From f0231c57a7d9d1746c0ded96d7d6d9927bc009a9 Mon Sep 17 00:00:00 2001 From: jokey Date: Sun, 7 Oct 2007 05:29:17 +0000 Subject: move stuff to root git-svn-id: http://overlays.gentoo.org/svn/proj/science/overlay@753 32389bae-6d03-0410-99cf-db05cde120eb --- sci-biology/glimmerhmm/ChangeLog | 16 -------- sci-biology/glimmerhmm/Manifest | 16 -------- .../glimmerhmm/files/digest-glimmerhmm-3.0.1 | 3 -- sci-biology/glimmerhmm/glimmerhmm-3.0.1.ebuild | 45 ---------------------- sci-biology/glimmerhmm/metadata.xml | 5 --- 5 files changed, 85 deletions(-) delete mode 100644 sci-biology/glimmerhmm/ChangeLog delete mode 100644 sci-biology/glimmerhmm/Manifest delete mode 100644 sci-biology/glimmerhmm/files/digest-glimmerhmm-3.0.1 delete mode 100644 sci-biology/glimmerhmm/glimmerhmm-3.0.1.ebuild delete mode 100644 sci-biology/glimmerhmm/metadata.xml (limited to 'sci-biology/glimmerhmm') diff --git a/sci-biology/glimmerhmm/ChangeLog b/sci-biology/glimmerhmm/ChangeLog deleted file mode 100644 index 918e4112f..000000000 --- a/sci-biology/glimmerhmm/ChangeLog +++ /dev/null @@ -1,16 +0,0 @@ -# ChangeLog for sci-biology/glimmerhmm -# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 27 Apr 2007; Andrey Kislyuk - +glimmerhmm-3.0.1.ebuild: - Mass import from sunrise - - 15 Mar 2007; Christian Faulhammer - glimmerhmm-3.0.1.ebuild: - Orthographic sex-up - - 14 Mar 2007; Andrey Kislyuk +glimmerhmm-3.0.1.ebuild, - +metadata.xml: - new package sci-biology/glimmerhmm (bug 170964) - diff --git a/sci-biology/glimmerhmm/Manifest b/sci-biology/glimmerhmm/Manifest deleted file mode 100644 index e07e63b79..000000000 --- a/sci-biology/glimmerhmm/Manifest +++ /dev/null @@ -1,16 +0,0 @@ -DIST GlimmerHMM-3.0.1.tar.gz 45475952 RMD160 273cb74458e3f444cd9f8ca9f6618335aea5465f SHA1 6caf10a3fb79660e48d88560869dee0394961f1a SHA256 c956838a398483003ff1af867c65aca082b82340d8b302b9ada77d1b246954e4 -EBUILD glimmerhmm-3.0.1.ebuild 1256 RMD160 63bbac5df129a0867aa0ab6e025710c8683cdcf6 SHA1 c517e20085e5e716435c0d29bd1a3bae9228e2d1 SHA256 0a9df33ae04c5b275999041573f0935b32be4797da0b48211e88dbe277d7dfe5 -MD5 660bd1edbd45fe60d64f23417d319a80 glimmerhmm-3.0.1.ebuild 1256 -RMD160 63bbac5df129a0867aa0ab6e025710c8683cdcf6 glimmerhmm-3.0.1.ebuild 1256 -SHA256 0a9df33ae04c5b275999041573f0935b32be4797da0b48211e88dbe277d7dfe5 glimmerhmm-3.0.1.ebuild 1256 -MISC ChangeLog 486 RMD160 7d213d91b90390472c3afbf1a921ccbbfc6111c3 SHA1 7c1d8b78c09b3c2344874ca9923aab99cf0656d8 SHA256 87dcfa56bc3f3a8f104c7fcf893596d6ab677a982af26651336a7b8854fd31f1 -MD5 6f733ec00f6a44d4d0e8c47297f1b91a ChangeLog 486 -RMD160 7d213d91b90390472c3afbf1a921ccbbfc6111c3 ChangeLog 486 -SHA256 87dcfa56bc3f3a8f104c7fcf893596d6ab677a982af26651336a7b8854fd31f1 ChangeLog 486 -MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 -MD5 1e678929a9fec6632e227bdf2262e9a1 metadata.xml 170 -RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 metadata.xml 170 -SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 metadata.xml 170 -MD5 6031057f170ba3e39d873476919294cf files/digest-glimmerhmm-3.0.1 256 -RMD160 30de1bc3c8be7819528bdbaea8be47a38d92b3a5 files/digest-glimmerhmm-3.0.1 256 -SHA256 a5ceb414b56313f97ef383cc3debda25408bcf877376fc456319a55e6f4f769e files/digest-glimmerhmm-3.0.1 256 diff --git a/sci-biology/glimmerhmm/files/digest-glimmerhmm-3.0.1 b/sci-biology/glimmerhmm/files/digest-glimmerhmm-3.0.1 deleted file mode 100644 index 9ab418485..000000000 --- a/sci-biology/glimmerhmm/files/digest-glimmerhmm-3.0.1 +++ /dev/null @@ -1,3 +0,0 @@ -MD5 e98e0bad04507b7f661e6b9876c3d1f6 GlimmerHMM-3.0.1.tar.gz 45475952 -RMD160 273cb74458e3f444cd9f8ca9f6618335aea5465f GlimmerHMM-3.0.1.tar.gz 45475952 -SHA256 c956838a398483003ff1af867c65aca082b82340d8b302b9ada77d1b246954e4 GlimmerHMM-3.0.1.tar.gz 45475952 diff --git a/sci-biology/glimmerhmm/glimmerhmm-3.0.1.ebuild b/sci-biology/glimmerhmm/glimmerhmm-3.0.1.ebuild deleted file mode 100644 index 61f3a2740..000000000 --- a/sci-biology/glimmerhmm/glimmerhmm-3.0.1.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -MY_P=GlimmerHMM - -DESCRIPTION="An eukaryotic gene finding system from TIGR" -HOMEPAGE="http://www.cbcb.umd.edu/software/GlimmerHMM/" -SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/glimmerhmm/${MY_P}-${PV}.tar.gz" - -LICENSE="Artistic" -SLOT="0" -IUSE="" -KEYWORDS="~x86" - -DEPEND="" -RDEPEND="" - -S=${WORKDIR}/${MY_P} - -src_compile() { - sed -i -e 's|\(my $scriptdir=\)$FindBin::Bin|\1"/usr/share/'${PN}'/training_utils"|' \ - -e 's|\(use lib\) $FindBin::Bin|\1 "/usr/share/'${PN}'/lib"|' train/trainGlimmerHMM || die "sed failed" - sed -i 's/^CFLAGS[ ]*=.*//' */makefile - - cd sources - emake || die "emake failed in sources" - cd "${S}/train" || die "failed to cd" - emake || die "emake failed in train" -} - -src_install() { - dobin sources/glimmerhmm train/trainGlimmerHMM - - dodir /usr/share/${PN}/{lib,models,training_utils} - insinto /usr/share/${PN}/lib - doins train/*.pm - insinto /usr/share/${PN}/models - doins -r trained_dir/* - insinto /usr/share/${PN}/training_utils - insopts -m755 - doins train/{build{1,2,-icm,-icm-noframe},erfapp,falsecomp,findsites,karlin,score,score{2,ATG,ATG2,STOP,STOP2},splicescore} - - dodoc README.first train/readme.train -} diff --git a/sci-biology/glimmerhmm/metadata.xml b/sci-biology/glimmerhmm/metadata.xml deleted file mode 100644 index 7e3286984..000000000 --- a/sci-biology/glimmerhmm/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ - - - -maintainer-wanted - -- cgit v1.2.3-65-gdbad