diff options
author | Gunnar Wrobel <wrobel@gentoo.org> | 2006-01-14 12:59:12 +0000 |
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committer | Gunnar Wrobel <wrobel@gentoo.org> | 2006-01-14 12:59:12 +0000 |
commit | 18419c9fe14d8a481a2804739c33d7295c0c6799 (patch) | |
tree | 47d876f10150c40f2932bc5f895651e706a44a46 | |
parent | More restructuring (diff) | |
parent | Cleanup (diff) | |
download | overlay-18419c9fe14d8a481a2804739c33d7295c0c6799.tar.gz overlay-18419c9fe14d8a481a2804739c33d7295c0c6799.tar.bz2 overlay-18419c9fe14d8a481a2804739c33d7295c0c6799.zip |
More restructuring
svn path=/testing/; revision=631
29 files changed, 714 insertions, 0 deletions
diff --git a/sci-biology/autoprime/Manifest b/sci-biology/autoprime/Manifest new file mode 100644 index 0000000..8550d31 --- /dev/null +++ b/sci-biology/autoprime/Manifest @@ -0,0 +1,6 @@ +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 new file mode 100644 index 0000000..659d86c --- /dev/null +++ b/sci-biology/autoprime/autoprime-2.0.0.ebuild @@ -0,0 +1,37 @@ +# 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 new file mode 100644 index 0000000..f6b2708 --- /dev/null +++ b/sci-biology/autoprime/autoprime-2.0.1.ebuild @@ -0,0 +1,37 @@ +# 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 new file mode 100644 index 0000000..cfac2ec --- /dev/null +++ b/sci-biology/autoprime/autoprime-2.0.ebuild @@ -0,0 +1,35 @@ +# 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 new file mode 100644 index 0000000..3d38458 --- /dev/null +++ b/sci-biology/autoprime/files/digest-autoprime-2.0 @@ -0,0 +1 @@ +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 new file mode 100644 index 0000000..bdee895 --- /dev/null +++ b/sci-biology/autoprime/files/digest-autoprime-2.0.0 @@ -0,0 +1 @@ +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 new file mode 100644 index 0000000..1a4558b --- /dev/null +++ b/sci-biology/autoprime/files/digest-autoprime-2.0.1 @@ -0,0 +1 @@ +MD5 70b857e0563898db9ad15acf8babd014 AutoPrime-2.0.1.tar.gz 25737 diff --git a/sci-biology/autoprimeweb/Manifest b/sci-biology/autoprimeweb/Manifest new file mode 100644 index 0000000..db785a4 --- /dev/null +++ b/sci-biology/autoprimeweb/Manifest @@ -0,0 +1,2 @@ +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 new file mode 100644 index 0000000..e2f427d --- /dev/null +++ b/sci-biology/autoprimeweb/autoprimeweb-2.0.0.ebuild @@ -0,0 +1,42 @@ +# 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 new file mode 100644 index 0000000..fa17cb1 --- /dev/null +++ b/sci-biology/autoprimeweb/files/digest-autoprimeweb-2.0.0 @@ -0,0 +1 @@ +MD5 580b9c0665889a1ababd05f3f14415be AutoPrimeWeb-2.0.0.tar.bz2 30337 diff --git a/sci-biology/ensembl-perl/Manifest b/sci-biology/ensembl-perl/Manifest new file mode 100644 index 0000000..cc791f2 --- /dev/null +++ b/sci-biology/ensembl-perl/Manifest @@ -0,0 +1,7 @@ +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 new file mode 100644 index 0000000..d00116e --- /dev/null +++ b/sci-biology/ensembl-perl/ensembl-perl-31.ebuild @@ -0,0 +1,45 @@ +# 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 ${WORKDIR} + + perl-module_src_install +} diff --git a/sci-biology/ensembl-perl/ensembl-perl-32.ebuild b/sci-biology/ensembl-perl/ensembl-perl-32.ebuild new file mode 100644 index 0000000..bcd7ff4 --- /dev/null +++ b/sci-biology/ensembl-perl/ensembl-perl-32.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +inherit cvs perl-module + +CATEGORY="sci-biology" + +DESCRIPTION="Additional perl modules for bioperl that can be used to easily access the EnsEMBL database" +HOMEPAGE="http://www.ensembl.org/" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="" + +ECVS_LOCALNAME="EnsEMBL" +ECVS_SERVER="cvsro.sanger.ac.uk:/cvsroot/CVSmaster" +ECVS_MODULE="ensembl/modules/Bio/EnsEMBL" +ECVS_BRANCH="branch-ensembl-${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 ${WORKDIR} + + perl-module_src_install +} diff --git a/sci-biology/ensembl-perl/ensembl-perl-33.ebuild b/sci-biology/ensembl-perl/ensembl-perl-33.ebuild new file mode 100644 index 0000000..bcd7ff4 --- /dev/null +++ b/sci-biology/ensembl-perl/ensembl-perl-33.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +inherit cvs perl-module + +CATEGORY="sci-biology" + +DESCRIPTION="Additional perl modules for bioperl that can be used to easily access the EnsEMBL database" +HOMEPAGE="http://www.ensembl.org/" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="" + +ECVS_LOCALNAME="EnsEMBL" +ECVS_SERVER="cvsro.sanger.ac.uk:/cvsroot/CVSmaster" +ECVS_MODULE="ensembl/modules/Bio/EnsEMBL" +ECVS_BRANCH="branch-ensembl-${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 new file mode 100644 index 0000000..cafb2aa --- /dev/null +++ b/sci-biology/ensembl-perl/files/Makefile.PL @@ -0,0 +1,10 @@ +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 new file mode 100644 index 0000000..e69de29 --- /dev/null +++ b/sci-biology/ensembl-perl/files/digest-ensembl-perl-31 diff --git a/sci-biology/ensembl-perl/files/digest-ensembl-perl-32 b/sci-biology/ensembl-perl/files/digest-ensembl-perl-32 new file mode 100644 index 0000000..e69de29 --- /dev/null +++ b/sci-biology/ensembl-perl/files/digest-ensembl-perl-32 diff --git a/sci-biology/ensembl-perl/files/digest-ensembl-perl-33 b/sci-biology/ensembl-perl/files/digest-ensembl-perl-33 new file mode 100644 index 0000000..e69de29 --- /dev/null +++ b/sci-biology/ensembl-perl/files/digest-ensembl-perl-33 diff --git a/sci-biology/repbase/Manifest b/sci-biology/repbase/Manifest new file mode 100644 index 0000000..f727e94 --- /dev/null +++ b/sci-biology/repbase/Manifest @@ -0,0 +1,9 @@ +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 new file mode 100755 index 0000000..37ee59c --- /dev/null +++ b/sci-biology/repbase/files/clean @@ -0,0 +1,59 @@ +#!/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 (<LIB>) +{ + 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 + { + $sequence .= uc($_); + $sequence =~ s/\n//g; + } +} diff --git a/sci-biology/repbase/files/digest-repbase-10.03 b/sci-biology/repbase/files/digest-repbase-10.03 new file mode 100644 index 0000000..c718f4e --- /dev/null +++ b/sci-biology/repbase/files/digest-repbase-10.03 @@ -0,0 +1 @@ +MD5 c530ff51d4f60a8ae2114f3185b0235f RepBase10.03.fasta.tar.gz 3530082 diff --git a/sci-biology/repbase/files/digest-repbase-10.04 b/sci-biology/repbase/files/digest-repbase-10.04 new file mode 100644 index 0000000..ede3594 --- /dev/null +++ b/sci-biology/repbase/files/digest-repbase-10.04 @@ -0,0 +1 @@ +MD5 76b1ac539ad79a64ab48904027631cea RepBase10.04.fasta.tar.gz 3562104 diff --git a/sci-biology/repbase/files/digest-repbase-10.07 b/sci-biology/repbase/files/digest-repbase-10.07 new file mode 100644 index 0000000..1a0810a --- /dev/null +++ b/sci-biology/repbase/files/digest-repbase-10.07 @@ -0,0 +1 @@ +MD5 54669e3eb561fa101903c681a594e2c7 RepBase10.07.fasta.tar.gz 4061677 diff --git a/sci-biology/repbase/files/digest-repbase-9.12 b/sci-biology/repbase/files/digest-repbase-9.12 new file mode 100644 index 0000000..3188ee7 --- /dev/null +++ b/sci-biology/repbase/files/digest-repbase-9.12 @@ -0,0 +1 @@ +MD5 fdf7cf4befd28b6b902da0f4a9263c72 RepBase9.12.fasta.tar.gz 3271264 diff --git a/sci-biology/repbase/repbase-10.03.ebuild b/sci-biology/repbase/repbase-10.03.ebuild new file mode 100644 index 0000000..32f0e4f --- /dev/null +++ b/sci-biology/repbase/repbase-10.03.ebuild @@ -0,0 +1,65 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +CATEGORY="sci-biology" + +MY_P="RepBase${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 new file mode 100644 index 0000000..90cfaa9 --- /dev/null +++ b/sci-biology/repbase/repbase-10.04.ebuild @@ -0,0 +1,65 @@ +# 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 new file mode 100644 index 0000000..50549fd --- /dev/null +++ b/sci-biology/repbase/repbase-10.07.ebuild @@ -0,0 +1,65 @@ +# 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 new file mode 100644 index 0000000..32f0e4f --- /dev/null +++ b/sci-biology/repbase/repbase-9.12.ebuild @@ -0,0 +1,65 @@ +# 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/skel.ChangeLog b/skel.ChangeLog new file mode 100644 index 0000000..8b65f19 --- /dev/null +++ b/skel.ChangeLog @@ -0,0 +1,67 @@ +# ChangeLog for <CATEGORY>/<PACKAGE_NAME> +# Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*<PACKAGE_NAME>-<PACKAGE_VERSION>-<PACKAGE_RELEASE> (DD MMM YYYY) + + DD MMM YYYY; YOUR_NAME <YOUR_EMAIL> changed_file1, changed_file2 : + Initial import. Ebuild submitted by submitter_name <submitter_email>. + Note that the "changed_file" listing is optional if you are simply bumping + the rev of the ebuild and are only making changes to the .ebuild file + itself. Also note that we now have a single unified paragraph rather than + having the first line separated from the rest by a newline. Everything + should be in one block like this. (note by drobbins, 16 Jul 2002) + + DD MMM YYYY; YOUR_NAME <YOUR_EMAIL> changed_file1, changed_file2: this is + an earlier ChangeLog entry. + +-- Explanation of ChangeLog format: + + *************************************************************************** + THIS IS IMPORTANT: The ChangeLog format is a *chronological* account of all + changes made to a set of ebuilds. That means that the most recent ChangeLog + entry *always* goes at the top of the file. More explanation below. + *************************************************************************** + + *************************************************************************** + ANOTHER IMPORTANT NOTE: There are some ChangeLogs that don't follow this + format and organize all changes under the "correct" "*" entry. This is not + correct. However, rather than making a concerted effort to fix these + ChangeLogs, we should spend our energy defining a comprehensive and strict + XML-based ChangeLog format which we then migrate to. But for any entries to + any ChangeLog that *you* make, please make sure to always add entries to the + top of the file like a good boy/girl. Even do this if it's clear that you're + adding an entry to a b0rked ChangeLog. + *************************************************************************** + + This changelog is targeted to users. This means that the comments should be + well explained and written in clean English. + + Every new version or revision of the package should be marked by a '*' + separator line as above to indicate where in the chronology it was first + added to our CVS tree. Any changes since the last revision, really _any + changes at all_ have to be added to the top of the file, underneath the + initial copyright and cvs header comments, in exactly the same format as this + comment. If you are modifying older ebuilds, simply note them as changed + files and add your entry to the top of the ChangeLog. Resist the temptation + to "organize" your ChangeLog entries by placing them under the "correct" "*" + entries -- this isn't the purpose of the "*" entries. + + This means that you start with header line that has the following format, + indented two spaces: + + DD MMM YYYY; your_name <your_email> changed_file1, changed_file2: Your + explanation should follow. It should be indented and wrapped at a line width + of 80 characters. The changed_files can be omitted if they are obvious; for + example, if you are only modifying the .ebuild file and committing a new rev + of a package. Any details about what exactly changed in the code should be + added as a message when the changes are committed to cvs, not in this file. + +-- A word regarding credit: + + Please add credit information ("ebuild submitted by ...", "patch submitted + by ...") to the ChangeLog. Do not add this information to the ebuilds + themselves. + + And remember: Give credit where credit is due. We're all doing this for + free, so the best we can hope (and expect!) to receive is credit. |