Added check for X support in the NCBI toolkit (fixes bug #112336)

Package-Manager: portage-2.0.51.22-r3

diff --git a/sci-biology/clustalx/ChangeLog b/sci-biology/clustalx/ChangeLog
index 6151a2c17fb2b478edaabc0dfa891d4da9e55d44..69c2f57623383d4ff7f3cf859596b2bc0ac82b21 100644 (file)
--- a/sci-biology/clustalx/ChangeLog
+++ b/sci-biology/clustalx/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/clustalx
 # Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalx/ChangeLog,v 1.6 2005/06/02 15:19:25 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalx/ChangeLog,v 1.7 2005/11/13 01:03:34 ribosome Exp $
+
+*clustalx-1.83-r2 (13 Nov 2005)
+
+  13 Nov 2005; Olivier Fisette <ribosome@gentoo.org>
+  +clustalx-1.83-r2.ebuild:
+  Added check for X support in the NCBI toolkit, as suggested by Brady
+  Catherman <bradyc@uidaho.edu> (fixes bug #112336).
 
   02 Jun 2005; Olivier Fisette <ribosome@gentoo.org>
   clustalx-1.83-r1.ebuild:

diff --git a/sci-biology/clustalx/Manifest b/sci-biology/clustalx/Manifest
index 4fcdfea9845897f9d835aa80918fd86d516bc492..9ca5545861cae2bb8978b37e4d1d8f439adfa38f 100644 (file)
--- a/sci-biology/clustalx/Manifest
+++ b/sci-biology/clustalx/Manifest
@@ -1,4 +1,6 @@
+MD5 ca93724bd9c8b5e1bfd755900185f2d8 clustalx-1.83-r2.ebuild 1825
 MD5 0f5a065a208f1b86c23cff8992d0c4b1 clustalx-1.83-r1.ebuild 1352
-MD5 85fc256f91737fa33c83b74019d519c1 ChangeLog 1538
+MD5 4d72fad3ef862b68d29358513d669462 ChangeLog 1777
 MD5 272b5b012593acd07a7a60b8b64e6761 metadata.xml 509
 MD5 800c4da737d4fb9af3d8ffb7f6f44892 files/digest-clustalx-1.83-r1 68
+MD5 800c4da737d4fb9af3d8ffb7f6f44892 files/digest-clustalx-1.83-r2 68

diff --git a/sci-biology/clustalx/clustalx-1.83-r2.ebuild b/sci-biology/clustalx/clustalx-1.83-r2.ebuild
new file mode 100644 (file)
index 0000000..1a8557e
--- /dev/null
+++ b/sci-biology/clustalx/clustalx-1.83-r2.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalx/clustalx-1.83-r2.ebuild,v 1.1 2005/11/13 01:03:34 ribosome Exp $
+
+inherit toolchain-funcs eutils
+
+DESCRIPTION="Graphical interface for the ClustalW multiple alignment program"
+HOMEPAGE="http://www-igbmc.u-strasbg.fr/BioInfo/ClustalX/"
+SRC_URI="ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/clustalx1.83.sun.tar.gz"
+LICENSE="public-domain"
+
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE=""
+
+DEPEND="sci-biology/clustalw
+       sci-biology/ncbi-tools
+       virtual/x11
+       virtual/motif"
+
+S="${WORKDIR}/${PN}${PV}.sun"
+
+pkg_setup() {
+       if ! built_with_use sci-biology/ncbi-tools X; then
+               echo
+               eerror "ClustalX requires the Vibrant toolkit, which is part of the"
+               eerror "optional X support in the \"sci-biology/ncbi-tools\" package."
+               eerror "To install ClustalX on your system, first recompile"
+               eerror "\"sci-biology/ncbi-tools\" with the \"X\" USE flag enabled,"
+               eerror "then try to install ClustalX again."
+               die "X support not enabled in \"sci-biology/ncbi-tools\""
+       fi
+}
+
+src_unpack() {
+       unpack ${A}
+       cd ${S}
+       cp makefile.linux makefile
+       sed -e "s/CC    = cc/CC = $(tc-getCC)/" \
+               -e "s/CFLAGS  = -c -O/CFLAGS  = -c ${CFLAGS}/" \
+               -e "s/LFLAGS    = -O -lm/LFLAGS = -lm ${CFLAGS}/" \
+               -e "s%-I/usr/bio/src/ncbi/include%-I/usr/include/ncbi%" \
+               -e "s%-L/usr/bio/src/ncbi/lib -L/usr/ccs/lib -L/usr/X11R6/lib%-L/usr/lib -L/usr/X11R6/lib%" \
+               -i makefile || die
+       sed -i -e "s%clustalx_help%/usr/share/doc/${PF}/clustalx_help%" clustalx.c || die
+       sed -i -e "s%clustalw.doc%../clustalw.doc%" clustalx.html || die
+}
+
+src_compile() {
+       make || die
+}
+
+src_install() {
+       dobin clustalx
+
+       dodoc README_X
+       dohtml clustalx.html
+
+       insinto /usr/share/doc/${PF}
+       doins clustalx_help clustalw.doc
+}

diff --git a/sci-biology/clustalx/files/digest-clustalx-1.83-r2 b/sci-biology/clustalx/files/digest-clustalx-1.83-r2
new file mode 100644 (file)
index 0000000..9d0832e
--- /dev/null
+++ b/sci-biology/clustalx/files/digest-clustalx-1.83-r2
@@ -0,0 +1 @@
+MD5 732538fe5fea04f4d5dd665e84c3b9ab clustalx1.83.sun.tar.gz 860205