From 57e05d7d06c7d4491321a25fcf3be152c58a167c Mon Sep 17 00:00:00 2001 From: Gunnar Wrobel Date: Wed, 23 Aug 2006 06:39:19 +0000 Subject: Moving sci-biology category to the stable overlay again svn path=/broken/; revision=748 --- sci-biology/autoprime/Manifest | 6 -- sci-biology/autoprime/autoprime-2.0.0.ebuild | 37 ------------ sci-biology/autoprime/autoprime-2.0.1.ebuild | 37 ------------ sci-biology/autoprime/autoprime-2.0.ebuild | 35 ------------ sci-biology/autoprime/files/digest-autoprime-2.0 | 1 - sci-biology/autoprime/files/digest-autoprime-2.0.0 | 1 - sci-biology/autoprime/files/digest-autoprime-2.0.1 | 1 - sci-biology/autoprimeweb/Manifest | 2 - sci-biology/autoprimeweb/autoprimeweb-2.0.0.ebuild | 42 -------------- .../autoprimeweb/files/digest-autoprimeweb-2.0.0 | 1 - sci-biology/ensembl-perl/Manifest | 7 --- sci-biology/ensembl-perl/ensembl-perl-31.ebuild | 45 --------------- sci-biology/ensembl-perl/ensembl-perl-32.ebuild | 45 --------------- sci-biology/ensembl-perl/ensembl-perl-33.ebuild | 45 --------------- sci-biology/ensembl-perl/files/Makefile.PL | 10 ---- .../ensembl-perl/files/digest-ensembl-perl-31 | 0 .../ensembl-perl/files/digest-ensembl-perl-32 | 0 .../ensembl-perl/files/digest-ensembl-perl-33 | 0 sci-biology/repbase/Manifest | 9 --- sci-biology/repbase/files/clean | 59 -------------------- sci-biology/repbase/files/digest-repbase-10.03 | 1 - sci-biology/repbase/files/digest-repbase-10.04 | 1 - sci-biology/repbase/files/digest-repbase-10.07 | 1 - sci-biology/repbase/files/digest-repbase-9.12 | 1 - sci-biology/repbase/repbase-10.03.ebuild | 65 ---------------------- sci-biology/repbase/repbase-10.04.ebuild | 65 ---------------------- sci-biology/repbase/repbase-10.07.ebuild | 65 ---------------------- sci-biology/repbase/repbase-9.12.ebuild | 65 ---------------------- 28 files changed, 647 deletions(-) delete mode 100644 sci-biology/autoprime/Manifest delete mode 100644 sci-biology/autoprime/autoprime-2.0.0.ebuild delete mode 100644 sci-biology/autoprime/autoprime-2.0.1.ebuild delete mode 100644 sci-biology/autoprime/autoprime-2.0.ebuild delete mode 100644 sci-biology/autoprime/files/digest-autoprime-2.0 delete mode 100644 sci-biology/autoprime/files/digest-autoprime-2.0.0 delete mode 100644 sci-biology/autoprime/files/digest-autoprime-2.0.1 delete mode 100644 sci-biology/autoprimeweb/Manifest delete mode 100644 sci-biology/autoprimeweb/autoprimeweb-2.0.0.ebuild delete mode 100644 sci-biology/autoprimeweb/files/digest-autoprimeweb-2.0.0 delete mode 100644 sci-biology/ensembl-perl/Manifest delete mode 100644 sci-biology/ensembl-perl/ensembl-perl-31.ebuild delete mode 100644 sci-biology/ensembl-perl/ensembl-perl-32.ebuild delete mode 100644 sci-biology/ensembl-perl/ensembl-perl-33.ebuild delete mode 100644 sci-biology/ensembl-perl/files/Makefile.PL delete mode 100644 sci-biology/ensembl-perl/files/digest-ensembl-perl-31 delete mode 100644 sci-biology/ensembl-perl/files/digest-ensembl-perl-32 delete mode 100644 sci-biology/ensembl-perl/files/digest-ensembl-perl-33 delete mode 100644 sci-biology/repbase/Manifest delete mode 100755 sci-biology/repbase/files/clean delete mode 100644 sci-biology/repbase/files/digest-repbase-10.03 delete mode 100644 sci-biology/repbase/files/digest-repbase-10.04 delete mode 100644 sci-biology/repbase/files/digest-repbase-10.07 delete mode 100644 sci-biology/repbase/files/digest-repbase-9.12 delete mode 100644 sci-biology/repbase/repbase-10.03.ebuild delete mode 100644 sci-biology/repbase/repbase-10.04.ebuild delete mode 100644 sci-biology/repbase/repbase-10.07.ebuild delete mode 100644 sci-biology/repbase/repbase-9.12.ebuild diff --git a/sci-biology/autoprime/Manifest b/sci-biology/autoprime/Manifest deleted file mode 100644 index 8550d31..0000000 --- a/sci-biology/autoprime/Manifest +++ /dev/null @@ -1,6 +0,0 @@ -MD5 9d92f632ade80a2f6e5ec60d82fb4cce autoprime-2.0.0.ebuild 761 -MD5 97c7532df6bbfd7ad008aec4887b4de3 autoprime-2.0.1.ebuild 649 -MD5 fbe4fdc3bebd9831e9990477561d72da autoprime-2.0.ebuild 746 -MD5 3460ece729b38b487daade18802c3285 files/digest-autoprime-2.0.0 66 -MD5 09a9c57f415ba24fcfa6fae440f49968 files/digest-autoprime-2.0.1 66 -MD5 7784311d2ac1eb36499051b488cbd1bc files/digest-autoprime-2.0 62 diff --git a/sci-biology/autoprime/autoprime-2.0.0.ebuild b/sci-biology/autoprime/autoprime-2.0.0.ebuild deleted file mode 100644 index 659d86c..0000000 --- a/sci-biology/autoprime/autoprime-2.0.0.ebuild +++ /dev/null @@ -1,37 +0,0 @@ -# Copyright 1999-2005 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /home/fsk/.cvsroot/AutoPrime/ebuilds/sci-biology/autoprime/autoprime-2.0.0.ebuild,v 1.1.1.1 2005/09/03 20:17:54 fsk Exp $ - -inherit perl-module - -MY_P=${P/autoprime/AutoPrime} - -CATEGORY="sci-biology" - -DESCRIPTION="A command line tool to generate primers for RT-PCR" -HOMEPAGE="http://www.autoprime.de/" -SRC_URI="http://www.gunnarwrobel.de/downloads/${MY_P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~x86" -IUSE="" - -DEPEND=">=sci-biology/bioperl-1.4 - >=sci-biology/repbase-9.12 - >=sci-biology/primer3-1.0.0 - " - -src_compile() -{ - cd ${WORKDIR}/${MY_P} - - perl-module_src_compile -} - -src_install() -{ - cd ${WORKDIR}/${MY_P} - - perl-module_src_install -} diff --git a/sci-biology/autoprime/autoprime-2.0.1.ebuild b/sci-biology/autoprime/autoprime-2.0.1.ebuild deleted file mode 100644 index f6b2708..0000000 --- a/sci-biology/autoprime/autoprime-2.0.1.ebuild +++ /dev/null @@ -1,37 +0,0 @@ -# Copyright 2004-2005 Gunnar Wrobel -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -inherit perl-module - -MY_P=${P/autoprime/AutoPrime} - -CATEGORY="sci-biology" - -DESCRIPTION="A command line tool to generate primers for RT-PCR" -HOMEPAGE="http://www.autoprime.de/" -SRC_URI="http://www.gunnarwrobel.de/downloads/${MY_P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~x86 ~amd64" -IUSE="" - -DEPEND=">=sci-biology/ensembl-perl-33 - >=sci-biology/repbase-10.07 - >=sci-biology/primer3-1.0.0 - " - -src_compile() -{ - cd ${WORKDIR}/${MY_P} - - perl-module_src_compile -} - -src_install() -{ - cd ${WORKDIR}/${MY_P} - - perl-module_src_install -} diff --git a/sci-biology/autoprime/autoprime-2.0.ebuild b/sci-biology/autoprime/autoprime-2.0.ebuild deleted file mode 100644 index cfac2ec..0000000 --- a/sci-biology/autoprime/autoprime-2.0.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2005 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /home/fsk/.cvsroot/AutoPrime/ebuilds/sci-biology/autoprime/autoprime-2.0.ebuild,v 1.1.1.1 2005/09/03 20:17:54 fsk Exp $ - -inherit perl-module - -CATEGORY="sci-biology" - -DESCRIPTION="A command line tool to generate primers for RT-PCR" -HOMEPAGE="http://www.autoprime.de/" -SRC_URI="http://www.gunnarwrobel.de/downloads/AutoPrime-2.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~x86" -IUSE="" - -DEPEND=">=sci-biology/bioperl-1.4 - >=sci-biology/repbase-9.12 - >=sci-biology/primer3-1.0.0 - " - -src_compile() -{ - cd ${WORKDIR}/${A/.tar.gz//} - - perl-module_src_compile -} - -src_install() -{ - cd ${WORKDIR}/${A/.tar.gz//} - - perl-module_src_install -} diff --git a/sci-biology/autoprime/files/digest-autoprime-2.0 b/sci-biology/autoprime/files/digest-autoprime-2.0 deleted file mode 100644 index 3d38458..0000000 --- a/sci-biology/autoprime/files/digest-autoprime-2.0 +++ /dev/null @@ -1 +0,0 @@ -MD5 6cfd9178f1d769aeebc45ae2b28cb71f AutoPrime-2.tar.gz 24042 diff --git a/sci-biology/autoprime/files/digest-autoprime-2.0.0 b/sci-biology/autoprime/files/digest-autoprime-2.0.0 deleted file mode 100644 index bdee895..0000000 --- a/sci-biology/autoprime/files/digest-autoprime-2.0.0 +++ /dev/null @@ -1 +0,0 @@ -MD5 ad8c629fa33cbff631a0413191f857dd AutoPrime-2.0.0.tar.gz 27658 diff --git a/sci-biology/autoprime/files/digest-autoprime-2.0.1 b/sci-biology/autoprime/files/digest-autoprime-2.0.1 deleted file mode 100644 index 1a4558b..0000000 --- a/sci-biology/autoprime/files/digest-autoprime-2.0.1 +++ /dev/null @@ -1 +0,0 @@ -MD5 70b857e0563898db9ad15acf8babd014 AutoPrime-2.0.1.tar.gz 25737 diff --git a/sci-biology/autoprimeweb/Manifest b/sci-biology/autoprimeweb/Manifest deleted file mode 100644 index db785a4..0000000 --- a/sci-biology/autoprimeweb/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -MD5 7cd78cb7228942db282ec1271aaa6319 autoprimeweb-2.0.0.ebuild 747 -MD5 2fbf1c8f321aa131fd60a5a0a5055308 files/digest-autoprimeweb-2.0.0 70 diff --git a/sci-biology/autoprimeweb/autoprimeweb-2.0.0.ebuild b/sci-biology/autoprimeweb/autoprimeweb-2.0.0.ebuild deleted file mode 100644 index e2f427d..0000000 --- a/sci-biology/autoprimeweb/autoprimeweb-2.0.0.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 2004-2005 Gunnar Wrobel -# $Header: $ - -inherit webapp - -MY_P=${P/autoprimeweb/AutoPrimeWeb} - -DESCRIPTION="A web frontend for AutoPrime" -HOMEPAGE="http://www.autoprime.de/" -SRC_URI="http://www.gunnarwrobel.de/downloads/${MY_P}.tar.bz2" - -LICENSE="GPL-2" -KEYWORDS="~x86 ~amd64" -IUSE="" - -DEPEND="virtual/httpd-php - dev-perl/XML-XSLT - sci-biology/autoprime" - -S=${WORKDIR}/${PN/autoprimeweb/AutoPrimeWeb} - -src_install () { - - webapp_src_preinst - - cp -r . ${D}${MY_HTDOCSDIR} - keepdir ${MY_HTDOCSDIR}/xmlfiles - - webapp_serverowned ${MY_HTDOCSDIR}/xmlfiles - - rm -rf ${D}${MY_HTDOCSDIR}/cgi - - mkdir -p ${D}${MY_CGIBINDIR}/autoprimeweb - cp -r cgi/* ${D}${MY_CGIBINDIR}/autoprimeweb - - webapp_src_install - -} - - - - diff --git a/sci-biology/autoprimeweb/files/digest-autoprimeweb-2.0.0 b/sci-biology/autoprimeweb/files/digest-autoprimeweb-2.0.0 deleted file mode 100644 index fa17cb1..0000000 --- a/sci-biology/autoprimeweb/files/digest-autoprimeweb-2.0.0 +++ /dev/null @@ -1 +0,0 @@ -MD5 580b9c0665889a1ababd05f3f14415be AutoPrimeWeb-2.0.0.tar.bz2 30337 diff --git a/sci-biology/ensembl-perl/Manifest b/sci-biology/ensembl-perl/Manifest deleted file mode 100644 index cc791f2..0000000 --- a/sci-biology/ensembl-perl/Manifest +++ /dev/null @@ -1,7 +0,0 @@ -MD5 4167bbcf0e0b05c834ac8b680e2e0955 ensembl-perl-31.ebuild 773 -MD5 92dcb9f863ac5144527c046e5b2d3746 ensembl-perl-32.ebuild 780 -MD5 92dcb9f863ac5144527c046e5b2d3746 ensembl-perl-33.ebuild 780 -MD5 b17aafa4efc4e955cbc2374091962976 files/Makefile.PL 311 -MD5 d41d8cd98f00b204e9800998ecf8427e files/digest-ensembl-perl-31 0 -MD5 d41d8cd98f00b204e9800998ecf8427e files/digest-ensembl-perl-32 0 -MD5 d41d8cd98f00b204e9800998ecf8427e files/digest-ensembl-perl-33 0 diff --git a/sci-biology/ensembl-perl/ensembl-perl-31.ebuild b/sci-biology/ensembl-perl/ensembl-perl-31.ebuild deleted file mode 100644 index d00116e..0000000 --- a/sci-biology/ensembl-perl/ensembl-perl-31.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2005 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -inherit cvs perl-module - -CATEGORY="sci-biology" - -DESCRIPTION="Additional perl modules for bioperl that can be used to easily access the EnsEMBL database" -HOMEPAGE="http://www.ensembl.org/" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~x86" -IUSE="" - -ECVS_LOCALNAME="EnsEMBL" -ECVS_SERVER="cvsro.sanger.ac.uk:/cvsroot/CVSmaster" -ECVS_MODULE="ensembl/modules/Bio/EnsEMBL" -ECVS_BRANCH="branch-ensembl-${PV}" -ECVS_USER="cvsuser" -ECVS_PASS="CVSUSER" - - -DEPEND="=sci-biology/bioperl-1.4" - -src_unpack() -{ - cvs_src_unpack - - cp ${FILESDIR}/Makefile.PL ${WORKDIR}/ -} - -src_compile() -{ - cd ${WORKDIR} - - perl-module_src_compile -} - -src_install() -{ - cd ${WORKDIR} - - perl-module_src_install -} diff --git a/sci-biology/ensembl-perl/ensembl-perl-32.ebuild b/sci-biology/ensembl-perl/ensembl-perl-32.ebuild deleted file mode 100644 index bcd7ff4..0000000 --- a/sci-biology/ensembl-perl/ensembl-perl-32.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2005 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -inherit cvs perl-module - -CATEGORY="sci-biology" - -DESCRIPTION="Additional perl modules for bioperl that can be used to easily access the EnsEMBL database" -HOMEPAGE="http://www.ensembl.org/" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~x86 ~amd64" -IUSE="" - -ECVS_LOCALNAME="EnsEMBL" -ECVS_SERVER="cvsro.sanger.ac.uk:/cvsroot/CVSmaster" -ECVS_MODULE="ensembl/modules/Bio/EnsEMBL" -ECVS_BRANCH="branch-ensembl-${PV}" -ECVS_USER="cvsuser" -ECVS_PASS="CVSUSER" - - -DEPEND="=sci-biology/bioperl-1.4" - -src_unpack() -{ - cvs_src_unpack - - cp ${FILESDIR}/Makefile.PL ${WORKDIR}/ -} - -src_compile() -{ - cd ${WORKDIR} - - perl-module_src_compile -} - -src_install() -{ - cd ${WORKDIR} - - perl-module_src_install -} diff --git a/sci-biology/ensembl-perl/ensembl-perl-33.ebuild b/sci-biology/ensembl-perl/ensembl-perl-33.ebuild deleted file mode 100644 index bcd7ff4..0000000 --- a/sci-biology/ensembl-perl/ensembl-perl-33.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2005 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -inherit cvs perl-module - -CATEGORY="sci-biology" - -DESCRIPTION="Additional perl modules for bioperl that can be used to easily access the EnsEMBL database" -HOMEPAGE="http://www.ensembl.org/" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~x86 ~amd64" -IUSE="" - -ECVS_LOCALNAME="EnsEMBL" -ECVS_SERVER="cvsro.sanger.ac.uk:/cvsroot/CVSmaster" -ECVS_MODULE="ensembl/modules/Bio/EnsEMBL" -ECVS_BRANCH="branch-ensembl-${PV}" -ECVS_USER="cvsuser" -ECVS_PASS="CVSUSER" - - -DEPEND="=sci-biology/bioperl-1.4" - -src_unpack() -{ - cvs_src_unpack - - cp ${FILESDIR}/Makefile.PL ${WORKDIR}/ -} - -src_compile() -{ - cd ${WORKDIR} - - perl-module_src_compile -} - -src_install() -{ - cd ${WORKDIR} - - perl-module_src_install -} diff --git a/sci-biology/ensembl-perl/files/Makefile.PL b/sci-biology/ensembl-perl/files/Makefile.PL deleted file mode 100644 index cafb2aa..0000000 --- a/sci-biology/ensembl-perl/files/Makefile.PL +++ /dev/null @@ -1,10 +0,0 @@ -use ExtUtils::MakeMaker 5.0; - -WriteMakefile( - NAME => "Bio::EnsEMBL", - VERSION => "31", - AUTHOR => "Sanger Center (ensembl-dev@ebi.ac.uk)", - ABSTRACT => "BioPerl modules to access ensembl", - INSTALLDIRS => "vendor", - PMLIBDIRS => [ "EnsEMBL" ] - ); diff --git a/sci-biology/ensembl-perl/files/digest-ensembl-perl-31 b/sci-biology/ensembl-perl/files/digest-ensembl-perl-31 deleted file mode 100644 index e69de29..0000000 diff --git a/sci-biology/ensembl-perl/files/digest-ensembl-perl-32 b/sci-biology/ensembl-perl/files/digest-ensembl-perl-32 deleted file mode 100644 index e69de29..0000000 diff --git a/sci-biology/ensembl-perl/files/digest-ensembl-perl-33 b/sci-biology/ensembl-perl/files/digest-ensembl-perl-33 deleted file mode 100644 index e69de29..0000000 diff --git a/sci-biology/repbase/Manifest b/sci-biology/repbase/Manifest deleted file mode 100644 index f727e94..0000000 --- a/sci-biology/repbase/Manifest +++ /dev/null @@ -1,9 +0,0 @@ -MD5 389a1a303497d5503f334e60466195a3 repbase-10.03.ebuild 1463 -MD5 91b78f561ed7a033faf48d1e4d5c68e3 repbase-10.04.ebuild 1456 -MD5 389a1a303497d5503f334e60466195a3 repbase-9.12.ebuild 1463 -MD5 24860972eb7dd95216a72d60acbd5d84 repbase-10.07.ebuild 1465 -MD5 943163c2456b74490a384738b63d6d94 files/clean 1161 -MD5 6d3280263178010862efcb1b59c4c816 files/digest-repbase-10.03 71 -MD5 3d53f3eb616d7665c620cf1ff30f5f99 files/digest-repbase-10.04 71 -MD5 6d171b2224c472ad2ab93a3033b09c96 files/digest-repbase-9.12 70 -MD5 899787e1cc59fab954e7331592a2d857 files/digest-repbase-10.07 71 diff --git a/sci-biology/repbase/files/clean b/sci-biology/repbase/files/clean deleted file mode 100755 index 37ee59c..0000000 --- a/sci-biology/repbase/files/clean +++ /dev/null @@ -1,59 +0,0 @@ -#!/usr/bin/perl -w - -use strict; - -my $name=""; -my $sequence=""; -my $infile = $ARGV[0]; -my $outfile = $ARGV[1]; - -open(LIB, $infile); - -open(CLIB, ">", $outfile); - -while () -{ - if (m/^>/) - { - if (not $name eq "") - { - if ($sequence eq "") - { - print "---------------------------------------------------------------------------------------\n"; - print "Empty sequence: " . $name . "\n"; - } - else - { - if ($sequence =~ m/^[ACGTNWSYRMHKXDVB]*$/) - { - $sequence =~ s/[WSYRMHKXDVB]/N/g; - if (not $sequence =~ m/NNNN/) - { - print CLIB $name; - print CLIB $sequence . "\n"; - } - else - { - print "---------------------------------------------------------------------------------------\n"; - print "Too many N's: " . $name; - } - } - else - { - print "---------------------------------------------------------------------------------------\n"; - print "Invalid entry: " . $name; - $sequence =~ s/[ACGTN]//g; - print "Reduced sequence:\n"; - print $sequence . "\n"; - } - $sequence = ""; - } - } - $name = $_; - } - else - { - $sequence .= uc($_); - $sequence =~ s/\n//g; - } -} diff --git a/sci-biology/repbase/files/digest-repbase-10.03 b/sci-biology/repbase/files/digest-repbase-10.03 deleted file mode 100644 index c718f4e..0000000 --- a/sci-biology/repbase/files/digest-repbase-10.03 +++ /dev/null @@ -1 +0,0 @@ -MD5 c530ff51d4f60a8ae2114f3185b0235f RepBase10.03.fasta.tar.gz 3530082 diff --git a/sci-biology/repbase/files/digest-repbase-10.04 b/sci-biology/repbase/files/digest-repbase-10.04 deleted file mode 100644 index ede3594..0000000 --- a/sci-biology/repbase/files/digest-repbase-10.04 +++ /dev/null @@ -1 +0,0 @@ -MD5 76b1ac539ad79a64ab48904027631cea RepBase10.04.fasta.tar.gz 3562104 diff --git a/sci-biology/repbase/files/digest-repbase-10.07 b/sci-biology/repbase/files/digest-repbase-10.07 deleted file mode 100644 index 1a0810a..0000000 --- a/sci-biology/repbase/files/digest-repbase-10.07 +++ /dev/null @@ -1 +0,0 @@ -MD5 54669e3eb561fa101903c681a594e2c7 RepBase10.07.fasta.tar.gz 4061677 diff --git a/sci-biology/repbase/files/digest-repbase-9.12 b/sci-biology/repbase/files/digest-repbase-9.12 deleted file mode 100644 index 3188ee7..0000000 --- a/sci-biology/repbase/files/digest-repbase-9.12 +++ /dev/null @@ -1 +0,0 @@ -MD5 fdf7cf4befd28b6b902da0f4a9263c72 RepBase9.12.fasta.tar.gz 3271264 diff --git a/sci-biology/repbase/repbase-10.03.ebuild b/sci-biology/repbase/repbase-10.03.ebuild deleted file mode 100644 index 32f0e4f..0000000 --- a/sci-biology/repbase/repbase-10.03.ebuild +++ /dev/null @@ -1,65 +0,0 @@ -# Copyright 1999-2005 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -CATEGORY="sci-biology" - -MY_P="RepBase${PV}.fasta" - -DESCRIPTION="A database of repetetive genetic elements in various organisms." -HOMEPAGE="http://www.girinst.org" -SRC_URI="${MY_P}.tar.gz" - -LICENSE="repbase-agreement" -SLOT="0" -KEYWORDS="~x86 ~amd64" -IUSE="" - -DEPEND="" -RDEPEND="" - -RESTRICT="fetch" - -REPBASELOC="${HOMEPAGE}/server/RepBase/" - -REPLIBRARIES=" -angrep.ref=repeat_lib_A.gambiae -cbrrep.ref=repeat_lib_C.briggsae -celrep.ref=repeat_lib_C.elegans -drorep.ref=repeat_lib_D.melanogaster -fugrep.ref=repeat_lib_F.rubripes -humrep.ref=repeat_lib_H.sapiens -prirep.ref=repeat_lib_P.troglodyte -rodrep.ref=repeat_lib_M.musculus -rodrep.ref=repeat_lib_R.norvegicus -zebrep.ref=repeat_lib_D.rerio -" - -pkg_nofetch() -{ - einfo "Please download ${SRC_URI}" - einfo "from ${REPBASELOC} and place it in ${DISTDIR}." - einfo "You will need to register as an academic user at" - einfo "${HOMEPAGE} in order to be" - einfo "allowed to download the file." -} - -src_compile() -{ - cp ${FILESDIR}/clean ${WORKDIR} - cd ${WORKDIR} - for lib in ${REPLIBRARIES} - do - einfo Cleaning library file ${lib/=*/} to ${lib/*=/} - ./clean ${MY_P}/${lib/=*/} ${lib/*=/} - done -} - -src_install() -{ - cd ${WORKDIR} - install -m 755 -d ${D}/usr/share/${P}/ - for lib in ${REPLIBRARIES} - do - install -m 644 ${lib/*=/} ${D}/usr/share/${P}/ - done -} diff --git a/sci-biology/repbase/repbase-10.04.ebuild b/sci-biology/repbase/repbase-10.04.ebuild deleted file mode 100644 index 90cfaa9..0000000 --- a/sci-biology/repbase/repbase-10.04.ebuild +++ /dev/null @@ -1,65 +0,0 @@ -# Copyright 1999-2005 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -CATEGORY="sci-biology" - -MY_P="RepBase${PV}.fasta" - -DESCRIPTION="A database of repetetive genetic elements in various organisms." -HOMEPAGE="http://www.girinst.org" -SRC_URI="${MY_P}.tar.gz" - -LICENSE="repbase-agreement" -SLOT="0" -KEYWORDS="~x86" -IUSE="" - -DEPEND="" -RDEPEND="" - -RESTRICT="fetch" - -REPBASELOC="${HOMEPAGE}/server/RepBase/" - -REPLIBRARIES=" -angrep.ref=repeat_lib_A.gambiae -cbrrep.ref=repeat_lib_C.briggsae -celrep.ref=repeat_lib_C.elegans -drorep.ref=repeat_lib_D.melanogaster -fugrep.ref=repeat_lib_F.rubripes -humrep.ref=repeat_lib_H.sapiens -prirep.ref=repeat_lib_P.troglodyte -rodrep.ref=repeat_lib_M.musculus -rodrep.ref=repeat_lib_R.norvegicus -zebrep.ref=repeat_lib_D.rerio -" - -pkg_nofetch() -{ - einfo "Please download ${SRC_URI}" - einfo "from ${REPBASELOC} and place it in ${DISTDIR}." - einfo "You will need to register as an academic user at" - einfo "${HOMEPAGE} in order to be" - einfo "allowed to download the file." -} - -src_compile() -{ - cp ${FILESDIR}/clean ${WORKDIR} - cd ${WORKDIR} - for lib in ${REPLIBRARIES} - do - einfo Cleaning library file ${lib/=*/} to ${lib/*=/} - ./clean ${MY_P}/${lib/=*/} ${lib/*=/} - done -} - -src_install() -{ - cd ${WORKDIR} - install -m 755 -d ${D}/usr/share/${P}/ - for lib in ${REPLIBRARIES} - do - install -m 644 ${lib/*=/} ${D}/usr/share/${P}/ - done -} diff --git a/sci-biology/repbase/repbase-10.07.ebuild b/sci-biology/repbase/repbase-10.07.ebuild deleted file mode 100644 index 50549fd..0000000 --- a/sci-biology/repbase/repbase-10.07.ebuild +++ /dev/null @@ -1,65 +0,0 @@ -# Copyright 1999-2005 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -CATEGORY="sci-biology" - -MY_P="RepBase${PV}.fasta" - -DESCRIPTION="A database of repetetive genetic elements in various organisms." -HOMEPAGE="http://www.girinst.org" -SRC_URI="${MY_P}.tar.gz" - -LICENSE="repbase-agreement" -SLOT="0" -KEYWORDS="~x86 ~amd64" -IUSE="" - -DEPEND="" -RDEPEND="" - -RESTRICT="fetch" - -REPBASELOC="${HOMEPAGE}/server/RepBase/" - -REPLIBRARIES=" -angrep.ref=repeat_lib_A.gambiae -cbrrep.ref=repeat_lib_C.briggsae -celrep.ref=repeat_lib_C.elegans -drorep.ref=repeat_lib_D.melanogaster -fugrep.ref=repeat_lib_F.rubripes -humrep.ref=repeat_lib_H.sapiens -prirep.ref=repeat_lib_P.troglodyte -rodrep.ref=repeat_lib_M.musculus -rodrep.ref=repeat_lib_R.norvegicus -zebrep.ref=repeat_lib_D.rerio -" - -pkg_nofetch() -{ - einfo "Please download ${SRC_URI}" - einfo "from ${REPBASELOC} and place it in ${DISTDIR}." - einfo "You will need to register as an academic user at" - einfo "${HOMEPAGE} in order to be" - einfo "allowed to download the file." -} - -src_compile() -{ - cp ${FILESDIR}/clean ${WORKDIR} - cd ${WORKDIR} - for lib in ${REPLIBRARIES} - do - einfo Cleaning library file ${lib/=*/} to ${lib/*=/} - ./clean ${MY_P}/${lib/=*/} ${lib/*=/} - done -} - -src_install() -{ - cd ${WORKDIR} - install -m 755 -d ${D}/usr/share/${PN}/ - for lib in ${REPLIBRARIES} - do - install -m 644 ${lib/*=/} ${D}/usr/share/${PN}/ - done -} diff --git a/sci-biology/repbase/repbase-9.12.ebuild b/sci-biology/repbase/repbase-9.12.ebuild deleted file mode 100644 index 32f0e4f..0000000 --- a/sci-biology/repbase/repbase-9.12.ebuild +++ /dev/null @@ -1,65 +0,0 @@ -# Copyright 1999-2005 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -CATEGORY="sci-biology" - -MY_P="RepBase${PV}.fasta" - -DESCRIPTION="A database of repetetive genetic elements in various organisms." -HOMEPAGE="http://www.girinst.org" -SRC_URI="${MY_P}.tar.gz" - -LICENSE="repbase-agreement" -SLOT="0" -KEYWORDS="~x86 ~amd64" -IUSE="" - -DEPEND="" -RDEPEND="" - -RESTRICT="fetch" - -REPBASELOC="${HOMEPAGE}/server/RepBase/" - -REPLIBRARIES=" -angrep.ref=repeat_lib_A.gambiae -cbrrep.ref=repeat_lib_C.briggsae -celrep.ref=repeat_lib_C.elegans -drorep.ref=repeat_lib_D.melanogaster -fugrep.ref=repeat_lib_F.rubripes -humrep.ref=repeat_lib_H.sapiens -prirep.ref=repeat_lib_P.troglodyte -rodrep.ref=repeat_lib_M.musculus -rodrep.ref=repeat_lib_R.norvegicus -zebrep.ref=repeat_lib_D.rerio -" - -pkg_nofetch() -{ - einfo "Please download ${SRC_URI}" - einfo "from ${REPBASELOC} and place it in ${DISTDIR}." - einfo "You will need to register as an academic user at" - einfo "${HOMEPAGE} in order to be" - einfo "allowed to download the file." -} - -src_compile() -{ - cp ${FILESDIR}/clean ${WORKDIR} - cd ${WORKDIR} - for lib in ${REPLIBRARIES} - do - einfo Cleaning library file ${lib/=*/} to ${lib/*=/} - ./clean ${MY_P}/${lib/=*/} ${lib/*=/} - done -} - -src_install() -{ - cd ${WORKDIR} - install -m 755 -d ${D}/usr/share/${P}/ - for lib in ${REPLIBRARIES} - do - install -m 644 ${lib/*=/} ${D}/usr/share/${P}/ - done -} -- cgit v1.2.3-65-gdbad