From a8f954cb3cf67663dbd5b5fa0eabb45747dd9ccc Mon Sep 17 00:00:00 2001 From: Olivier Fisette Date: Thu, 23 Dec 2004 22:50:57 +0000 Subject: [PATCH] Moving to sci-biology/emboss --- app-sci/emboss-kaptain/Manifest | 2 +- app-sci/emboss/ChangeLog | 73 ------------------------ app-sci/emboss/Manifest | 5 -- app-sci/emboss/emboss-2.9.0.ebuild | 58 ------------------- app-sci/emboss/files/22emboss-r1 | 4 -- app-sci/emboss/files/digest-emboss-2.9.0 | 1 - app-sci/emboss/metadata.xml | 22 ------- 7 files changed, 1 insertion(+), 164 deletions(-) delete mode 100644 app-sci/emboss/ChangeLog delete mode 100644 app-sci/emboss/Manifest delete mode 100644 app-sci/emboss/emboss-2.9.0.ebuild delete mode 100644 app-sci/emboss/files/22emboss-r1 delete mode 100644 app-sci/emboss/files/digest-emboss-2.9.0 delete mode 100644 app-sci/emboss/metadata.xml diff --git a/app-sci/emboss-kaptain/Manifest b/app-sci/emboss-kaptain/Manifest index e965174a0e22..c731883fbf72 100644 --- a/app-sci/emboss-kaptain/Manifest +++ b/app-sci/emboss-kaptain/Manifest @@ -1,4 +1,4 @@ MD5 93acc378715490b14d7d7364ef5f8ab8 ChangeLog 536 MD5 f189a3c4ff5ae55bcee4f8ed0ace5d20 metadata.xml 254 -MD5 c1da1f0f37f8ca81f41fd5301dce076d emboss-kaptain-0.97.ebuild 1187 +MD5 0edcb6525c935d961ec670db04336972 emboss-kaptain-0.97.ebuild 1191 MD5 25e58e7c514be03e50f128e66179551d files/digest-emboss-kaptain-0.97 70 diff --git a/app-sci/emboss/ChangeLog b/app-sci/emboss/ChangeLog deleted file mode 100644 index a09bff4dc2c0..000000000000 --- a/app-sci/emboss/ChangeLog +++ /dev/null @@ -1,73 +0,0 @@ -# ChangeLog for app-sci/emboss -# Copyright 2000-2004 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/app-sci/emboss/ChangeLog,v 1.15 2004/11/01 01:28:06 ribosome Exp $ - - 31 Oct 2004; Olivier Fisette emboss-2.9.0.ebuild, - -emboss-2.8.0-r3.ebuild: - Removed old version. Added 2.9.0 to x86. - - 10 Aug 2004; Olivier Fisette - emboss-2.8.0-r3.ebuild: - Added to x86. - emboss-2.8.0-r2.ebuild: - Removed obsolete ebuild. - - 21 Jul 2004; David Holm emboss-2.9.0.ebuild: - Added to ~ppc. - - 20 Jul 2004; Olivier Fisette - emboss-2.8.0-r3.ebuild, emboss-2.9.0.ebuild: - Removed icc support since no patching is needed. - - 19 Jul 2004; Olivier Fisette emboss-2.9.0.ebuild: - Version bump. Changed the configuration and install steps a bit to - reflect the fact that header files are now installed automatically. - - 14 Jul 2004; Olivier Fisette - emboss-2.8.0-r3.ebuild: Modified configuration step to make the X and png - USE flags independent; Added support for icc; Added primer3 and clustalw - to the dependencies since some EMBOSS programs won't work without them; - Added support for the biological databases aaindex, cutg, prints, prosite, - rebase and transfac, which are needed for many EMBOSS programs (the databases - are PDEPENDencies since they all must be indexed with an EMBOSS program before - use) (this database support is optional); Added header files installation for - EMBOSS development. - emboss-2.8.0-r2.ebuild: Added to x86. - emboss-2.8.0-r1.ebuild, emboss-2.8.0.ebuild, emboss-2.7.1.ebuild: Removed files. - metadata.xml: Added long description; Set myself as maintainer. - - 02 Jun 2004; Aron Griffis emboss-2.8.0-r1.ebuild, - emboss-2.8.0-r2.ebuild: - Fix use invocation - - 12 May 2004; David Holm emboss-2.8.0-r2.ebuild: - Added to ~ppc. - -*emboss-2.8.0-r2 (11 May 2004) - - 11 May 2004; Patrick Kursawe emboss-2.8.0-r2.ebuild, - files/22emboss-r1: - Adjusted value of PLPLOT_LIB, see bug #50176 - -*emboss-2.8.0-r1 (30 Jan 2004) - - 30 Jan 2004; Stephen Diener emboss-2.8.0-r1.ebuild: - Modified to use X and png properly for servers - - 28 Jan 2004; Stephen Diener emboss-2.8.0.ebuild: - Modified 2.8.0 ebuild to require X not just USE it. - -*emboss-2.8.0 (13 Dec 2003) - - 13 Dec 2003; Stephen Diener emboss-2.7.1.ebuild, - emboss-2.8.0.ebuild: - Version bump... - - 20 Oct 2003; George Shapovalov metdata.xml : - added metadata.xml, marked ebuild stable - -*emboss-2.7.1 (03 Sep 2003) - - 03 Sep 2003; emboss-2.7.1.ebuild: - Initial ebuild - diff --git a/app-sci/emboss/Manifest b/app-sci/emboss/Manifest deleted file mode 100644 index 87e3b32a9144..000000000000 --- a/app-sci/emboss/Manifest +++ /dev/null @@ -1,5 +0,0 @@ -MD5 02e17352ecec7dabbaa1aab84769e746 emboss-2.9.0.ebuild 1779 -MD5 1b0826c48804a608a2bb548e7c27dc93 ChangeLog 2789 -MD5 6051afb1f26bf343082490327784b958 metadata.xml 1013 -MD5 68e42b6377bb0887a0aeac76cf530854 files/digest-emboss-2.9.0 66 -MD5 ef2dfa3d13837026f59c0cf5f04f67c5 files/22emboss-r1 110 diff --git a/app-sci/emboss/emboss-2.9.0.ebuild b/app-sci/emboss/emboss-2.9.0.ebuild deleted file mode 100644 index 753a865f9576..000000000000 --- a/app-sci/emboss/emboss-2.9.0.ebuild +++ /dev/null @@ -1,58 +0,0 @@ -# Copyright 1999-2004 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/app-sci/emboss/emboss-2.9.0.ebuild,v 1.7 2004/12/23 21:29:30 ribosome Exp $ - -DESCRIPTION="The European Molecular Biology Open Software Suite: a sequence analysis package." -HOMEPAGE="http://emboss.sourceforge.net/" -SRC_URI="ftp://ftp.uk.embnet.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz" -LICENSE="GPL-2 LGPL-2" - -SLOT="0" -KEYWORDS="x86 ~ppc" -IUSE="X png no-biodata" - -DEPEND="X? ( virtual/x11 ) - png? ( - sys-libs/zlib - media-libs/libpng - >=media-libs/gd-1.8 - ) - sci-biology/primer3 - sci-biology/clustalw" - -PDEPEND="!no-biodata? ( - sci-biology/aaindex - sci-biology/cutg - sci-biology/prints - sci-biology/prosite - sci-biology/rebase - sci-biology/transfac - )" - -S=${WORKDIR}/EMBOSS-${PV} - -src_compile() { - EXTRA_CONF="--includedir=${D}/usr/include/emboss" - ! use X && EXTRA_CONF="${EXTRA_CONF} --without-x" - ! use png && EXTRA_CONF="${EXTRA_CONF} --without-pngdriver" - - econf ${EXTRA_CONF} || die - # Do not install the JEMBOSS component (the --without-java configure option - # does not work). JEMBOSS will be available as a separate package. - sed -i -e 's/SUBDIRS = plplot ajax nucleus emboss test doc jemboss/SUBDIRS = plplot ajax nucleus emboss test doc/' Makefile - emake || die -} - -src_install() { - einstall || die - dodoc AUTHORS ChangeLog FAQ NEWS README THANKS - - # Install env file for setting libplplot and acd files path. - insinto /etc/env.d - newins ${FILESDIR}/22emboss-r1 22emboss - - # Symlink preinstalled docs to /usr/share/doc. - dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals - dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${PF}/programs - dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials -} diff --git a/app-sci/emboss/files/22emboss-r1 b/app-sci/emboss/files/22emboss-r1 deleted file mode 100644 index 177643ced11f..000000000000 --- a/app-sci/emboss/files/22emboss-r1 +++ /dev/null @@ -1,4 +0,0 @@ -# plplot libs dir -PLPLOT_LIB="/usr/share/EMBOSS/" -# ACD files location -EMBOSS_ACDROOT="/usr/share/EMBOSS/acd" diff --git a/app-sci/emboss/files/digest-emboss-2.9.0 b/app-sci/emboss/files/digest-emboss-2.9.0 deleted file mode 100644 index ab9c2bc595ca..000000000000 --- a/app-sci/emboss/files/digest-emboss-2.9.0 +++ /dev/null @@ -1 +0,0 @@ -MD5 c6facfd1750e88a0c8b7bb7ac826d472 EMBOSS-2.9.0.tar.gz 14479274 diff --git a/app-sci/emboss/metadata.xml b/app-sci/emboss/metadata.xml deleted file mode 100644 index ff86b6a3a444..000000000000 --- a/app-sci/emboss/metadata.xml +++ /dev/null @@ -1,22 +0,0 @@ - - - - - ribosome@gentoo.org - Olivier Fisette - - sci - - EMBOSS is "The European Molecular Biology Open Software Suite". - EMBOSS is a free Open Source software analysis package specially - developed for the needs of the molecular biology (e.g. EMBnet) user - community. The software automatically copes with data in a variety - of formats and even allows transparent retrieval of sequence data - from the web. Also, as extensive libraries are provided with the - package, it is a platform to allow other scientists to develop and - release software in true open source spirit. EMBOSS also integrates - a range of currently available packages and tools for sequence - analysis into a seamless whole. EMBOSS breaks the historical trend - towards commercial software packages. - - -- 2.26.2