diff options
| -rw-r--r-- | sci-biology/emboss/ChangeLog | 13 | ||||
| -rw-r--r-- | sci-biology/emboss/Manifest | 2 | ||||
| -rw-r--r-- | sci-biology/emboss/emboss-3.0.0-r1.ebuild | 80 | ||||
| -rw-r--r-- | sci-biology/emboss/files/digest-emboss-3.0.0-r1 | 1 | ||||
| -rw-r--r-- | sci-biology/rebase/ChangeLog | 8 | ||||
| -rw-r--r-- | sci-biology/rebase/Manifest | 2 | ||||
| -rw-r--r-- | sci-biology/rebase/files/digest-rebase-601-r1 | 1 | ||||
| -rw-r--r-- | sci-biology/rebase/rebase-601-r1.ebuild | 43 |
8 files changed, 147 insertions, 3 deletions
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog index 3e860d6d3867..99d686c9f63a 100644 --- a/sci-biology/emboss/ChangeLog +++ b/sci-biology/emboss/ChangeLog @@ -1,6 +1,15 @@ # ChangeLog for sci-biology/emboss -# Copyright 2000-2005 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.24 2005/12/14 03:28:52 spyderous Exp $ +# Copyright 2000-2006 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.25 2006/01/21 17:19:43 ribosome Exp $ + +*emboss-3.0.0-r1 (21 Jan 2006) + + 21 Jan 2006; Olivier Fisette <ribosome@gentoo.org> + +emboss-3.0.0-r1.ebuild: + Install codons and restriction enzyme equivalence files in alternative + directories. This avoids file collisions on case insensitive filesystems + (see bug #115446), allows the installation of an updated enzyme prototypes + file that will give more consistent results (see bug #118832). 14 Dec 2005; Donnie Berkholz <spyderous@gentoo.org>; emboss-3.0.0.ebuild: Add modular X dependencies. diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest index 02c46adea9d5..5031a68e7fc5 100644 --- a/sci-biology/emboss/Manifest +++ b/sci-biology/emboss/Manifest @@ -1,5 +1,7 @@ MD5 6747fe89baf91e10880d44ecd28bd5f3 ChangeLog 5216 +MD5 12a9ce7a5e8cecb45348e897130fa529 emboss-3.0.0-r1.ebuild 2926 MD5 ecb49ecef824e368a8ad751b90f19186 emboss-3.0.0.ebuild 1854 MD5 ef2dfa3d13837026f59c0cf5f04f67c5 files/22emboss-r1 110 MD5 84fbde044d74a82c084fa22d5d59ae8e files/digest-emboss-3.0.0 66 +MD5 84fbde044d74a82c084fa22d5d59ae8e files/digest-emboss-3.0.0-r1 66 MD5 6051afb1f26bf343082490327784b958 metadata.xml 1013 diff --git a/sci-biology/emboss/emboss-3.0.0-r1.ebuild b/sci-biology/emboss/emboss-3.0.0-r1.ebuild new file mode 100644 index 000000000000..3f27832a6330 --- /dev/null +++ b/sci-biology/emboss/emboss-3.0.0-r1.ebuild @@ -0,0 +1,80 @@ +# Copyright 1999-2006 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-3.0.0-r1.ebuild,v 1.1 2006/01/21 17:19:43 ribosome Exp $ + +DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package" +HOMEPAGE="http://emboss.sourceforge.net/" +SRC_URI="ftp://${PN}.open-bio.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz" +LICENSE="GPL-2 LGPL-2" + +SLOT="0" +KEYWORDS="~amd64 ~ppc ~ppc-macos ~ppc64 ~x86" +IUSE="X png minimal" + +DEPEND="X? ( || ( x11-libs/libXt virtual/x11 ) ) + png? ( + sys-libs/zlib + media-libs/libpng + >=media-libs/gd-1.8 + ) + !minimal? ( + sci-biology/primer3 + sci-biology/clustalw + )" + +PDEPEND="!minimal? ( + sci-biology/aaindex + sci-biology/cutg + sci-biology/prints + >=sci-biology/prosite-19.7 + >=sci-biology/rebase-601-r1 + 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 ${EXTRA_CONF} || die + # Do not install the JEMBOSS component (the --without-java configure option + # does not work). JEMBOSS will be available as a separate package. + sed -i -e 's/SUBDIRS = plplot ajax nucleus emboss test doc jemboss/SUBDIRS = plplot ajax nucleus emboss test doc/' Makefile || die + emake || die +} + +src_install() { + einstall || die "Failed to install program files." + dodoc AUTHORS ChangeLog FAQ NEWS README THANKS "${FILESDIR}"/README.Gentoo \ + || die "Failed to install documentation." + + # Install env file for setting libplplot and acd files path. + insinto /etc/env.d + newins ${FILESDIR}/22emboss-r1 22emboss || \ + die "Failed to install environment file." + + # Symlink preinstalled docs to /usr/share/doc. + dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals || die + dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${PF}/programs || die + dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials || die + + # Remove useless dummy files from the image. + rm "${D}"/usr/share/EMBOSS/data/{AAINDEX,PRINTS,PROSITE,REBASE}/dummyfile \ + || die "Failed to remove dummy files." + + # Move the provided codon files to a different directory. This will avoid + # user confusion and file collisions on case-insensitive file systems (see + # bug #115446). This change is documented in "README.Gentoo". + mv "${D}"/usr/share/EMBOSS/data/CODONS \ + "${D}"/usr/share/EMBOSS/data/CODONS.orig || \ + die "Failed to move CODON directory." + + # Move the provided restriction enzyme prototypes file to a different name. + # This will avoid file collisions with future versions of rebase that will + # install their own enzyme prototypes file (see bug #118832). + mv "${D}"/usr/share/EMBOSS/data/embossre.equ \ + "${D}"/usr/share/EMBOSS/data/embossre.equ.orig || \ + die "Failed to move enzyme equivalence file." +} diff --git a/sci-biology/emboss/files/digest-emboss-3.0.0-r1 b/sci-biology/emboss/files/digest-emboss-3.0.0-r1 new file mode 100644 index 000000000000..5dfd3480a664 --- /dev/null +++ b/sci-biology/emboss/files/digest-emboss-3.0.0-r1 @@ -0,0 +1 @@ +MD5 fa72feded9ab9272e3e731c09f545dcc EMBOSS-3.0.0.tar.gz 16257908 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 +} |