diff options
Diffstat (limited to 'sci-biology/gbrowse')
| -rw-r--r-- | sci-biology/gbrowse/ChangeLog | 17 | ||||
| -rw-r--r-- | sci-biology/gbrowse/Manifest | 26 | ||||
| -rw-r--r-- | sci-biology/gbrowse/files/GBrowseInstall.pm-2.26.patch | 72 | ||||
| -rw-r--r-- | sci-biology/gbrowse/files/GBrowseInstall.pm-2.38.patch (renamed from sci-biology/gbrowse/files/GBrowseInstall.pm-2.33.patch) | 0 | ||||
| -rw-r--r-- | sci-biology/gbrowse/files/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm-2.26.patch | 21 | ||||
| -rw-r--r-- | sci-biology/gbrowse/gbrowse-1.70.ebuild | 68 | ||||
| -rw-r--r-- | sci-biology/gbrowse/gbrowse-2.00.ebuild | 76 | ||||
| -rw-r--r-- | sci-biology/gbrowse/gbrowse-2.26.ebuild | 167 | ||||
| -rw-r--r-- | sci-biology/gbrowse/gbrowse-2.38.ebuild (renamed from sci-biology/gbrowse/gbrowse-2.33.ebuild) | 33 |
9 files changed, 46 insertions, 434 deletions
diff --git a/sci-biology/gbrowse/ChangeLog b/sci-biology/gbrowse/ChangeLog index 8024f81e1..e36ad4701 100644 --- a/sci-biology/gbrowse/ChangeLog +++ b/sci-biology/gbrowse/ChangeLog @@ -1,7 +1,20 @@ -# ChangeLog for sci-biology/generic-genome-browser -# Copyright 2000-2010 Gentoo Foundation; Distributed under the GPL v2 +# ChangeLog for sci-biology/gbrowse +# Copyright 1999-2011 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 $ +*gbrowse-2.38 (26 Jun 2011) + + 26 Jun 2011; Justin Lecher <jlec@gentoo.org> -gbrowse-2.26.ebuild, + -files/GBrowseInstall.pm-2.26.patch, + -files/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm-2.26.patch, + -gbrowse-2.33.ebuild, -files/GBrowseInstall.pm-2.33.patch, + +gbrowse-2.38.ebuild, +files/GBrowseInstall.pm-2.38.patch: + Version Bump + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> -gbrowse-1.70.ebuild, + -gbrowse-2.00.ebuild, gbrowse-2.26.ebuild, gbrowse-2.33.ebuild: + Cleaned ebuild, 'http://search.cpan.org/CPAN' found in thirdpartymirrors + 05 Feb 2010; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: Version bump diff --git a/sci-biology/gbrowse/Manifest b/sci-biology/gbrowse/Manifest index 96f87cdb3..101b58a14 100644 --- a/sci-biology/gbrowse/Manifest +++ b/sci-biology/gbrowse/Manifest @@ -1,13 +1,11 @@ -AUX GBrowseInstall.pm-2.26.patch 2647 RMD160 5acd26d95bf0c26edb0f816e840b43ef99a88ea3 SHA1 39362a38cff41097ead8c49de5eaf94d77c59f02 SHA256 1aee7359bc1b036f5d214975a5ea2395a507f04b0ee839ed3a1543a0ab4fb3c6 -AUX GBrowseInstall.pm-2.33.patch 1278 RMD160 96c7f2c66537c6e01cf2619018f608607c0927dc SHA1 a3cb874018d2c7a5acf34381971cc09d83a13f73 SHA256 5a1018f582c2e0ffca034d04ce73f678dd879d90932e4e89ea664c7c113f4b7c -AUX GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm-2.26.patch 1001 RMD160 6784a8d01714be237247d56df13de96681f3aea5 SHA1 55c3eac7eb1e11c766b8d430c7dd36336347ef50 SHA256 a25f49dba6609a25c799d0290713038b608f8aef1a4275eff5f1f12e5225a19a +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +AUX GBrowseInstall.pm-2.38.patch 1278 RMD160 96c7f2c66537c6e01cf2619018f608607c0927dc SHA1 a3cb874018d2c7a5acf34381971cc09d83a13f73 SHA256 5a1018f582c2e0ffca034d04ce73f678dd879d90932e4e89ea664c7c113f4b7c AUX gbrowse-slave.default 210 RMD160 77245190ab0d3a543f3103bb6f21864f73ea1cde SHA1 a19d60edd3fdc1f059ed8fa58f7e91fc47ec92dc SHA256 e4e6d68ade29681f442b2e1c7f8abbc7ff3255b3b8db3c59ed6368ba561d7d66 AUX gbrowse-slave.init.d 2196 RMD160 8b565d1be23c89cbae0f9fd5cd2201f47a564b94 SHA1 738bc8f06486a0e6caa72642f79f9b7dbb356524 SHA256 de511a92757153ee648eb6cd39e3c69c1e30fa2c2ed406f24c08571c72609219 AUX gbrowse.conf.vhosts.d 740 RMD160 e24f5132e37a84dd0bb9a39e2de99cd11d260844 SHA1 2c44fdcf04bef92eb6210d4e6667b994e5643a13 SHA256 8acd5a067ab3dd42cff0ab7cb0d783b2409ccb872590eba32ea55d4929f65f21 -DIST GBrowse-2.00.tar.gz 3844690 RMD160 f3856ca620d8adc10172d8dfb644dfbbd25cbf88 SHA1 9d78393ca21d2569a975cfff7588cb7fe62d1082 SHA256 62c96ae1c6c1494ff67fbea1fde0d80d5051705c22167a55db317a0d33b1b8ea -DIST GBrowse-2.26.tar.gz 11937473 RMD160 c2c9d988e3183637b0a97f00e8de1387ad107eab SHA1 3153afc0ef7e6ea8ca6879343028673fdb062501 SHA256 4ac5c0fd87c5ab64b3c52ebb51f51433cb8c6062fd80a56d3de91f24594d3a3f -DIST GBrowse-2.33.tar.gz 11915644 RMD160 0e2f054b4bcc2748895a856620af7e50f5e15038 SHA1 f31cbe960904b5a2ea4b7eae7a9d78baaf29fce0 SHA256 063114b844776a9500528437fb3dbc60f47a8ac380d910bd6b3148ec7cc0cc4b -DIST Generic-Genome-Browser-1.70.tar.gz 3331393 RMD160 056f72fc17bdbf803fce7e6bdde406566a80c204 SHA1 7a83abaedc4d2b061e1247972036025a713a845f SHA256 e08ef0d1ffff8186bffd30177808ad3dd7991a99abf3ea6350c8d487ba835486 +DIST GBrowse-2.38.tar.gz 11966992 RMD160 dde50d49ee1b228103dffc9701e450ac9e3be3cd SHA1 4228a4938cbdbc409ddb23f81cd3186cdf15391d SHA256 acf7d3d0f32d0138640b2773ed580572ff63d646d4538f354dec8986607aa275 DIST README-gff-files 5309 RMD160 8ba184fa8a6b921f925143cf53de06e3da353023 SHA1 ad2d2b3133c73a05ace4a0107ff1a3a4221bc8f8 SHA256 21f4f026b212698c5aac0e82045670f8397ab50fdfe74b938fcbc71a1d36c82a DIST Refseq_Genome_TBLASTX.tar.gz 56482234 RMD160 e188d9dfe12bed3fd299be4625f7e658f54bb8c4 SHA1 72ec3de9b9ca0e10c2dd8dcda24f9be74f98cf09 SHA256 7036bdd9aefbf44e384df83f4c1e973c1ab3eac8fe74b37499c4a3f1c55a18af DIST fly.fasta.gz 37349852 RMD160 4bedfcc5d0ea3d325f3d3e446713251a8ce34ca3 SHA1 8f2c7a2f24dbab0f27c73009fe51efb8f41d6769 SHA256 892ed03e17edd3469f1ed00cb9967fb905bbac57c1cb7858667381f34a6bfeea @@ -18,9 +16,13 @@ DIST worm.fasta.gz 30593662 RMD160 674ef3d09cdfaa5d748f18c0e769f0a5ca3d48cf SHA1 DIST worm.gff.gz 65789458 RMD160 ddced7c965963ce41a10bdecae949731ed305121 SHA1 ccfb0f287e27ff7849b099c81d811f468a7e617c SHA256 afd63c65c3fdb0ba8a1cf455bd4477a2d5d27d5b0e88c6a5a10d156d0567374f DIST yeast.fasta.gz 3801757 RMD160 5545054cf6ffa5381c7992141144107076fdf62e SHA1 c36fddc5fd2c79e01292f66644088654304bc438 SHA256 bf51cbced31aa6a30bca43cc72fdb53194fbb403407e2ebb9d70c901ab072e6d DIST yeast.gff.gz 249814 RMD160 64538d18de23d930915938bd00ae4a94a52f3960 SHA1 ec753b1ae409e1377f568531a53be8985a7bfa2e SHA256 20c93e6ba9457896a693d13e8fd8fa00d77acbb55aee9b19a31c2b29c4b7e9b1 -EBUILD gbrowse-1.70.ebuild 1670 RMD160 e9bf6980abebabc6ff807ea3c682a3988d0a5f14 SHA1 0413b93216348184e79b3feea36cd68618bed688 SHA256 ecb0b9290e48b82a0d29520d8418593db7baa564bb3731ed7ed808f1b4b5ff3f -EBUILD gbrowse-2.00.ebuild 1932 RMD160 5a0d15a10c2f6f9e4ac1f60ce048efcd2311cdb4 SHA1 186d5a91fbae9b6894091ac376addb84784d6a03 SHA256 21b035ef921900bc893a4de0fe123b6192860265e0594b73723c24b03dd5a23c -EBUILD gbrowse-2.26.ebuild 6959 RMD160 a3b966bad08410ea7e619b4cb6497a78836c6094 SHA1 ec109df87df0cfc0d72c35a1c662b2c85f495a10 SHA256 3020b2c5953e7bc02ed1e1e98a8b63bb69feda55101725d019201e748394e5b6 -EBUILD gbrowse-2.33.ebuild 6207 RMD160 20e3780fe421c5b83add7a52d4629a9e169994f0 SHA1 cb5c80a5e6f558f41b71a832e4384501a846271d SHA256 1dfe2823194c4ac30ffd2530d96c04c4a533592fbd1a6931584c0af74422cca3 -MISC ChangeLog 1985 RMD160 9695d7522c6165b842087b67938629377f9cc82b SHA1 3edd2e74f9b26289d95ad7609b838edb3ccb9561 SHA256 76c1d0553f09390397af4354dc653677f25d06828e42e57a60b2f35a869222ac +EBUILD gbrowse-2.38.ebuild 6136 RMD160 9da72299772f44f80f9a653840fa167d04c1d3e5 SHA1 9a65efd853905e653b5a781128e45cc0e00e611a SHA256 db0cc819ad165d509c935e4cef5be3ee1f47d0e0a0a1ecb697ef6290b7259ad5 +MISC ChangeLog 2531 RMD160 a666bbe4d2aa432f678eb56d321db77686990b45 SHA1 d4950185a71e503373f25af3466fd876d2996249 SHA256 2c805b6e02263dfaf7b2c87ed68e8da2a8cbc1d23409968c36037105338038da MISC metadata.xml 572 RMD160 bc941571413238acb3d77e61d49b959737ed4f5a SHA1 0c05303509c0e2dd21b37fc93c936809db49e530 SHA256 89b9964a9404a95dbb622a91735348da8e66d34d7dd7e7f144ed8c0159c43e31 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4G56MACgkQgAnW8HDreRaXVQCgwiv8qpUdbIu7rc522SjTi/lq +cQ4AoMbh/D6qOR+v7qwowOCzPKmTktJb +=+CVr +-----END PGP SIGNATURE----- diff --git a/sci-biology/gbrowse/files/GBrowseInstall.pm-2.26.patch b/sci-biology/gbrowse/files/GBrowseInstall.pm-2.26.patch deleted file mode 100644 index 4c17f8d9a..000000000 --- a/sci-biology/gbrowse/files/GBrowseInstall.pm-2.26.patch +++ /dev/null @@ -1,72 +0,0 @@ ---- install_util/GBrowseInstall.pm.ori 2010-11-27 12:01:58.000000000 +0100 -+++ install_util/GBrowseInstall.pm 2010-11-27 12:02:15.000000000 +0100 -@@ -436,8 +436,8 @@ - $self->ownership_warning($databases,$user); - } - -- chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave'); -- $self->fix_selinux; -+ # chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave'); -+ # $self->fix_selinux; - - my $base = basename($self->install_path->{htdocs}); - ---- install_util/GBrowseInstall.pm.ori 2011-02-14 13:39:46.000000000 +0100 -+++ install_util/GBrowseInstall.pm 2011-02-14 13:41:50.000000000 +0100 -@@ -438,25 +438,25 @@ - $gid =~ /^(\d+)$/; - $gid = $1; - -- unless (chown $uid,$gid,$tmp) { -- $self->ownership_warning($tmp,$user); -- } -+# unless (chown $uid,$gid,$tmp) { -+# $self->ownership_warning($tmp,$user); -+# } - - my $htdocs_i = File::Spec->catfile($self->install_path->{htdocs},'i'); - my $images = File::Spec->catfile($tmp,'images'); - my $htdocs = $self->install_path->{htdocs}; -- chown $uid,-1,$htdocs; -- { -- local $> = $uid; -- symlink($images,$htdocs_i); # so symlinkifowner match works! -- } -- chown $>,-1,$self->install_path->{htdocs}; -+# chown $uid,-1,$htdocs; -+# { -+# local $> = $uid; -+# symlink($images,$htdocs_i); # so symlinkifowner match works! -+# } -+# chown $>,-1,$self->install_path->{htdocs}; - - my $databases = $self->install_path->{'databases'}; - -- unless (chown $uid,$gid,glob(File::Spec->catfile($databases,'').'*')) { -- $self->ownership_warning($databases,$user); -- } -+# unless (chown $uid,$gid,glob(File::Spec->catfile($databases,'').'*')) { -+# $self->ownership_warning($databases,$user); -+# } - - # chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave'); - # $self->fix_selinux; ---- install_util/GBrowseInstall.pm.ori 2011-02-14 13:50:41.000000000 +0100 -+++ install_util/GBrowseInstall.pm 2011-02-14 13:51:46.000000000 +0100 -@@ -470,11 +470,11 @@ - my @inc = map{"-I$_"} split ':',$self->added_to_INC; - system $perl,@inc,$metadb_script; - -- if (Module::Build->y_n( -- "It is recommended that you restart Apache. Shall I try this for you?",'y' -- )) { -- system "sudo /etc/init.d/apache2 restart"; -- } -+# if (Module::Build->y_n( -+# "It is recommended that you restart Apache. Shall I try this for you?",'y' -+# )) { -+# system "sudo /etc/init.d/apache2 restart"; -+# } - - print STDERR "\n***INSTALLATION COMPLETE***\n"; - print STDERR "Load http://localhost/$base for demo and documentation.\n"; diff --git a/sci-biology/gbrowse/files/GBrowseInstall.pm-2.33.patch b/sci-biology/gbrowse/files/GBrowseInstall.pm-2.38.patch index e91fe1634..e91fe1634 100644 --- a/sci-biology/gbrowse/files/GBrowseInstall.pm-2.33.patch +++ b/sci-biology/gbrowse/files/GBrowseInstall.pm-2.38.patch diff --git a/sci-biology/gbrowse/files/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm-2.26.patch b/sci-biology/gbrowse/files/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm-2.26.patch deleted file mode 100644 index 0dde70406..000000000 --- a/sci-biology/gbrowse/files/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm-2.26.patch +++ /dev/null @@ -1,21 +0,0 @@ ---- install_util/GBrowseInstall.pm.ori 2011-05-11 04:10:08.000000000 +0200 -+++ install_util/GBrowseInstall.pm 2011-05-11 04:10:26.000000000 +0200 -@@ -463,12 +463,12 @@ - - my $base = basename($self->install_path->{htdocs}); - -- # Configure the databases, if needed. -- print STDERR "Updating user account database...\n"; -- my $metadb_script = File::Spec->catfile("bin", "gbrowse_metadb_config.pl"); -- my $perl = $self->perl; -- my @inc = map{"-I$_"} split ':',$self->added_to_INC; -- system $perl,@inc,$metadb_script; -+# # Configure the databases, if needed. -+# print STDERR "Updating user account database...\n"; -+# my $metadb_script = File::Spec->catfile("bin", "gbrowse_metadb_config.pl"); -+# my $perl = $self->perl; -+# my @inc = map{"-I$_"} split ':',$self->added_to_INC; -+# system $perl,@inc,$metadb_script; - - # if (Module::Build->y_n( - # "It is recommended that you restart Apache. Shall I try this for you?",'y' diff --git a/sci-biology/gbrowse/gbrowse-1.70.ebuild b/sci-biology/gbrowse/gbrowse-1.70.ebuild deleted file mode 100644 index 9bf0f47ce..000000000 --- a/sci-biology/gbrowse/gbrowse-1.70.ebuild +++ /dev/null @@ -1,68 +0,0 @@ -# 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/gbrowse/gbrowse-2.00.ebuild b/sci-biology/gbrowse/gbrowse-2.00.ebuild deleted file mode 100644 index cce42a39b..000000000 --- a/sci-biology/gbrowse/gbrowse-2.00.ebuild +++ /dev/null @@ -1,76 +0,0 @@ -# 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="GBrowse-${PV}" - -DESCRIPTION="The generic genome browser provides a display of genomic annotations on interactive web pages" -HOMEPAGE="http://gmod.org" -SRC_URI="mirror://sourceforge/gmod/${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/Safe-World (not compatible w/perl-5.10) -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 - dev-perl/JSON - dev-perl/libwww-perl" -RDEPEND="${DEPEND} - >=www-servers/apache-2.0.47 - dev-perl/DBI - || ( dev-perl/DBD-Pg dev-perl/DBD-mysql ) - !minimal? ( - dev-perl/File-NFSLock - dev-perl/FCGI - perl-core/Math-BigInt - dev-perl/Digest-SHA1 - dev-perl/Crypt-SSLeay - dev-perl/Net-SMTP-SSL - dev-perl/GD-SVG - dev-perl/Net-OpenID-Consumer - virtual/perl-DB_File - dev-perl/DB_File-Lock - )" - -src_prepare() { - sed -i 's/return unless -t STDIN/return/' install_util/GBrowseInstall.pm || die -} - -src_configure() { - webapp_src_preinst - perl Makefile.PL \ - HTDOCS="${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 -# find "${D}" -type f | xargs sed -i "s|${D}||" || die -} diff --git a/sci-biology/gbrowse/gbrowse-2.26.ebuild b/sci-biology/gbrowse/gbrowse-2.26.ebuild deleted file mode 100644 index 89000cfd4..000000000 --- a/sci-biology/gbrowse/gbrowse-2.26.ebuild +++ /dev/null @@ -1,167 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ -EAPI="2" - -inherit perl-module webapp - -MY_P="GBrowse-${PV}" - -DESCRIPTION="The generic genome browser provides a display of genomic annotations on interactive web pages" -HOMEPAGE="http://gmod.org" -SRC_URI="mirror://sourceforge/gmod/${MY_P}.tar.gz - test? ( http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/saccharomyces_cerevisiae.gff.bz2 - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/Refseq_Genome_TBLASTX.tar.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/README-gff-files - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/human.gff.tar.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.fasta.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.gff.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.fasta.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.gff.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.fasta.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.gff.gz )" - -LICENSE="Artistic" -# webapp ebuilds do not set SLOT -KEYWORDS="~x86 ~amd64" -IUSE="-minimal svg test" # lwp moby scf - -S="${WORKDIR}/${MY_P}" - -# TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/Safe-World (not compatible w/perl-5.10) -# TODO: make sure www-servers/apache +cgi -DEPEND=">=dev-lang/perl-5.8.8 - dev-perl/Capture-Tiny - >=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 - dev-perl/JSON - dev-perl/libwww-perl - svg? ( dev-perl/GD-SVG )" - -# TODO: based on the following message in apache/error_log the list of deps should be longer -# GBROWSE NOTICE: To enable PDF generation, please enter the directory "/home/httpd" and run the commands: "sudo mkdir .inkscape .gnome2" and "sudo chown apache .inkscape .gnome2". To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://127.0.0.1/gbrowse/cgi-bin/gbrowse_details/yeast?ref=chrII;start=90739;end=92028;name=YBL069W;class=Sequence;feature_id=881;db_id=annotations%3Adatabase - -# * Bio::DB::BigFile is not installed -# * Bio::DB::Sam is not installed -# * DBD::Pg is not installed - -RDEPEND="${DEPEND} - >=www-servers/apache-2.0.47 - www-apache/mod_fastcgi - dev-perl/DBI - || ( dev-perl/DBD-Pg dev-perl/DBD-mysql ) - !minimal? ( - dev-perl/File-NFSLock - dev-perl/FCGI - perl-core/Math-BigInt - perl-core/Math-BigInt-FastCalc - dev-perl/Math-BigInt-GMP - dev-perl/Digest-SHA1 - dev-perl/Crypt-SSLeay - dev-perl/Net-SMTP-SSL - dev-perl/Net-OpenID-Consumer - virtual/perl-DB_File - dev-perl/DB_File-Lock - dev-perl/GD-SVG - dev-perl/Text-Shellwords - dev-perl/XML-Twig - dev-perl/XML-DOM - dev-perl/XML-Writer - dev-perl/XML-Parser - dev-perl/Bio-Das - dev-perl/Text-Shellwords - )" - -src_prepare() { - sed -i 's/return unless -t STDIN/return/' install_util/GBrowseInstall.pm || die - sed -i 's/process_/bp_process_/g' INSTALL || die - epatch "${FILESDIR}"/GBrowseInstall.pm-"${PV}".patch || die "Failed to patch" - epatch "${FILESDIR}"/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl"${PV}".pm.patch || die "Failed to patch" -} - -src_configure() { - # GBROWSE_ROOT is the root path in SRC_URI to be prepended - # /usr/share/webapps/gbrowse/2.03/htdocs/etc/gbrowse/GBrowse.conf - - # if we use CONF="${D}${MY_HTDOCSDIR}"/etc/gbrowse the the install process - # will not find currently installed config files and therefore place *.conf - # files into "{$S}"/blib/conf/*.conf instead of creating "{$S}"/blib/conf/*.conf.new - webapp_src_preinst - perl Makefile.PL \ - HTDOCS="${MY_HTDOCSDIR}" \ - CGIBIN="${MY_HTDOCSDIR}"/cgi-bin \ - CONF="${MY_HTDOCSDIR}"/etc/gbrowse \ - PACKAGE_DIR="${D}" \ - INSTALLDIRS=vendor \ - GBROWSE_ROOT="gbrowse" \ - DESTDIR="${D}" \ - DATABASES="/var/www/gbrowse2/databases/" \ - TMP="/var/tmp/gbrowse2" \ - INSTALLETC="n" \ - INSTALLCONF="n" \ - WWWUSER="apache" \ - DO_XS=1 \ - NONROOT=1 \ - || die - - #sed -i 's#DBI:SQLite:#DBI:SQLite:'${D}'#' "${S}"/install_util/GBrowseInstall.pm || die - #sed -i 's#DBI:SQLite:#DBI:SQLite:'${D}'#' "${S}"/conf/GBrowse.conf || die - #sed -i 's#/var/www/gbrowse2/databases/#'${D}'/var/www/gbrowse2/databases/#' "${S}"/_build/build_params - #sed -i 's#/var/www/gbrowse2/databases/#'${D}'/var/www/gbrowse2/databases/#' "${S}"/_build/config_data - #sed -i 's#/var/www/gbrowse2/databases/#'${D}'/var/www/gbrowse2/databases/#' "${S}"/_build/runtime_params -} - -src_install() { - mydoc="Changes README TODO INSTALL" - perl-module_src_install - - # TODO: write our own readme - webapp_src_preinst - webapp_postinst_txt en "${S}"/INSTALL || die - webapp_src_install - - # should create a /etc/init.d/ startup script based on this - # /var/tmp/portage/sci-biology/gbrowse-2.03/work/GBrowse-2.03/etc/init.d/gbrowse-slave - - # pre-create the directory so we can force its owner later on - mkdir -p "${D}"/var/www/gbrowse2/databases || die - chown -R apache.apache "${D}"/var/www/gbrowse2/databases || die - mkdir -p "${D}"/var/www/localhost/htdocs/gbrowse || die - - ln -s "${D}"/var/tmp/gbrowse2/images "${D}"/var/www/localhost/htdocs/gbrowse/i || die - - einfo "Probably you want to install a cron job to remove the generated temporary images:" - einfo "find /var/tmp/gbrowse2/images -type f -atime +20 -print -exec rm {}" - - einfo "Make sure you compiled apache with +cgi and copy ${FILESDIR}/gbrowse.conf.vhosts.d to /etc/apache2/vhosts.d/" - - sed -i "s#"${D}"##g" "${S}"/install_util/GBrowseInstall.pm || die - sed -i "s#"${D}"##" "${S}"/blib/conf/GBrowse.conf* - sed -i 's#DBI:SQLite:'${D}'/var/www/gbrowse2/databases/#DBI:SQLite:/var/www/gbrowse2/databases/#' "${S}"/install_util/GBrowseInstall.pm || die -} - -pkg_postinst() { - webapp_pkg_postinst || die "webapp_pkg_postinst failed" - - einfo "Please run gbrowse_metadb_config.pl to upate SQlite flatfiles or the live database" - einfo "This was disabled by "${FILESDIR}"/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm.patch" -} - -src_test() { - mysql -uroot -p password -e 'create database yeast' - mysql -uroot -p password -e 'grant all privileges on yeast.* to gbrowse@localhost' - mysql -uroot -p password -e 'grant file on *.* to gbrowse@localhost' - mysql -uroot -p password -e 'grant select on yeast.* to nobody@localhost' - - cd /usr/portage/distfiles || die - gzip -d yeast.fasta.gz || die - gzip -d yeast.gff.gz || die - #gzip -d fly.fasta.gz - #gzip -d fly.gff.gz - bp_bulk_load_gff.pl -d yeast -fasta yeast.fasta yeast.gff || die -} diff --git a/sci-biology/gbrowse/gbrowse-2.33.ebuild b/sci-biology/gbrowse/gbrowse-2.38.ebuild index e2bcfc3be..9cc3ce479 100644 --- a/sci-biology/gbrowse/gbrowse-2.33.ebuild +++ b/sci-biology/gbrowse/gbrowse-2.38.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI="2" @@ -7,21 +7,23 @@ inherit perl-module webapp MY_P="GBrowse-${PV}" -DESCRIPTION="The generic genome browser provides a display of genomic annotations on interactive web pages" -HOMEPAGE="http://gmod.org" +DESCRIPTION="Display of genomic annotations on interactive web pages" +HOMEPAGE="http://gmod.org/" # mirror://sourceforge/gmod/${MY_P}.tar.gz -# http://search.cpan.org/CPAN/authors/id/L/LD/LDS/GBrowse-2.33.tar.gz -SRC_URI="http://search.cpan.org/CPAN/authors/id/L/LD/LDS/${MY_P}.tar.gz - test? ( http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/saccharomyces_cerevisiae.gff.bz2 - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/Refseq_Genome_TBLASTX.tar.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/README-gff-files - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/human.gff.tar.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.fasta.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.gff.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.fasta.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.gff.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.fasta.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.gff.gz )" +# mirror://cpan/authors/id/L/LD/LDS/GBrowse-2.33.tar.gz +SRC_URI=" + mirror://cpan/authors/id/L/LD/LDS/${MY_P}.tar.gz + test? ( + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/saccharomyces_cerevisiae.gff.bz2 + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/Refseq_Genome_TBLASTX.tar.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/README-gff-files + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/human.gff.tar.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.fasta.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.gff.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.fasta.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.gff.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.fasta.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.gff.gz )" LICENSE="Artistic" # webapp ebuilds do not set SLOT @@ -54,7 +56,6 @@ DEPEND=" # * Bio::DB::Sam is not installed # * DBD::Pg is not installed - RDEPEND="${DEPEND} >=www-servers/apache-2.0.47 www-apache/mod_fastcgi |