++++++++ |
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sci-biology/biopieces/metadata.xml | 9 +++++ |
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4 files changed, 146 insertions(+) |
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|
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diff --git a/sci-biology/biopieces/ChangeLog b/sci-biology/biopieces/ChangeLog |
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new file mode 100644 |
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index 0000000..58b781a |
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--- /dev/null |
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+++ b/sci-biology/biopieces/ChangeLog |
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@@ -0,0 +1,11 @@ |
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+# ChangeLog for sci-biology/biopieces |
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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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+*biopieces-0.51 (28 Mar 2014) |
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+*biopieces-9999 (28 Mar 2014) |
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+ |
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+ 28 Mar 2014; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> |
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+ +biopieces-0.51.ebuild, +biopieces-9999.ebuild, +metadata.xml: |
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+ sci-biology/biopieces: skeleton for a new package; has it's own install.sh |
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+ script |
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|
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diff --git a/sci-biology/biopieces/biopieces-0.51.ebuild b/sci-biology/biopieces/biopieces-0.51.ebuild |
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new file mode 100644 |
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index 0000000..0135966 |
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--- /dev/null |
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+++ b/sci-biology/biopieces/biopieces-0.51.ebuild |
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@@ -0,0 +1,63 @@ |
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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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+# $Header: $ |
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+ |
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+EAPI=5 |
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+ |
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+[ "$PV" == "9999" ] && inherit subversion |
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+ |
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+DESCRIPTION="Toolkit to find and trim adaptors, plot read lengths, qualities, map reads and submit to GenBank" |
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+HOMEPAGE="http://code.google.com/p/biopieces" |
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+SRC_URI="" |
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+if [ "$PV" == "9999" ]; then |
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+ ESVN_REPO_URI="http://biopieces.googlecode.com/svn/trunk" |
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+ KEYWORDS="" |
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+else |
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+ SRC_URI="http://biopieces.googlecode.com/files/biopieces_installer-"${PV}".sh" |
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+ KEYWORDS="" |
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+fi |
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+ |
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+LICENSE="GPL-2" |
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+SLOT="0" |
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+IUSE="" |
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+ |
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+# Ruby terminal-table ? |
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+ |
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+DEPEND=">=dev-lang/perl-5.8 |
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+ dev-perl/Bit-Vector |
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+ dev-perl/SVG |
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+ dev-perl/TermReadKey |
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+ perl-core/Time-HiRes |
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+ dev-perl/DBI |
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+ dev-perl/XML-Parser |
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+ dev-perl/Carp-Clan |
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+ dev-perl/Class-Inspector |
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+ dev-perl/HTML-Parser |
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+ dev-perl/libwww-perl |
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+ dev-perl/SOAP-Lite |
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+ dev-perl/URI |
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+ dev-perl/Inline |
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+ dev-perl/Parse-RecDescent |
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+ perl-core/version |
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+ perl-core/DB_File |
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+ dev-perl/DBD-mysql |
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+ >=dev-lang/python-2.6 |
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+ dev-lang/ruby |
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+ dev-ruby/gnuplot |
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+ dev-ruby/narray |
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+ dev-ruby/RubyInline" |
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+ |
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+# sci-biology/vmatch # http://www.vmatch.de/ # fecth restrict |
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+# sci-biology/usearch-bin # http://www.drive5.com/usearch/ # fecth restrict |
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+ |
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+RDEPEND="${DEPEND} |
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+ sci-biology/ncbi-tools |
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+ sci-biology/muscle |
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+ sci-biology/mummer |
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+ sci-biology/blat |
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+ sci-biology/bowtie |
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+ sci-biology/bwa |
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+ sci-biology/velvet |
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+ sci-biology/idba |
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+ sci-biology/Ray |
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+ sci-biology/scan_for_matches" |
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|
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diff --git a/sci-biology/biopieces/biopieces-9999.ebuild b/sci-biology/biopieces/biopieces-9999.ebuild |
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new file mode 100644 |
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index 0000000..0135966 |
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--- /dev/null |
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+++ b/sci-biology/biopieces/biopieces-9999.ebuild |
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@@ -0,0 +1,63 @@ |
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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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+# $Header: $ |
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+ |
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+EAPI=5 |
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+ |
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+[ "$PV" == "9999" ] && inherit subversion |
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+ |
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+DESCRIPTION="Toolkit to find and trim adaptors, plot read lengths, qualities, map reads and submit to GenBank" |
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+HOMEPAGE="http://code.google.com/p/biopieces" |
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+SRC_URI="" |
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+if [ "$PV" == "9999" ]; then |
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+ ESVN_REPO_URI="http://biopieces.googlecode.com/svn/trunk" |
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+ KEYWORDS="" |
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+else |
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+ SRC_URI="http://biopieces.googlecode.com/files/biopieces_installer-"${PV}".sh" |
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+ KEYWORDS="" |
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+fi |
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+ |
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+LICENSE="GPL-2" |
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+SLOT="0" |
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+IUSE="" |
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+ |
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+# Ruby terminal-table ? |
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+ |
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+DEPEND=">=dev-lang/perl-5.8 |
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+ dev-perl/Bit-Vector |
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+ dev-perl/SVG |
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+ dev-perl/TermReadKey |
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+ perl-core/Time-HiRes |
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+ dev-perl/DBI |
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+ dev-perl/XML-Parser |
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+ dev-perl/Carp-Clan |
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+ dev-perl/Class-Inspector |
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+ dev-perl/HTML-Parser |
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+ dev-perl/libwww-perl |
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+ dev-perl/SOAP-Lite |
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+ dev-perl/URI |
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+ dev-perl/Inline |
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+ dev-perl/Parse-RecDescent |
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+ perl-core/version |
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+ perl-core/DB_File |
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+ dev-perl/DBD-mysql |
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+ >=dev-lang/python-2.6 |
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+ dev-lang/ruby |
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+ dev-ruby/gnuplot |
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+ dev-ruby/narray |
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+ dev-ruby/RubyInline" |
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+ |
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+# sci-biology/vmatch # http://www.vmatch.de/ # fecth restrict |
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+# sci-biology/usearch-bin # http://www.drive5.com/usearch/ # fecth restrict |
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+ |
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+RDEPEND="${DEPEND} |
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+ sci-biology/ncbi-tools |
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+ sci-biology/muscle |
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+ sci-biology/mummer |
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+ sci-biology/blat |
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+ sci-biology/bowtie |
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+ sci-biology/bwa |
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+ sci-biology/velvet |
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+ sci-biology/idba |
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+ sci-biology/Ray |
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+ sci-biology/scan_for_matches" |
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|
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diff --git a/sci-biology/biopieces/metadata.xml b/sci-biology/biopieces/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/biopieces/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> |