[gentoo-commits] proj/sci:master commit in: sci-biology/biopieces/

[gentoo-commits] proj/sci:master commit in: sci-biology/biopieces/

[Martin Mokrejs]

commit:     35ad68a597e8b049437e248e0edbd0811fca83cb
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 28 14:00:53 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 28 14:00:53 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=35ad68a5

sci-biology/biopieces: skeleton for a new package; has it's own install.sh script

Package-Manager: portage-2.2.7

---
 sci-biology/biopieces/ChangeLog             | 11 +++++
 sci-biology/biopieces/biopieces-0.51.ebuild | 63 +++++++++++++++++++++++++++++
 sci-biology/biopieces/biopieces-9999.ebuild | 63 +++++++++++++++++++++++++++++
 sci-biology/biopieces/metadata.xml          |  9 +++++
 4 files changed, 146 insertions(+)

diff --git a/sci-biology/biopieces/ChangeLog b/sci-biology/biopieces/ChangeLog
new file mode 100644
index 0000000..58b781a
--- /dev/null
+++ b/sci-biology/biopieces/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-biology/biopieces
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*biopieces-0.51 (28 Mar 2014)
+*biopieces-9999 (28 Mar 2014)
+
+  28 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +biopieces-0.51.ebuild, +biopieces-9999.ebuild, +metadata.xml:
+  sci-biology/biopieces: skeleton for a new package; has it's own install.sh
+  script

diff --git a/sci-biology/biopieces/biopieces-0.51.ebuild b/sci-biology/biopieces/biopieces-0.51.ebuild
new file mode 100644
index 0000000..0135966
--- /dev/null
+++ b/sci-biology/biopieces/biopieces-0.51.ebuild
@@ -0,0 +1,63 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+[ "$PV" == "9999" ] && inherit subversion
+
+DESCRIPTION="Toolkit to find and trim adaptors, plot read lengths, qualities, map reads and submit to GenBank"
+HOMEPAGE="http://code.google.com/p/biopieces"
+SRC_URI=""
+if [ "$PV" == "9999" ]; then
+	ESVN_REPO_URI="http://biopieces.googlecode.com/svn/trunk"
+	KEYWORDS=""
+else
+	SRC_URI="http://biopieces.googlecode.com/files/biopieces_installer-"${PV}".sh"
+	KEYWORDS=""
+fi
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+
+#    Ruby terminal-table ?
+
+DEPEND=">=dev-lang/perl-5.8
+	dev-perl/Bit-Vector
+	dev-perl/SVG
+	dev-perl/TermReadKey
+	perl-core/Time-HiRes
+	dev-perl/DBI
+	dev-perl/XML-Parser
+	dev-perl/Carp-Clan
+	dev-perl/Class-Inspector
+	dev-perl/HTML-Parser
+	dev-perl/libwww-perl
+	dev-perl/SOAP-Lite
+	dev-perl/URI
+	dev-perl/Inline
+	dev-perl/Parse-RecDescent
+	perl-core/version
+	perl-core/DB_File
+	dev-perl/DBD-mysql
+	>=dev-lang/python-2.6
+	dev-lang/ruby
+	dev-ruby/gnuplot
+	dev-ruby/narray
+	dev-ruby/RubyInline"
+
+# sci-biology/vmatch # http://www.vmatch.de/ # fecth restrict
+# sci-biology/usearch-bin # http://www.drive5.com/usearch/ # fecth restrict
+
+RDEPEND="${DEPEND}
+	sci-biology/ncbi-tools
+	sci-biology/muscle
+	sci-biology/mummer
+	sci-biology/blat
+	sci-biology/bowtie
+	sci-biology/bwa
+	sci-biology/velvet
+	sci-biology/idba
+	sci-biology/Ray
+	sci-biology/scan_for_matches"

diff --git a/sci-biology/biopieces/biopieces-9999.ebuild b/sci-biology/biopieces/biopieces-9999.ebuild
new file mode 100644
index 0000000..0135966
--- /dev/null
+++ b/sci-biology/biopieces/biopieces-9999.ebuild
@@ -0,0 +1,63 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+[ "$PV" == "9999" ] && inherit subversion
+
+DESCRIPTION="Toolkit to find and trim adaptors, plot read lengths, qualities, map reads and submit to GenBank"
+HOMEPAGE="http://code.google.com/p/biopieces"
+SRC_URI=""
+if [ "$PV" == "9999" ]; then
+	ESVN_REPO_URI="http://biopieces.googlecode.com/svn/trunk"
+	KEYWORDS=""
+else
+	SRC_URI="http://biopieces.googlecode.com/files/biopieces_installer-"${PV}".sh"
+	KEYWORDS=""
+fi
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+
+#    Ruby terminal-table ?
+
+DEPEND=">=dev-lang/perl-5.8
+	dev-perl/Bit-Vector
+	dev-perl/SVG
+	dev-perl/TermReadKey
+	perl-core/Time-HiRes
+	dev-perl/DBI
+	dev-perl/XML-Parser
+	dev-perl/Carp-Clan
+	dev-perl/Class-Inspector
+	dev-perl/HTML-Parser
+	dev-perl/libwww-perl
+	dev-perl/SOAP-Lite
+	dev-perl/URI
+	dev-perl/Inline
+	dev-perl/Parse-RecDescent
+	perl-core/version
+	perl-core/DB_File
+	dev-perl/DBD-mysql
+	>=dev-lang/python-2.6
+	dev-lang/ruby
+	dev-ruby/gnuplot
+	dev-ruby/narray
+	dev-ruby/RubyInline"
+
+# sci-biology/vmatch # http://www.vmatch.de/ # fecth restrict
+# sci-biology/usearch-bin # http://www.drive5.com/usearch/ # fecth restrict
+
+RDEPEND="${DEPEND}
+	sci-biology/ncbi-tools
+	sci-biology/muscle
+	sci-biology/mummer
+	sci-biology/blat
+	sci-biology/bowtie
+	sci-biology/bwa
+	sci-biology/velvet
+	sci-biology/idba
+	sci-biology/Ray
+	sci-biology/scan_for_matches"

diff --git a/sci-biology/biopieces/metadata.xml b/sci-biology/biopieces/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/biopieces/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>

[gentoo-commits] proj/sci:master commit in: sci-biology/biopieces/

[Nicolas Bock]

commit:     ae7eb86ca691a1713ac4afef719d7baeb376e45f
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 28 14:00:53 2014 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Mon Mar 31 15:27:34 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ae7eb86c

sci-biology/biopieces: skeleton for a new package; has it's own install.sh script

Package-Manager: portage-2.2.7

---
 sci-biology/biopieces/ChangeLog             | 11 +++++
 sci-biology/biopieces/biopieces-0.51.ebuild | 63 +++++++++++++++++++++++++++++
 sci-biology/biopieces/biopieces-9999.ebuild | 63 +++++++++++++++++++++++++++++
 sci-biology/biopieces/metadata.xml          |  9 +++++
 4 files changed, 146 insertions(+)

diff --git a/sci-biology/biopieces/ChangeLog b/sci-biology/biopieces/ChangeLog
new file mode 100644
index 0000000..58b781a
--- /dev/null
+++ b/sci-biology/biopieces/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-biology/biopieces
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*biopieces-0.51 (28 Mar 2014)
+*biopieces-9999 (28 Mar 2014)
+
+  28 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +biopieces-0.51.ebuild, +biopieces-9999.ebuild, +metadata.xml:
+  sci-biology/biopieces: skeleton for a new package; has it's own install.sh
+  script

diff --git a/sci-biology/biopieces/biopieces-0.51.ebuild b/sci-biology/biopieces/biopieces-0.51.ebuild
new file mode 100644
index 0000000..0135966
--- /dev/null
+++ b/sci-biology/biopieces/biopieces-0.51.ebuild
@@ -0,0 +1,63 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+[ "$PV" == "9999" ] && inherit subversion
+
+DESCRIPTION="Toolkit to find and trim adaptors, plot read lengths, qualities, map reads and submit to GenBank"
+HOMEPAGE="http://code.google.com/p/biopieces"
+SRC_URI=""
+if [ "$PV" == "9999" ]; then
+	ESVN_REPO_URI="http://biopieces.googlecode.com/svn/trunk"
+	KEYWORDS=""
+else
+	SRC_URI="http://biopieces.googlecode.com/files/biopieces_installer-"${PV}".sh"
+	KEYWORDS=""
+fi
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+
+#    Ruby terminal-table ?
+
+DEPEND=">=dev-lang/perl-5.8
+	dev-perl/Bit-Vector
+	dev-perl/SVG
+	dev-perl/TermReadKey
+	perl-core/Time-HiRes
+	dev-perl/DBI
+	dev-perl/XML-Parser
+	dev-perl/Carp-Clan
+	dev-perl/Class-Inspector
+	dev-perl/HTML-Parser
+	dev-perl/libwww-perl
+	dev-perl/SOAP-Lite
+	dev-perl/URI
+	dev-perl/Inline
+	dev-perl/Parse-RecDescent
+	perl-core/version
+	perl-core/DB_File
+	dev-perl/DBD-mysql
+	>=dev-lang/python-2.6
+	dev-lang/ruby
+	dev-ruby/gnuplot
+	dev-ruby/narray
+	dev-ruby/RubyInline"
+
+# sci-biology/vmatch # http://www.vmatch.de/ # fecth restrict
+# sci-biology/usearch-bin # http://www.drive5.com/usearch/ # fecth restrict
+
+RDEPEND="${DEPEND}
+	sci-biology/ncbi-tools
+	sci-biology/muscle
+	sci-biology/mummer
+	sci-biology/blat
+	sci-biology/bowtie
+	sci-biology/bwa
+	sci-biology/velvet
+	sci-biology/idba
+	sci-biology/Ray
+	sci-biology/scan_for_matches"

diff --git a/sci-biology/biopieces/biopieces-9999.ebuild b/sci-biology/biopieces/biopieces-9999.ebuild
new file mode 100644
index 0000000..0135966
--- /dev/null
+++ b/sci-biology/biopieces/biopieces-9999.ebuild
@@ -0,0 +1,63 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+[ "$PV" == "9999" ] && inherit subversion
+
+DESCRIPTION="Toolkit to find and trim adaptors, plot read lengths, qualities, map reads and submit to GenBank"
+HOMEPAGE="http://code.google.com/p/biopieces"
+SRC_URI=""
+if [ "$PV" == "9999" ]; then
+	ESVN_REPO_URI="http://biopieces.googlecode.com/svn/trunk"
+	KEYWORDS=""
+else
+	SRC_URI="http://biopieces.googlecode.com/files/biopieces_installer-"${PV}".sh"
+	KEYWORDS=""
+fi
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+
+#    Ruby terminal-table ?
+
+DEPEND=">=dev-lang/perl-5.8
+	dev-perl/Bit-Vector
+	dev-perl/SVG
+	dev-perl/TermReadKey
+	perl-core/Time-HiRes
+	dev-perl/DBI
+	dev-perl/XML-Parser
+	dev-perl/Carp-Clan
+	dev-perl/Class-Inspector
+	dev-perl/HTML-Parser
+	dev-perl/libwww-perl
+	dev-perl/SOAP-Lite
+	dev-perl/URI
+	dev-perl/Inline
+	dev-perl/Parse-RecDescent
+	perl-core/version
+	perl-core/DB_File
+	dev-perl/DBD-mysql
+	>=dev-lang/python-2.6
+	dev-lang/ruby
+	dev-ruby/gnuplot
+	dev-ruby/narray
+	dev-ruby/RubyInline"
+
+# sci-biology/vmatch # http://www.vmatch.de/ # fecth restrict
+# sci-biology/usearch-bin # http://www.drive5.com/usearch/ # fecth restrict
+
+RDEPEND="${DEPEND}
+	sci-biology/ncbi-tools
+	sci-biology/muscle
+	sci-biology/mummer
+	sci-biology/blat
+	sci-biology/bowtie
+	sci-biology/bwa
+	sci-biology/velvet
+	sci-biology/idba
+	sci-biology/Ray
+	sci-biology/scan_for_matches"

diff --git a/sci-biology/biopieces/metadata.xml b/sci-biology/biopieces/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/biopieces/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>

[gentoo-commits] proj/sci:master commit in: sci-biology/biopieces/

[Justin Lecher]

commit:     560c4c1875f38a0b7279acd0dea4ba97eac3106a
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Nov 13 12:42:43 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Nov 13 12:42:43 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=560c4c18

sci-biology/biopieces: Use perl virtuals instead of core

Package-Manager: portage-2.2.14

---
 sci-biology/biopieces/ChangeLog             | 4 ++++
 sci-biology/biopieces/biopieces-0.51.ebuild | 6 +++---
 sci-biology/biopieces/biopieces-9999.ebuild | 6 +++---
 3 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/sci-biology/biopieces/ChangeLog b/sci-biology/biopieces/ChangeLog
index 58b781a..3e269ec 100644
--- a/sci-biology/biopieces/ChangeLog
+++ b/sci-biology/biopieces/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  13 Nov 2014; Justin Lecher <jlec@gentoo.org> biopieces-0.51.ebuild,
+  biopieces-9999.ebuild:
+  Use perl virtuals instead of core
+
 *biopieces-0.51 (28 Mar 2014)
 *biopieces-9999 (28 Mar 2014)
 

diff --git a/sci-biology/biopieces/biopieces-0.51.ebuild b/sci-biology/biopieces/biopieces-0.51.ebuild
index 0135966..6be82b8 100644
--- a/sci-biology/biopieces/biopieces-0.51.ebuild
+++ b/sci-biology/biopieces/biopieces-0.51.ebuild
@@ -27,7 +27,7 @@ DEPEND=">=dev-lang/perl-5.8
 	dev-perl/Bit-Vector
 	dev-perl/SVG
 	dev-perl/TermReadKey
-	perl-core/Time-HiRes
+	virtual/perl-Time-HiRes
 	dev-perl/DBI
 	dev-perl/XML-Parser
 	dev-perl/Carp-Clan
@@ -38,8 +38,8 @@ DEPEND=">=dev-lang/perl-5.8
 	dev-perl/URI
 	dev-perl/Inline
 	dev-perl/Parse-RecDescent
-	perl-core/version
-	perl-core/DB_File
+	virtual/perl-version
+	virtual/perl-DB_File
 	dev-perl/DBD-mysql
 	>=dev-lang/python-2.6
 	dev-lang/ruby

diff --git a/sci-biology/biopieces/biopieces-9999.ebuild b/sci-biology/biopieces/biopieces-9999.ebuild
index 0135966..6be82b8 100644
--- a/sci-biology/biopieces/biopieces-9999.ebuild
+++ b/sci-biology/biopieces/biopieces-9999.ebuild
@@ -27,7 +27,7 @@ DEPEND=">=dev-lang/perl-5.8
 	dev-perl/Bit-Vector
 	dev-perl/SVG
 	dev-perl/TermReadKey
-	perl-core/Time-HiRes
+	virtual/perl-Time-HiRes
 	dev-perl/DBI
 	dev-perl/XML-Parser
 	dev-perl/Carp-Clan
@@ -38,8 +38,8 @@ DEPEND=">=dev-lang/perl-5.8
 	dev-perl/URI
 	dev-perl/Inline
 	dev-perl/Parse-RecDescent
-	perl-core/version
-	perl-core/DB_File
+	virtual/perl-version
+	virtual/perl-DB_File
 	dev-perl/DBD-mysql
 	>=dev-lang/python-2.6
 	dev-lang/ruby

[gentoo-commits] proj/sci:master commit in: sci-biology/biopieces/

[Justin Lecher]

commit:     c921e9ffb851dcb6c90beb29502aff76d7436fd1
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 18 13:12:38 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 18 13:12:38 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c921e9ff

sci-biology/biopieces: fix SLOT operators; correct ruby and python deps

Package-Manager: portage-2.2.17

---
 sci-biology/biopieces/ChangeLog             |  5 ++-
 sci-biology/biopieces/biopieces-9999.ebuild | 49 ++++++++++++++++-------------
 2 files changed, 32 insertions(+), 22 deletions(-)

diff --git a/sci-biology/biopieces/ChangeLog b/sci-biology/biopieces/ChangeLog
index 3e269ec..db06e76 100644
--- a/sci-biology/biopieces/ChangeLog
+++ b/sci-biology/biopieces/ChangeLog
@@ -1,7 +1,10 @@
 # ChangeLog for sci-biology/biopieces
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  18 Feb 2015; Justin Lecher <jlec@gentoo.org> -Manifest, biopieces-9999.ebuild:
+  sci-biology/biopieces: fix SLOT operators; correct ruby and python deps
+
   13 Nov 2014; Justin Lecher <jlec@gentoo.org> biopieces-0.51.ebuild,
   biopieces-9999.ebuild:
   Use perl virtuals instead of core

diff --git a/sci-biology/biopieces/biopieces-9999.ebuild b/sci-biology/biopieces/biopieces-9999.ebuild
index 6be82b8..d33a63f 100644
--- a/sci-biology/biopieces/biopieces-9999.ebuild
+++ b/sci-biology/biopieces/biopieces-9999.ebuild
@@ -1,51 +1,58 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
 EAPI=5
 
-[ "$PV" == "9999" ] && inherit subversion
+PYTHON_COMPAT=( python2_7 )
+
+USE_RUBY="ruby19"
 
-DESCRIPTION="Toolkit to find and trim adaptors, plot read lengths, qualities, map reads and submit to GenBank"
-HOMEPAGE="http://code.google.com/p/biopieces"
-SRC_URI=""
 if [ "$PV" == "9999" ]; then
 	ESVN_REPO_URI="http://biopieces.googlecode.com/svn/trunk"
 	KEYWORDS=""
+	inherit subversion
 else
-	SRC_URI="http://biopieces.googlecode.com/files/biopieces_installer-"${PV}".sh"
+	SRC_URI="http://biopieces.googlecode.com/files/biopieces_installer-${PV}.sh"
 	KEYWORDS=""
 fi
 
+inherit ruby-fakegem python-single-r1
+
+DESCRIPTION="Toolkit to find and trim adaptors, plot read lengths, qualities, map reads and submit to GenBank"
+HOMEPAGE="http://code.google.com/p/biopieces"
+SRC_URI=""
+
 LICENSE="GPL-2"
 SLOT="0"
 IUSE=""
 
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
 #    Ruby terminal-table ?
 
-DEPEND=">=dev-lang/perl-5.8
+DEPEND="
+	>=dev-lang/perl-5.8
+	dev-perl/libwww-perl
 	dev-perl/Bit-Vector
-	dev-perl/SVG
-	dev-perl/TermReadKey
-	virtual/perl-Time-HiRes
-	dev-perl/DBI
-	dev-perl/XML-Parser
 	dev-perl/Carp-Clan
 	dev-perl/Class-Inspector
+	dev-perl/DBD-mysql
+	dev-perl/DBI
 	dev-perl/HTML-Parser
-	dev-perl/libwww-perl
-	dev-perl/SOAP-Lite
-	dev-perl/URI
 	dev-perl/Inline
 	dev-perl/Parse-RecDescent
+	dev-perl/SOAP-Lite
+	dev-perl/SVG
+	dev-perl/TermReadKey
+	dev-perl/URI
+	dev-perl/XML-Parser
 	virtual/perl-version
 	virtual/perl-DB_File
-	dev-perl/DBD-mysql
-	>=dev-lang/python-2.6
-	dev-lang/ruby
-	dev-ruby/gnuplot
-	dev-ruby/narray
-	dev-ruby/RubyInline"
+	virtual/perl-Time-HiRes"
+
+ruby_add_bdepend "dev-ruby/RubyInline"
+ruby_add_rdepend "dev-ruby/gnuplot dev-ruby/narray"
 
 # sci-biology/vmatch # http://www.vmatch.de/ # fecth restrict
 # sci-biology/usearch-bin # http://www.drive5.com/usearch/ # fecth restrict

[gentoo-commits] proj/sci:master commit in: sci-biology/biopieces/

[Justin Lecher]

commit:     5494a57d02f531afe13a2fa22065946824b6e2d5
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 18 13:16:16 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 18 13:16:16 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5494a57d

Add symlink

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 sci-biology/biopieces/biopieces-0.51.ebuild | 64 +----------------------------
 1 file changed, 1 insertion(+), 63 deletions(-)

diff --git a/sci-biology/biopieces/biopieces-0.51.ebuild b/sci-biology/biopieces/biopieces-0.51.ebuild
deleted file mode 100644
index 6be82b8..0000000
--- a/sci-biology/biopieces/biopieces-0.51.ebuild
+++ /dev/null
@@ -1,63 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-[ "$PV" == "9999" ] && inherit subversion
-
-DESCRIPTION="Toolkit to find and trim adaptors, plot read lengths, qualities, map reads and submit to GenBank"
-HOMEPAGE="http://code.google.com/p/biopieces"
-SRC_URI=""
-if [ "$PV" == "9999" ]; then
-	ESVN_REPO_URI="http://biopieces.googlecode.com/svn/trunk"
-	KEYWORDS=""
-else
-	SRC_URI="http://biopieces.googlecode.com/files/biopieces_installer-"${PV}".sh"
-	KEYWORDS=""
-fi
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE=""
-
-#    Ruby terminal-table ?
-
-DEPEND=">=dev-lang/perl-5.8
-	dev-perl/Bit-Vector
-	dev-perl/SVG
-	dev-perl/TermReadKey
-	virtual/perl-Time-HiRes
-	dev-perl/DBI
-	dev-perl/XML-Parser
-	dev-perl/Carp-Clan
-	dev-perl/Class-Inspector
-	dev-perl/HTML-Parser
-	dev-perl/libwww-perl
-	dev-perl/SOAP-Lite
-	dev-perl/URI
-	dev-perl/Inline
-	dev-perl/Parse-RecDescent
-	virtual/perl-version
-	virtual/perl-DB_File
-	dev-perl/DBD-mysql
-	>=dev-lang/python-2.6
-	dev-lang/ruby
-	dev-ruby/gnuplot
-	dev-ruby/narray
-	dev-ruby/RubyInline"
-
-# sci-biology/vmatch # http://www.vmatch.de/ # fecth restrict
-# sci-biology/usearch-bin # http://www.drive5.com/usearch/ # fecth restrict
-
-RDEPEND="${DEPEND}
-	sci-biology/ncbi-tools
-	sci-biology/muscle
-	sci-biology/mummer
-	sci-biology/blat
-	sci-biology/bowtie
-	sci-biology/bwa
-	sci-biology/velvet
-	sci-biology/idba
-	sci-biology/Ray
-	sci-biology/scan_for_matches"

diff --git a/sci-biology/biopieces/biopieces-0.51.ebuild b/sci-biology/biopieces/biopieces-0.51.ebuild
new file mode 120000
index 0000000..f048b8a
--- /dev/null
+++ b/sci-biology/biopieces/biopieces-0.51.ebuild
@@ -0,0 +1 @@
+biopieces-9999.ebuild
\ No newline at end of file

[gentoo-commits] proj/sci:master commit in: sci-biology/biopieces/

[Justin Lecher]

commit:     3f85d74886bd2349d66353e35fd902730e2cf8d7
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar  8 17:43:37 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar  8 17:43:37 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3f85d748

Fix missing test in IUSE and missing dep in python

Package-Manager: portage-2.2.17
RepoMan-Options: --force

 sci-biology/biopieces/ChangeLog             | 3 +++
 sci-biology/biopieces/biopieces-9999.ebuild | 8 +++++---
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/sci-biology/biopieces/ChangeLog b/sci-biology/biopieces/ChangeLog
index db06e76..615109a 100644
--- a/sci-biology/biopieces/ChangeLog
+++ b/sci-biology/biopieces/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  08 Mar 2015; Justin Lecher <jlec@gentoo.org> biopieces-9999.ebuild:
+  Fix missing test in IUSE and missing dep in python
+
   18 Feb 2015; Justin Lecher <jlec@gentoo.org> -Manifest, biopieces-9999.ebuild:
   sci-biology/biopieces: fix SLOT operators; correct ruby and python deps
 

diff --git a/sci-biology/biopieces/biopieces-9999.ebuild b/sci-biology/biopieces/biopieces-9999.ebuild
index d33a63f..0e3731d 100644
--- a/sci-biology/biopieces/biopieces-9999.ebuild
+++ b/sci-biology/biopieces/biopieces-9999.ebuild
@@ -25,13 +25,13 @@ SRC_URI=""
 
 LICENSE="GPL-2"
 SLOT="0"
-IUSE=""
+IUSE="test"
 
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 #    Ruby terminal-table ?
 
-DEPEND="
+CDEPEND="${PYTHON_DEPS}
 	>=dev-lang/perl-5.8
 	dev-perl/libwww-perl
 	dev-perl/Bit-Vector
@@ -51,13 +51,15 @@ DEPEND="
 	virtual/perl-DB_File
 	virtual/perl-Time-HiRes"
 
+DEPEND="${CDEPEND}"
+
 ruby_add_bdepend "dev-ruby/RubyInline"
 ruby_add_rdepend "dev-ruby/gnuplot dev-ruby/narray"
 
 # sci-biology/vmatch # http://www.vmatch.de/ # fecth restrict
 # sci-biology/usearch-bin # http://www.drive5.com/usearch/ # fecth restrict
 
-RDEPEND="${DEPEND}
+RDEPEND="${CDEPEND}
 	sci-biology/ncbi-tools
 	sci-biology/muscle
 	sci-biology/mummer

[gentoo-commits] proj/sci:master commit in: sci-biology/biopieces/

[Martin Mokrejs]

commit:     853d6c57b51915231367ba298190d8035a909ce1
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jun 22 09:36:56 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jun 22 09:36:56 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=853d6c57

sci-biology/biopieces: minor ebuild cleanup, ruby vers, copyright line, deps

remove optional RDEPEND while sci-biology/idba is missing, see github issue #381

Package-Manager: portage-2.2.28

 sci-biology/biopieces/biopieces-0.51.ebuild | 8 ++++----
 sci-biology/biopieces/biopieces-9999.ebuild | 8 ++++----
 sci-biology/biopieces/metadata.xml          | 2 +-
 3 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/sci-biology/biopieces/biopieces-0.51.ebuild b/sci-biology/biopieces/biopieces-0.51.ebuild
index ed5a251..f3f4079 100644
--- a/sci-biology/biopieces/biopieces-0.51.ebuild
+++ b/sci-biology/biopieces/biopieces-0.51.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -6,7 +6,7 @@ EAPI=5
 
 PYTHON_COMPAT=( python2_7 )
 
-USE_RUBY="ruby19"
+USE_RUBY="ruby20 ruby21"
 
 if [ "$PV" == "9999" ]; then
 	ESVN_REPO_URI="http://biopieces.googlecode.com/svn/trunk"
@@ -19,7 +19,7 @@ fi
 
 inherit ruby-fakegem python-single-r1
 
-DESCRIPTION="Toolkit to find and trim adaptors, plot read lengths, qualities, map reads and submit to GenBank"
+DESCRIPTION="Trim adaptors, plot read lengths, qualities, map reads and submit to GenBank"
 HOMEPAGE="http://code.google.com/p/biopieces"
 SRC_URI=""
 
@@ -67,6 +67,6 @@ RDEPEND="${CDEPEND}
 	sci-biology/bowtie
 	sci-biology/bwa
 	sci-biology/velvet
-	sci-biology/idba
 	sci-biology/Ray
 	sci-biology/scan_for_matches"
+# sci-biology/idba

diff --git a/sci-biology/biopieces/biopieces-9999.ebuild b/sci-biology/biopieces/biopieces-9999.ebuild
index ed5a251..f3f4079 100644
--- a/sci-biology/biopieces/biopieces-9999.ebuild
+++ b/sci-biology/biopieces/biopieces-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -6,7 +6,7 @@ EAPI=5
 
 PYTHON_COMPAT=( python2_7 )
 
-USE_RUBY="ruby19"
+USE_RUBY="ruby20 ruby21"
 
 if [ "$PV" == "9999" ]; then
 	ESVN_REPO_URI="http://biopieces.googlecode.com/svn/trunk"
@@ -19,7 +19,7 @@ fi
 
 inherit ruby-fakegem python-single-r1
 
-DESCRIPTION="Toolkit to find and trim adaptors, plot read lengths, qualities, map reads and submit to GenBank"
+DESCRIPTION="Trim adaptors, plot read lengths, qualities, map reads and submit to GenBank"
 HOMEPAGE="http://code.google.com/p/biopieces"
 SRC_URI=""
 
@@ -67,6 +67,6 @@ RDEPEND="${CDEPEND}
 	sci-biology/bowtie
 	sci-biology/bwa
 	sci-biology/velvet
-	sci-biology/idba
 	sci-biology/Ray
 	sci-biology/scan_for_matches"
+# sci-biology/idba

diff --git a/sci-biology/biopieces/metadata.xml b/sci-biology/biopieces/metadata.xml
index 1699e58..f68a1b6 100644
--- a/sci-biology/biopieces/metadata.xml
+++ b/sci-biology/biopieces/metadata.xml
@@ -5,7 +5,7 @@
     <email>mmokrejs@fold.natur.cuni.cz</email>
     <name>Martin Mokrejs</name>
   </maintainer>
-<maintainer type="project">
+  <maintainer type="project">
     <email>sci-biology@gentoo.org</email>
     <name>Gentoo Biology Project</name>
   </maintainer>

[gentoo-commits] proj/sci:master commit in: sci-biology/biopieces/

[Martin Mokrejs]

commit:     0f38e9552bf34f6c99d9afd35af1290d005309b8
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Sep 24 11:26:40 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Sep 24 11:26:40 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0f38e955

sci-biology/biopieces: re-add just landed sci-biology/idba to DEPENDencies, github issue 381#

Package-Manager: portage-2.3.0

 sci-biology/biopieces/biopieces-0.51.ebuild | 4 ++--
 sci-biology/biopieces/biopieces-9999.ebuild | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/sci-biology/biopieces/biopieces-0.51.ebuild b/sci-biology/biopieces/biopieces-0.51.ebuild
index f3f4079..0deacba 100644
--- a/sci-biology/biopieces/biopieces-0.51.ebuild
+++ b/sci-biology/biopieces/biopieces-0.51.ebuild
@@ -68,5 +68,5 @@ RDEPEND="${CDEPEND}
 	sci-biology/bwa
 	sci-biology/velvet
 	sci-biology/Ray
-	sci-biology/scan_for_matches"
-# sci-biology/idba
+	sci-biology/scan_for_matches
+	sci-biology/idba"

diff --git a/sci-biology/biopieces/biopieces-9999.ebuild b/sci-biology/biopieces/biopieces-9999.ebuild
index f3f4079..0deacba 100644
--- a/sci-biology/biopieces/biopieces-9999.ebuild
+++ b/sci-biology/biopieces/biopieces-9999.ebuild
@@ -68,5 +68,5 @@ RDEPEND="${CDEPEND}
 	sci-biology/bwa
 	sci-biology/velvet
 	sci-biology/Ray
-	sci-biology/scan_for_matches"
-# sci-biology/idba
+	sci-biology/scan_for_matches
+	sci-biology/idba"

[gentoo-commits] proj/sci:master commit in: sci-biology/biopieces/

[David Seifert]

commit:     d75563d482ad25f5355ae6f8ee781c612027fc20
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Sep  2 11:55:22 2017 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Sep  2 11:55:22 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d75563d4

sci-biology/biopieces: Update USE_RUBY to fix breakages

Package-Manager: Portage-2.3.8, Repoman-2.3.3

 sci-biology/biopieces/biopieces-0.51.ebuild | 4 ++--
 sci-biology/biopieces/biopieces-9999.ebuild | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/sci-biology/biopieces/biopieces-0.51.ebuild b/sci-biology/biopieces/biopieces-0.51.ebuild
index 6b504cb11..03a9d78cc 100644
--- a/sci-biology/biopieces/biopieces-0.51.ebuild
+++ b/sci-biology/biopieces/biopieces-0.51.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
 
 PYTHON_COMPAT=( python2_7 )
 
-USE_RUBY="ruby20 ruby21"
+USE_RUBY="ruby22 ruby23 ruby24"
 
 if [ "$PV" == "9999" ]; then
 	ESVN_REPO_URI="http://biopieces.googlecode.com/svn/trunk"

diff --git a/sci-biology/biopieces/biopieces-9999.ebuild b/sci-biology/biopieces/biopieces-9999.ebuild
index 6b504cb11..03a9d78cc 100644
--- a/sci-biology/biopieces/biopieces-9999.ebuild
+++ b/sci-biology/biopieces/biopieces-9999.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
 
 PYTHON_COMPAT=( python2_7 )
 
-USE_RUBY="ruby20 ruby21"
+USE_RUBY="ruby22 ruby23 ruby24"
 
 if [ "$PV" == "9999" ]; then
 	ESVN_REPO_URI="http://biopieces.googlecode.com/svn/trunk"

[gentoo-commits] proj/sci:master commit in: sci-biology/biopieces/

[Horea Christian]

commit:     39df6200aad813e9488a21850b8b7b954b521dbd
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sat Sep 26 09:40:59 2020 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sat Sep 26 09:40:59 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=39df6200

sci-biology/biopieces: Removed package with deprecated dep

Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 sci-biology/biopieces/biopieces-0.51.ebuild | 71 -----------------------------
 sci-biology/biopieces/biopieces-9999.ebuild | 71 -----------------------------
 sci-biology/biopieces/metadata.xml          | 12 -----
 3 files changed, 154 deletions(-)

diff --git a/sci-biology/biopieces/biopieces-0.51.ebuild b/sci-biology/biopieces/biopieces-0.51.ebuild
deleted file mode 100644
index 03a9d78cc..000000000
--- a/sci-biology/biopieces/biopieces-0.51.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-USE_RUBY="ruby22 ruby23 ruby24"
-
-if [ "$PV" == "9999" ]; then
-	ESVN_REPO_URI="http://biopieces.googlecode.com/svn/trunk"
-	KEYWORDS=""
-	inherit subversion
-else
-	SRC_URI="http://biopieces.googlecode.com/files/biopieces_installer-${PV}.sh"
-	KEYWORDS=""
-fi
-
-inherit ruby-fakegem python-single-r1
-
-DESCRIPTION="Trim adaptors, plot read lengths, qualities, map reads and submit to GenBank"
-HOMEPAGE="http://code.google.com/p/biopieces"
-SRC_URI=""
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE="test"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-#    Ruby terminal-table ?
-
-CDEPEND="${PYTHON_DEPS}
-	>=dev-lang/perl-5.8
-	dev-perl/libwww-perl
-	dev-perl/Bit-Vector
-	dev-perl/Carp-Clan
-	dev-perl/Class-Inspector
-	dev-perl/DBD-mysql
-	dev-perl/DBI
-	dev-perl/HTML-Parser
-	dev-perl/Inline
-	dev-perl/Parse-RecDescent
-	dev-perl/SOAP-Lite
-	dev-perl/SVG
-	dev-perl/TermReadKey
-	dev-perl/URI
-	dev-perl/XML-Parser
-	virtual/perl-version
-	virtual/perl-DB_File
-	virtual/perl-Time-HiRes"
-
-DEPEND="${CDEPEND}"
-
-ruby_add_bdepend "dev-ruby/RubyInline"
-ruby_add_rdepend "dev-ruby/gnuplot dev-ruby/narray"
-
-# sci-biology/vmatch # http://www.vmatch.de/ # fecth restrict
-# sci-biology/usearch-bin # http://www.drive5.com/usearch/ # fecth restrict
-
-RDEPEND="${CDEPEND}
-	sci-biology/ncbi-tools
-	sci-biology/muscle
-	sci-biology/mummer
-	sci-biology/blat
-	sci-biology/bowtie
-	sci-biology/bwa
-	sci-biology/velvet
-	sci-biology/Ray
-	sci-biology/scan_for_matches
-	sci-biology/idba"

diff --git a/sci-biology/biopieces/biopieces-9999.ebuild b/sci-biology/biopieces/biopieces-9999.ebuild
deleted file mode 100644
index 03a9d78cc..000000000
--- a/sci-biology/biopieces/biopieces-9999.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-USE_RUBY="ruby22 ruby23 ruby24"
-
-if [ "$PV" == "9999" ]; then
-	ESVN_REPO_URI="http://biopieces.googlecode.com/svn/trunk"
-	KEYWORDS=""
-	inherit subversion
-else
-	SRC_URI="http://biopieces.googlecode.com/files/biopieces_installer-${PV}.sh"
-	KEYWORDS=""
-fi
-
-inherit ruby-fakegem python-single-r1
-
-DESCRIPTION="Trim adaptors, plot read lengths, qualities, map reads and submit to GenBank"
-HOMEPAGE="http://code.google.com/p/biopieces"
-SRC_URI=""
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE="test"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-#    Ruby terminal-table ?
-
-CDEPEND="${PYTHON_DEPS}
-	>=dev-lang/perl-5.8
-	dev-perl/libwww-perl
-	dev-perl/Bit-Vector
-	dev-perl/Carp-Clan
-	dev-perl/Class-Inspector
-	dev-perl/DBD-mysql
-	dev-perl/DBI
-	dev-perl/HTML-Parser
-	dev-perl/Inline
-	dev-perl/Parse-RecDescent
-	dev-perl/SOAP-Lite
-	dev-perl/SVG
-	dev-perl/TermReadKey
-	dev-perl/URI
-	dev-perl/XML-Parser
-	virtual/perl-version
-	virtual/perl-DB_File
-	virtual/perl-Time-HiRes"
-
-DEPEND="${CDEPEND}"
-
-ruby_add_bdepend "dev-ruby/RubyInline"
-ruby_add_rdepend "dev-ruby/gnuplot dev-ruby/narray"
-
-# sci-biology/vmatch # http://www.vmatch.de/ # fecth restrict
-# sci-biology/usearch-bin # http://www.drive5.com/usearch/ # fecth restrict
-
-RDEPEND="${CDEPEND}
-	sci-biology/ncbi-tools
-	sci-biology/muscle
-	sci-biology/mummer
-	sci-biology/blat
-	sci-biology/bowtie
-	sci-biology/bwa
-	sci-biology/velvet
-	sci-biology/Ray
-	sci-biology/scan_for_matches
-	sci-biology/idba"

diff --git a/sci-biology/biopieces/metadata.xml b/sci-biology/biopieces/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/biopieces/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>