Moved from app-sci/bioperl-run to sci-biology/bioperl-run.

8 files changed, 174 insertions, 0 deletions

diff --git a/sci-biology/bioperl-run/ChangeLog b/sci-biology/bioperl-run/ChangeLog
new file mode 100644
index 000000000000..d48ccf5e0899
--- /dev/null
+++ b/sci-biology/bioperl-run/ChangeLog
@@ -0,0 +1,35 @@
+# ChangeLog for app-sci/bioperl-run
+# Copyright 2000-2004 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-run/ChangeLog,v 1.1 2004/12/23 22:09:47 ribosome Exp $
+
+*bioperl-run-1.2.2 (23 Dec 2004)
+
+  23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
+  +files/bioperl-run-Pise-test-patch.diff, +bioperl-run-1.2.2.ebuild,
+  +bioperl-run-1.4.ebuild:
+  Moved from app-sci/bioperl-run to sci-biology/bioperl-run.
+
+  23 Sep 2004; Stephen Diener <sediener@gentoo.org> bioperl-run-1.4.ebuild:
+  Bumped 1.4 to stable on x86
+
+  03 Aug 2004; David Holm <dholm@gentoo.org> bioperl-run-1.4.ebuild:
+  Added to ~ppc.
+
+  22 Mar 2004; Patrick Kursawe <phosphan@gentoo.org> bioperl-run-1.2.2.ebuild,
+  bioperl-run-1.4.ebuild:
+  removing DEPEND="${RDEPEND}"
+
+*bioperl-run-1.4 (08 Jan 2004)
+
+  08 Jan 2004; Stephen Diener <sediener@gentoo.org> bioperl-run-1.4.ebuild:
+  version bump to 1.4
+
+  14 Dec 2003; Stephen Diener <sediener@gentoo.org> bioperl-run-1.2.2.ebuild:
+  Bump to stable
+
+*bioperl-run-1.2.2 (29 Sep 2003)
+
+  29 Sep 2003; <sediener@gentoo.org> bioperl-run-1.2.2.ebuild, metadata.xml,
+  files/bioperl-run-Pise-test-patch.diff:
+  Initial Import. Built of of the bioperl ebuild from Gontran Zepeda.
+
diff --git a/sci-biology/bioperl-run/Manifest b/sci-biology/bioperl-run/Manifest
new file mode 100644
index 000000000000..20d30ca0abaf
--- /dev/null
+++ b/sci-biology/bioperl-run/Manifest
@@ -0,0 +1,7 @@
+MD5 4cd3241aa707d6a6d276fd13d119e7d6 bioperl-run-1.4.ebuild 1306
+MD5 5c2ee510b374b6726d8b226c24662a5c bioperl-run-1.2.2.ebuild 1456
+MD5 81eb9eddaa9c418106d796b152b14ed0 ChangeLog 995
+MD5 e8b4df3df76800c376905734d8043cfa metadata.xml 216
+MD5 47db6a1f839dd45f8c891b5f6ab2ff2a files/digest-bioperl-run-1.4 67
+MD5 21ad123058f1e670f289ee1a87de4e82 files/bioperl-run-Pise-test-patch.diff 722
+MD5 b23d441d6d3f1d4ed3dead4c3dc2799b files/digest-bioperl-run-1.2.2 69
diff --git a/sci-biology/bioperl-run/bioperl-run-1.2.2.ebuild b/sci-biology/bioperl-run/bioperl-run-1.2.2.ebuild
new file mode 100644
index 000000000000..d1e6cc22ee8f
--- /dev/null
+++ b/sci-biology/bioperl-run/bioperl-run-1.2.2.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2004 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-run/bioperl-run-1.2.2.ebuild,v 1.1 2004/12/23 22:09:47 ribosome Exp $
+
+inherit perl-module eutils
+CATEGORY="app-sci"
+
+DESCRIPTION="collection of tools for bioinformatics, genomics and life science research : subset required to run analyses"
+HOMEPAGE="http://www.bioperl.org/"
+#SRC_URI="http://www.cpan.org/modules/by-module/Bio/${P}.tar.gz"
+SRC_URI="http://www.bioperl.org/ftp/DIST/${P}.tar.gz"
+
+LICENSE="Artistic GPL-2"
+SLOT="0"
+KEYWORDS="x86"
+IUSE=""
+
+RDEPEND="
+	dev-perl/Algorithm-Diff
+	dev-perl/File-Temp
+	dev-perl/IO-String
+	dev-perl/XML-Parser"
+
+DEPEND=""
+
+src_unpack() {
+	unpack ${A}
+	cd ${S}
+	# remove interactiveness
+	epatch ${FILESDIR}/bioperl-run-Pise-test-patch.diff
+}
+
+src_compile() {
+	# there's a test to run for BioGFFDB if using mysql
+	perl-module_src_compile || die "compile failed"
+	# make test
+##	perl-module_src_test || die "src test failed"
+}
+
+src_install() {
+	mydoc="AUTHORS BUGS FAQ"
+	perl-module_src_install
+
+	# bioperl scripts and examples
+	einfo 'Adding bioperl examples and scripts to /usr/share/...'
+	dodir /usr/share/${PF}/scripts
+	#insinto /usr/share/${PF}/scripts
+	cd ${S}/scripts/
+	tar cf - ./ | ( cd ${D}/usr/share/${PF}/scripts; tar xf -)
+	dodir /usr/share/${PF}/examples
+	cd ${S}/examples/
+	tar cf - ./ | ( cd ${D}/usr/share/${PF}/examples; tar xf -)
+	cd ${S}
+
+}
diff --git a/sci-biology/bioperl-run/bioperl-run-1.4.ebuild b/sci-biology/bioperl-run/bioperl-run-1.4.ebuild
new file mode 100644
index 000000000000..f6b9aaae4247
--- /dev/null
+++ b/sci-biology/bioperl-run/bioperl-run-1.4.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2004 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-run/bioperl-run-1.4.ebuild,v 1.1 2004/12/23 22:09:47 ribosome Exp $
+
+inherit perl-module eutils
+CATEGORY="app-sci"
+
+DESCRIPTION="collection of tools for bioinformatics, genomics and life science research : subset required to run analyses"
+HOMEPAGE="http://www.bioperl.org/"
+#SRC_URI="http://www.cpan.org/modules/by-module/Bio/${P}.tar.gz"
+SRC_URI="http://www.bioperl.org/ftp/DIST/${P}.tar.gz"
+
+LICENSE="Artistic GPL-2"
+SLOT="0"
+KEYWORDS="x86 ~ppc"
+IUSE=""
+
+RDEPEND="
+	dev-perl/Algorithm-Diff
+	dev-perl/File-Temp
+	dev-perl/IO-String
+	dev-perl/XML-Parser"
+
+DEPEND=""
+
+src_compile() {
+	perl-module_src_compile || die "compile failed"
+	# make test
+	#perl-module_src_test || die "src test failed"
+}
+
+src_install() {
+	mydoc="AUTHORS BUGS INSTALL.PROGRAMS README"
+	perl-module_src_install
+
+	# bioperl scripts and examples
+	einfo 'Adding bioperl examples and scripts to /usr/share/...'
+	dodir /usr/share/${PF}/scripts
+	#insinto /usr/share/${PF}/scripts
+	cd ${S}/scripts/
+	tar cf - ./ | ( cd ${D}/usr/share/${PF}/scripts; tar xf -)
+	dodir /usr/share/${PF}/examples
+	cd ${S}/examples/
+	tar cf - ./ | ( cd ${D}/usr/share/${PF}/examples; tar xf -)
+	cd ${S}
+
+}
diff --git a/sci-biology/bioperl-run/files/bioperl-run-Pise-test-patch.diff b/sci-biology/bioperl-run/files/bioperl-run-Pise-test-patch.diff
new file mode 100644
index 000000000000..5683347a6b52
--- /dev/null
+++ b/sci-biology/bioperl-run/files/bioperl-run-Pise-test-patch.diff
@@ -0,0 +1,22 @@
+--- Makefile.PL.original	2003-09-28 23:33:16.000000000 -0400
++++ Makefile.PL	2003-09-28 23:33:50.000000000 -0400
+@@ -73,19 +73,6 @@
+ my $DISTNAME = "bioperl-run";
+ my $VERSION  = "1.2.2";
+ 
+-my $proceed = prompt("Do you want to run the Pise tests (requires a network connection) y/n",'n');
+-if( $proceed =~ /^[yY]/) {
+-    my $address = prompt("Enter your email address (no default)",'');
+-   
+-    if (open T,">t/pise-email.test") {
+-print T "$address\n";
+-close T;
+-    } else { warn("Cannot open file t/pise-email.test for writing - no Pise tests will be run"); }
+-} else {
+-    if( -e "t/pise-email.test" ) {
+-unlink "t/pise-email.test";
+-    }
+-}
+ #$do_autoload_finesse = 0;
+ #$NAME     = 'Bio';
+ #$DISTNAME = "GFD";
diff --git a/sci-biology/bioperl-run/files/digest-bioperl-run-1.2.2 b/sci-biology/bioperl-run/files/digest-bioperl-run-1.2.2
new file mode 100644
index 000000000000..cf92f27aa20d
--- /dev/null
+++ b/sci-biology/bioperl-run/files/digest-bioperl-run-1.2.2
@@ -0,0 +1 @@
+MD5 2ffbaa69e713f102f86c7b7462ccff52 bioperl-run-1.2.2.tar.gz 811989
diff --git a/sci-biology/bioperl-run/files/digest-bioperl-run-1.4 b/sci-biology/bioperl-run/files/digest-bioperl-run-1.4
new file mode 100644
index 000000000000..5c20eceaee32
--- /dev/null
+++ b/sci-biology/bioperl-run/files/digest-bioperl-run-1.4
@@ -0,0 +1 @@
+MD5 25914ab48d1ab0393ebb067a8f68a821 bioperl-run-1.4.tar.gz 830774
diff --git a/sci-biology/bioperl-run/metadata.xml b/sci-biology/bioperl-run/metadata.xml
new file mode 100644
index 000000000000..8a4bcd47220d
--- /dev/null
+++ b/sci-biology/bioperl-run/metadata.xml
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer><email>sediener@gentoo.org</email></maintainer>
+</pkgmetadata>