diff options
| -rw-r--r-- | sci-biology/gbrowse/ChangeLog (renamed from sci-biology/generic-genome-browser/ChangeLog) | 5 | ||||
| -rw-r--r-- | sci-biology/gbrowse/Manifest | 4 | ||||
| -rw-r--r-- | sci-biology/gbrowse/gbrowse-1.70.ebuild | 68 | ||||
| -rw-r--r-- | sci-biology/gbrowse/metadata.xml (renamed from sci-biology/generic-genome-browser/metadata.xml) | 4 | ||||
| -rw-r--r-- | sci-biology/generic-genome-browser/Manifest | 4 | ||||
| -rw-r--r-- | sci-biology/generic-genome-browser/generic-genome-browser-1.68.ebuild | 82 |
6 files changed, 80 insertions, 87 deletions
diff --git a/sci-biology/generic-genome-browser/ChangeLog b/sci-biology/gbrowse/ChangeLog index c23f8b8cc..73671bed1 100644 --- a/sci-biology/generic-genome-browser/ChangeLog +++ b/sci-biology/gbrowse/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-biology/generic-genome-browser -# Copyright 2000-2007 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 2000-2009 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/generic-genome-browser/ChangeLog,v 1.10 2007/07/29 17:07:38 phreak Exp $ + 11 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: + Version bump, rewrite and rename to gbrowse + 29 Jul 2007; Christian Heim <phreak@gentoo.org> generic-genome-browser-1.58.ebuild: Fixing the DEPEND/RDEPEND for the move of net-www/apache to diff --git a/sci-biology/gbrowse/Manifest b/sci-biology/gbrowse/Manifest new file mode 100644 index 000000000..37780cde9 --- /dev/null +++ b/sci-biology/gbrowse/Manifest @@ -0,0 +1,4 @@ +DIST Generic-Genome-Browser-1.70.tar.gz 3331393 RMD160 056f72fc17bdbf803fce7e6bdde406566a80c204 SHA1 7a83abaedc4d2b061e1247972036025a713a845f SHA256 e08ef0d1ffff8186bffd30177808ad3dd7991a99abf3ea6350c8d487ba835486 +EBUILD gbrowse-1.70.ebuild 1670 RMD160 e9bf6980abebabc6ff807ea3c682a3988d0a5f14 SHA1 0413b93216348184e79b3feea36cd68618bed688 SHA256 ecb0b9290e48b82a0d29520d8418593db7baa564bb3731ed7ed808f1b4b5ff3f +MISC ChangeLog 1908 RMD160 41b276f789eeaa01a1a0b5b2485b1c52531c5030 SHA1 ef564f0fa4036e9cf48ea26011b50362d32de621 SHA256 6c6d481b2bb0ace16946a1758bebfe134dbd4d7213d553027e388dd7d62391f9 +MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 diff --git a/sci-biology/gbrowse/gbrowse-1.70.ebuild b/sci-biology/gbrowse/gbrowse-1.70.ebuild new file mode 100644 index 000000000..9bf0f47ce --- /dev/null +++ b/sci-biology/gbrowse/gbrowse-1.70.ebuild @@ -0,0 +1,68 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/generic-genome-browser/generic-genome-browser-1.58.ebuild,v 1.9 2007/07/29 17:07:38 phreak Exp $ + +EAPI="2" + +inherit perl-module webapp + +MY_P="Generic-Genome-Browser-${PV}" + +DESCRIPTION="The generic genome browser provides a display of genomic annotations on interactive web pages" +HOMEPAGE="http://gmod.org" +SRC_URI="mirror://sourceforge/gmod/${MY_P}.tar.gz" + +LICENSE="Artistic" +# webapp ebuilds do not set SLOT +KEYWORDS="~x86 ~amd64" +IUSE="-minimal" # lwp moby scf + +S="${WORKDIR}/${MY_P}" + +# TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/libwww-perl, LWP +DEPEND=">=dev-lang/perl-5.8.8 + >=sci-biology/bioperl-1.6 + >=dev-perl/GD-2.07 + dev-perl/IO-String + virtual/perl-Digest-MD5 + >=dev-perl/CGI-Session-4.03 + dev-perl/Statistics-Descriptive + >=dev-perl/Bio-Graphics-1.97" +RDEPEND="${DEPEND} + >=www-servers/apache-2.0.47 + >=virtual/perl-CGI-2.56 + dev-perl/DBI + dev-perl/DBD-mysql + dev-perl/Class-Base + dev-perl/Text-Shellwords + !minimal? ( + dev-perl/XML-Parser + dev-perl/XML-Writer + dev-perl/XML-Twig + dev-perl/XML-DOM + dev-perl/GD-SVG + dev-perl/Bio-Das + )" + +src_configure() { + webapp_src_preinst + perl Makefile.PL \ + HTDOCS="${D}/${MY_HTDOCSDIR}" \ + CGIBIN="${D}/${MY_HTDOCSDIR}/cgi-bin" \ + CONF="${D}/etc" \ + PREFIX="${D}/usr" \ + PACKAGE_DIR="${D}" \ + INSTALLDIRS=vendor \ + GBROWSE_ROOT=gbrowse \ + DESTDIR="${ROOT}" \ + || die +} + +src_install() { + mydoc="Changes README TODO INSTALL" + perl-module_src_install + + # TODO: write our own readme + webapp_postinst_txt en "${S}/INSTALL" + webapp_src_install +} diff --git a/sci-biology/generic-genome-browser/metadata.xml b/sci-biology/gbrowse/metadata.xml index d4648212c..3302123e5 100644 --- a/sci-biology/generic-genome-browser/metadata.xml +++ b/sci-biology/gbrowse/metadata.xml @@ -1,5 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> + <maintainer> + <email>weaver@gentoo.org</email> + <name>Andrey Kislyuk</name> + </maintainer> <herd>sci-biology</herd> </pkgmetadata> diff --git a/sci-biology/generic-genome-browser/Manifest b/sci-biology/generic-genome-browser/Manifest deleted file mode 100644 index 8dcab2cc1..000000000 --- a/sci-biology/generic-genome-browser/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -DIST Generic-Genome-Browser--1.68.tar.gz 2145950 RMD160 093df1e5e170e7fa33c63865ca54ea90b9f0d4fd SHA1 487b8453f722c63ada9c62a4190235be6684897b SHA256 5b5ed7f504a9646d158f0a99d37c0e2b45e3d602b140a5eac261c92478c4ae6b -EBUILD generic-genome-browser-1.68.ebuild 2284 RMD160 fded262e1cbe15982c38fb473acf6dfe16f15df3 SHA1 03ed326d6023126ac0bfdb70215f4f688e1be099 SHA256 212598ace888fa337c7931b414d0c7291741c36fc25c3e67e0a96eb184bd58a8 -MISC ChangeLog 1800 RMD160 945635f595dee6335828affd4d042c173e570cf3 SHA1 419375011a04db77048ac39dfdaffc613dfdcb86 SHA256 a59e36913cf1616e2e125dfa1a5e0f2c5140a61e3701bf0e80107298053f5f9d -MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 diff --git a/sci-biology/generic-genome-browser/generic-genome-browser-1.68.ebuild b/sci-biology/generic-genome-browser/generic-genome-browser-1.68.ebuild deleted file mode 100644 index 45ee5b82f..000000000 --- a/sci-biology/generic-genome-browser/generic-genome-browser-1.68.ebuild +++ /dev/null @@ -1,82 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/generic-genome-browser/generic-genome-browser-1.58.ebuild,v 1.9 2007/07/29 17:07:38 phreak Exp $ - -inherit perl-app - -MY_PN="Generic-Genome-Browser" - -# I don't know if the '--' is a typo... TODO contact somebody and find out. -MY_P="${MY_PN}--${PV}" - -DESCRIPTION="The generic genome browser provides a display of genomic annotations on interactive web pages" -HOMEPAGE="http://www.gmod.org" -SRC_URI="mirror://sourceforge/gmod/${MY_P}.tar.gz" - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~x86 ~ppc ~amd64" -IUSE="mysql gd" - -S="${WORKDIR}/${MY_PN}-${PV}" - -DEPEND=" - >=sci-biology/bioperl-1.4 - >=virtual/perl-CGI-2.56 - >=dev-perl/GD-2.07 - dev-perl/DBI - virtual/perl-Digest-MD5 - dev-perl/Text-Shellwords - dev-perl/libwww-perl - dev-perl/XML-Parser - dev-perl/XML-Writer - dev-perl/XML-Twig - dev-perl/XML-DOM - dev-perl/Bio-Das - gd? ( - dev-perl/GD-SVG - ) - mysql? - ( - >=virtual/mysql-4.0 - dev-perl/DBD-mysql - ) - >=www-servers/apache-2.0.47" - -RDEPEND="${DEPEND}" - -src_compile() { - - cd ${S} -# ewarn "Modifying Makefile.PL to avoid sandbox violation" - sed -e "s:WriteMakefile(:WriteMakefile(\n 'PREFIX'=>'${D}/usr',\n'INSTALLDIRS' => 'vendor',:" -i Makefile.PL \ - || die "Failed to sed Makefile.PL" - - perl Makefile.PL \ - HTDOCS=/var/www/localhost/htdocs \ - CGIBIN=/var/www/localhost/cgi-bin \ - CONF=/etc \ - PREFIX=/var/www/localhost \ - DESTDIR=${D} \ - INSTALLDIRS=vendor - #perl-module_src_compile || die "Make failed" - perl-module_src_test || die "Test Failed" -} - -# Might want to look at how to use webapp with this. - -src_install() { - dodir /etc - dodir /var/www/localhost/htdocs - dodir /var/www/localhost/cgi-bin - mydoc="History README TODO INSTALL" - dodir /usr/share/${PF}/tutorial - cd ${S}/docs/tutorial - tar cf - ./ | ( cd ${D}/usr/share/${PF}/scripts; tar xf -) - cd ${S} - sed -e "s:my \$dir = \":my \$dir = \"${D}/:" -i install_util/conf_install.PLS || die "sed1 failed" - sed -e "s:my \$ht_target = \":my \$ht_target = \"${D}/:" -i install_util/htdocs_install.PLS || die "sed2 failed" - sed -e "s:my \$cgi_target = :my \$cgi_target = \"${D}\"\.:" -i install_util/cgi_install.PLS || die "sed3 failed" - - perl-module_src_install -} |