Initial import

Package-Manager: portage-2.1.1

5 files changed, 131 insertions, 0 deletions

diff --git a/sci-biology/staden-bin/ChangeLog b/sci-biology/staden-bin/ChangeLog
new file mode 100644
index 000000000000..7b36f8386a81
--- /dev/null
+++ b/sci-biology/staden-bin/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/staden-bin
+# Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/staden-bin/ChangeLog,v 1.1 2006/10/22 16:37:35 ribosome Exp $
+
+*staden-bin-1.7.0 (22 Oct 2006)
+
+  22 Oct 2006; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
+  +staden-bin-1.7.0.ebuild:
+  Initial import.
+
diff --git a/sci-biology/staden-bin/Manifest b/sci-biology/staden-bin/Manifest
new file mode 100644
index 000000000000..6b44478eeb18
--- /dev/null
+++ b/sci-biology/staden-bin/Manifest
@@ -0,0 +1,16 @@
+DIST staden-linux-x86-1-7-0.tar.gz 38515727 RMD160 99dd575a9682719cdd8cff35dbd13c5073c61b32 SHA1 31014bb1a453b024fd4e969664da5acf6f7fc169 SHA256 38c96b2df886ebb2407e21bd3c0059d632c2db9a6a7ab707f31c90f6db9e5e0e
+EBUILD staden-bin-1.7.0.ebuild 2962 RMD160 2dc74d1d108edadbd169b1ebf7fc07468efc1a54 SHA1 70cc7b549ecb57a8e061f5d2f0c4ff07dcffe036 SHA256 e58bbde11b045c1aee63379e7c6010931fb20436e98d94465c0a0293dd225d58
+MD5 e6060d0fa70c00b15b3ff9a20542d941 staden-bin-1.7.0.ebuild 2962
+RMD160 2dc74d1d108edadbd169b1ebf7fc07468efc1a54 staden-bin-1.7.0.ebuild 2962
+SHA256 e58bbde11b045c1aee63379e7c6010931fb20436e98d94465c0a0293dd225d58 staden-bin-1.7.0.ebuild 2962
+MISC ChangeLog 367 RMD160 8e26e1a8fca2e8ab44244928682bae452ed21cf9 SHA1 d9c6df6269ef3f9abec3d4051c9ea52c88f4802f SHA256 dcf44067e50be6e033bc73b0d782322293be48b12bb706c7211f0cf3e43bcad9
+MD5 9860577ebc39061d2d92c3a4d5e10f33 ChangeLog 367
+RMD160 8e26e1a8fca2e8ab44244928682bae452ed21cf9 ChangeLog 367
+SHA256 dcf44067e50be6e033bc73b0d782322293be48b12bb706c7211f0cf3e43bcad9 ChangeLog 367
+MISC metadata.xml 262 RMD160 4eabcbcb990d4d5e3b34db8c27bcd2c0cfcf7501 SHA1 3c024ca60a2b93ed0e0311f6b05ef5ef117bee31 SHA256 89af818a993faf14a4a87e2f254943420156c2a317c385480a9533ba682b650f
+MD5 5f35ae4b4cb1cd144db7c7c093d3fd80 metadata.xml 262
+RMD160 4eabcbcb990d4d5e3b34db8c27bcd2c0cfcf7501 metadata.xml 262
+SHA256 89af818a993faf14a4a87e2f254943420156c2a317c385480a9533ba682b650f metadata.xml 262
+MD5 da06914b2f9e2bb9617639db1578c5e4 files/digest-staden-bin-1.7.0 274
+RMD160 20d65fe0e81a5feed63f41e2925108ab088edf44 files/digest-staden-bin-1.7.0 274
+SHA256 022e1e0c801b0084bd0293706997f38a28fdbd929e83276e12d20ae4711a7a4f files/digest-staden-bin-1.7.0 274
diff --git a/sci-biology/staden-bin/files/digest-staden-bin-1.7.0 b/sci-biology/staden-bin/files/digest-staden-bin-1.7.0
new file mode 100644
index 000000000000..42feae6f3546
--- /dev/null
+++ b/sci-biology/staden-bin/files/digest-staden-bin-1.7.0
@@ -0,0 +1,3 @@
+MD5 57edef52b055c42fbef307673e844677 staden-linux-x86-1-7-0.tar.gz 38515727
+RMD160 99dd575a9682719cdd8cff35dbd13c5073c61b32 staden-linux-x86-1-7-0.tar.gz 38515727
+SHA256 38c96b2df886ebb2407e21bd3c0059d632c2db9a6a7ab707f31c90f6db9e5e0e staden-linux-x86-1-7-0.tar.gz 38515727
diff --git a/sci-biology/staden-bin/metadata.xml b/sci-biology/staden-bin/metadata.xml
new file mode 100644
index 000000000000..ebbff811d3b4
--- /dev/null
+++ b/sci-biology/staden-bin/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer>
+		<email>ribosome@gentoo.org</email>
+		<name>Olivier Fisette</name>
+	</maintainer>
+	<herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/staden-bin/staden-bin-1.7.0.ebuild b/sci-biology/staden-bin/staden-bin-1.7.0.ebuild
new file mode 100644
index 000000000000..09b51b987431
--- /dev/null
+++ b/sci-biology/staden-bin/staden-bin-1.7.0.ebuild
@@ -0,0 +1,93 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/staden-bin/staden-bin-1.7.0.ebuild,v 1.1 2006/10/22 16:37:35 ribosome Exp $
+
+inherit multilib
+
+DESCRIPTION="The Staden Package - Biological sequence handling and analysis"
+LICENSE="staden"
+HOMEPAGE="http://staden.sourceforge.net"
+SRC_URI="mirror://sourceforge/staden/staden-linux-x86-${PV//./-}.tar.gz"
+
+SLOT="0"
+IUSE=""
+KEYWORDS="~x86"
+
+ITCLTK_PV="3.3"
+IWIDGETS_PV="4.0.1"
+
+RDEPEND="app-shells/pdksh
+	=media-libs/libpng-1.2*
+	=sci-libs/io_lib-1.10*
+	~dev-tcltk/itcl-${ITCLTK_PV}
+	~dev-tcltk/itk-${ITCLTK_PV}
+	~dev-tcltk/iwidgets-${IWIDGETS_PV}
+	x11-libs/libX11"
+
+S="${WORKDIR}/staden-linux-x86-${PV//./-}"
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+
+	# Remove Gentoo-provided libraries.
+	rm lib/linux-binaries/libpng* || die "Could not remove libpng."
+	rm -r lib/itcl${ITCLTK_PV} || die "Could not remove itcl."
+	rm -r lib/itk${ITCLTK_PV} || die "Could not remove itk."
+	rm lib/iwidgets || die "Could not remove iwidgets."
+
+	# Remove executables provided by the io_lib package.
+	for i in append_sff convert_trace extract_seq get_comment hash_extract \
+			hash_sff hash_tar index_tar makeSCF scf_dump scf_info scf_update \
+			trace_dump ztr_dump; do
+		rm linux-bin/${i} || die "Could not remove io_lib program: ${i}."
+	done
+
+	# Remove the help program, which is only a wrapper to launch netscape
+	# with a non-existent hypertext file.
+	rm linux-bin/staden_help || die "Could not remove staden-help."
+
+	# Remove broken prebuilt EMBOSS tcl/tk GUIs.
+	rm tables/emboss_menu
+	rm -r lib/spin_emboss/acdtcl
+	rm -r lib/spin2_emboss/acdtcl
+
+	sed -e 's:/usr/bin/nawk:/usr/bin/awk:' -i linux-bin/fasta-split || \
+			die "Could not patch fasta-split."
+	sed -e 's:/usr/local/badger/gap4_test:/opt/staden:' \
+			-i linux-bin/finish_cDNA -i linux-bin/finish_cDNA_ends_only || \
+			die "Could not patch finish_cDNA"
+}
+
+src_compile() {
+	echo; einfo "Nothing to compile"; echo
+}
+
+src_install() {
+	# There is no Makefile.
+	dodir /opt/staden
+	cp -R "${S}"/* "${D}"/opt/staden/ || die "Could not copy package files."
+	dosym /opt/staden/doc /usr/share/doc/${PF} || die "Could not symlink docs."
+
+	# Staden programs look for the tcl/tk/itcl/itk/iwidgets libraries in the
+	# package root.
+	dosym /usr/$(get_libdir)/itcl${ITCLTK_PV} /opt/staden/lib/itcl${ITCLTK_PV} \
+			|| die "Could not symlink itcl."
+	dosym /usr/$(get_libdir)/itk${ITCLTK_PV} /opt/staden/lib/itk${ITCLTK_PV} \
+			|| die "Could not symlink itk."
+	dosym /usr/$(get_libdir)/iwidgets${IWIDGETS_PV} /opt/staden/lib/iwidgets \
+			|| die "Could not symlink iwidgets."
+
+	dodir /etc/env.d
+	cat <<- EOF > "${D}"/etc/env.d/60staden
+		STADENROOT="/opt/staden"
+	EOF
+}
+
+pkg_postinst() {
+	echo
+	einfo "Before using Staden applications, csh users should source"
+	einfo "\"/opt/staden/staden.login\", whilst bash users should source"
+	einfo "\"/opt/staden/staden.profile\"."
+	echo
+}