Fixed issues with duplicated CODON files, case-insensitive filesystems (ppc-macos) and restriction enzymes equivalences (see bugs #118832 and #115446)

(Portage version: 2.0.53)

4 files changed, 53 insertions, 1 deletions

diff --git a/sci-biology/rebase/ChangeLog b/sci-biology/rebase/ChangeLog
index bcc87a245910..f7c2a8b74e07 100644
--- a/sci-biology/rebase/ChangeLog
+++ b/sci-biology/rebase/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/rebase
 # Copyright 2000-2006 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/rebase/ChangeLog,v 1.51 2006/01/18 21:28:24 corsair Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/rebase/ChangeLog,v 1.52 2006/01/21 17:19:43 ribosome Exp $
+
+*rebase-601-r1 (21 Jan 2006)
+
+  21 Jan 2006; Olivier Fisette <ribosome@gentoo.org> +rebase-601-r1.ebuild:
+  Install an enzymes prototypes file, replacing the one distributed with
+  EMBOSS. This will solve the inconsistencies reported in bug #118832.
 
   18 Jan 2006; Markus Rothe <corsair@gentoo.org> rebase-512.ebuild:
   Stable on ppc64; bug #118832
diff --git a/sci-biology/rebase/Manifest b/sci-biology/rebase/Manifest
index 9db7760c6724..e5af18ff6bb0 100644
--- a/sci-biology/rebase/Manifest
+++ b/sci-biology/rebase/Manifest
@@ -3,8 +3,10 @@ MD5 8b72021e3a53e0c9ab7acaf2d016637e files/digest-rebase-509 63
 MD5 de0923d154ca7a32f45ee6bb9d3a40c4 files/digest-rebase-511 63
 MD5 0327e485fe0040317dd1016583b0d76d files/digest-rebase-512 63
 MD5 9b37c587b84cf914d6f9a9b616c493db files/digest-rebase-601 63
+MD5 9b37c587b84cf914d6f9a9b616c493db files/digest-rebase-601-r1 63
 MD5 550f8d428f3e75690b43d32df6aa60cd metadata.xml 900
 MD5 b4f7769279c4301bacb9c4b78f136d08 rebase-509.ebuild 1097
 MD5 fe94217aa8122be5dc5855d73772d8b0 rebase-511.ebuild 1237
 MD5 292928f0068bac8ab37a29c223af581e rebase-512.ebuild 1238
+MD5 ef9d51f417289656336e9f1f26edf920 rebase-601-r1.ebuild 1360
 MD5 ac62c4563f22a49719f3623d9e163ce1 rebase-601.ebuild 1244
diff --git a/sci-biology/rebase/files/digest-rebase-601-r1 b/sci-biology/rebase/files/digest-rebase-601-r1
new file mode 100644
index 000000000000..514623f4bd95
--- /dev/null
+++ b/sci-biology/rebase/files/digest-rebase-601-r1
@@ -0,0 +1 @@
+MD5 473a812ec6119fb8b02ac3e0bfec6884 rebase-601.tar.bz2 181829
diff --git a/sci-biology/rebase/rebase-601-r1.ebuild b/sci-biology/rebase/rebase-601-r1.ebuild
new file mode 100644
index 000000000000..8cb1c680615e
--- /dev/null
+++ b/sci-biology/rebase/rebase-601-r1.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/rebase/rebase-601-r1.ebuild,v 1.1 2006/01/21 17:19:43 ribosome Exp $
+
+DESCRIPTION="A restriction enzyme database"
+LICENSE="public-domain"
+HOMEPAGE="http://rebase.neb.com"
+SRC_URI="mirror://gentoo/${P}.tar.bz2"
+
+SLOT="0"
+# Minimal build keeps only the indexed files (if applicable) and the
+# documentation. The non-indexed database is not installed.
+IUSE="emboss minimal"
+KEYWORDS="~x86 ~ppc ~amd64 ~ppc-macos ~ppc64"
+
+DEPEND="emboss? ( >=sci-biology/emboss-3.0.0-r1 )"
+
+src_compile() {
+	if use emboss; then
+		echo
+		einfo "Indexing ${PN} for usage with EMBOSS."
+		mkdir REBASE
+		EMBOSS_DATA=. rebaseextract -auto -infile withrefm.${PV} \
+			-protofile proto.${PV} || die "Indexing ${PN} failed."
+		echo
+	fi
+}
+
+src_install() {
+	if ! use minimal; then
+		insinto /usr/share/${PN}
+		doins withrefm.${PV} proto.${PV} || die \
+			"Failed to install raw database."
+	fi
+	newdoc REBASE.DOC README || die "Failed to install documentation."
+	if use emboss; then
+		insinto /usr/share/EMBOSS/data/REBASE
+		doins REBASE/{embossre.enz,embossre.ref,embossre.sup} || die \
+			"Failed to install EMBOSS data files."
+		insinto /usr/share/EMBOSS/data
+		doins embossre.equ || die "Failed to install enzyme prototypes file."
+	fi
+}