diff options
Diffstat (limited to 'sci-biology')
-rw-r--r-- | sci-biology/gbrowse/ChangeLog | 6 | ||||
-rw-r--r-- | sci-biology/gbrowse/Manifest | 1 | ||||
-rw-r--r-- | sci-biology/gbrowse/files/GBrowseInstall.pm-2.45.patch | 32 | ||||
-rw-r--r-- | sci-biology/gbrowse/gbrowse-2.45.ebuild | 199 |
4 files changed, 238 insertions, 0 deletions
diff --git a/sci-biology/gbrowse/ChangeLog b/sci-biology/gbrowse/ChangeLog index c63914ae5..41e233429 100644 --- a/sci-biology/gbrowse/ChangeLog +++ b/sci-biology/gbrowse/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2012 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-2.45 (17 Jan 2012) + + 17 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +gbrowse-2.45.ebuild, +files/GBrowseInstall.pm-2.45.patch: + version bump and some fixes so that it works with webappconfig again? + 17 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> gbrowse-2.39.ebuild: added dev-perl/TermReadKey to dependencies diff --git a/sci-biology/gbrowse/Manifest b/sci-biology/gbrowse/Manifest index 5d79df93e..6e6d8a7ef 100644 --- a/sci-biology/gbrowse/Manifest +++ b/sci-biology/gbrowse/Manifest @@ -1,4 +1,5 @@ DIST GBrowse-2.39.tar.gz 11969088 SHA256 b4e76acfa1d8f64d5f227c3ba0258666928b4f357428549be85f05c944337d44 SHA512 4297192236a297a4f6a25892e245e3f5a4951b561ae167d7d402ff09b50a9a8a0d924094136d191d9068f735f77795a166e37aac67cd964d70cc805a15f8c26d WHIRLPOOL a0fc2c882d9e11f76d739a824152f9b5482f2b352583dc2e92fcfb60cf1b19ff1a9684c543ee6b8e69b3ed441548d5dd9b1d2da9e8779f0d157a7fe73f6e7af8 +DIST GBrowse-2.45.tar.gz 11954151 SHA256 8f8c9054d48199ccfe0a536ef892461a9e197d49ac99dd67381f9ad45377c35c SHA512 8b330ccb5468a4dd6b2f409a97350578788eb857a8db79715314f12875a69c5f37c6679b1efa23aaae77b978f93f35dbe8113a2714e3bbd45fb02273edf1a119 WHIRLPOOL 2bd2e7a47788b31861dc0d0f8654f56c5e078b9a99b9bab74c89422800b8e9a8bfb3e0b64e99dc9eb53bcfe04f3106322f8da2c978ad2873adc3ef06e64d37a4 DIST README-gff-files 5309 SHA256 21f4f026b212698c5aac0e82045670f8397ab50fdfe74b938fcbc71a1d36c82a SHA512 b591d269400c28f8908e5cc7bd27815b35b1750661cd4bb2c34e94f712ce100f71c7e9934800477425747e75fdd487192c3a2c05cf7249e28006c986feb54cca WHIRLPOOL f4080b582ac52adc76536cb7dcd646e4ce85b0f8210ef2010e037db7d114b436077f3b7d7d84216030e92130ad5be649442ece1e281273b13c39c537542270b6 DIST Refseq_Genome_TBLASTX.tar.gz 56482234 SHA256 7036bdd9aefbf44e384df83f4c1e973c1ab3eac8fe74b37499c4a3f1c55a18af SHA512 d49dc91f1246a881acf1b4fa0f336fe25ee0317f04a5bc42f2750509f95af3768eabfa0d4517f97ee14bb5de9e59700e0a7ef9018e577d2a87874809d313fdfb WHIRLPOOL 0cc86c1987d5399b952ba05cb441035a03ef5e47242e7f2ce95a73cc5420ff8b581ab6b097b66c96d65dc73b9ef4e301473b89a29c60413dd4d4d5e39508b6df DIST fly.fasta.gz 37349852 SHA256 892ed03e17edd3469f1ed00cb9967fb905bbac57c1cb7858667381f34a6bfeea SHA512 f3c0864d82be03c5e06a2e420ecd42df254318b7ee18f7dbb982b1c716ff5db465da69991ab009cf157b6a3601220fadd58d91d68732570af453e2bd329e09b7 WHIRLPOOL e914a4082913fff82687b0282e9ddcb01cfdd50712dbc30dba9ba697fcacc2b4b168f2b6b587479c84e2b51370ea7285fb6c5a8ce3961a55f3ee2ee29f27d169 diff --git a/sci-biology/gbrowse/files/GBrowseInstall.pm-2.45.patch b/sci-biology/gbrowse/files/GBrowseInstall.pm-2.45.patch new file mode 100644 index 000000000..e91fe1634 --- /dev/null +++ b/sci-biology/gbrowse/files/GBrowseInstall.pm-2.45.patch @@ -0,0 +1,32 @@ +--- 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 13:50:41.000000000 +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/gbrowse-2.45.ebuild b/sci-biology/gbrowse/gbrowse-2.45.ebuild new file mode 100644 index 000000000..f9148443c --- /dev/null +++ b/sci-biology/gbrowse/gbrowse-2.45.ebuild @@ -0,0 +1,199 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ +EAPI="2" + +inherit perl-module webapp + +MY_P="GBrowse-${PV}" + +DESCRIPTION="Display of genomic annotations on interactive web pages" +HOMEPAGE="http://gmod.org/" +# mirror://sourceforge/gmod/${MY_P}.tar.gz +# mirror://cpan/authors/id/L/LD/LDS/GBrowse-2.33.tar.gz +SRC_URI=" + mirror://cpan/authors/id/L/LD/LDS/${MY_P}.tar.gz + test? ( + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/saccharomyces_cerevisiae.gff.bz2 + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/Refseq_Genome_TBLASTX.tar.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/README-gff-files + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/human.gff.tar.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.fasta.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.gff.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.fasta.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.gff.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.fasta.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.gff.gz )" + +LICENSE="Artistic" +# webapp ebuilds do not set SLOT +KEYWORDS="~x86 ~amd64" +IUSE="cgi fastcgi minimal mysql pdf postgres svg test" # lwp moby scf + +S="${WORKDIR}/${MY_P}" + +# TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/Safe-World (not compatible w/perl-5.10) +# how about mod_fcgi and dev-libs/fcgi and mod_scgi? +DEPEND="!!sci-biology/GBrowse + >=perl-core/Module-Build-0.380.0 + >=dev-lang/perl-5.8.8 + dev-perl/Capture-Tiny + >=sci-biology/bioperl-1.6.901 + >=dev-perl/GD-2.07 + dev-perl/IO-String + virtual/perl-Digest-MD5 + >=dev-perl/CGI-Session-4.03 + dev-perl/Statistics-Descriptive + >=dev-perl/Bio-Graphics-1.97 + >=dev-perl/JSON-2.510.0 + dev-perl/TermReadKey + dev-perl/libwww-perl + svg? ( dev-perl/GD-SVG ) + pdf? ( media-gfx/inkscape ) + mysql? ( dev-perl/DBD-mysql ) + postgres? ( dev-perl/DBD-Pg ) + sci-biology/ucsc-genome-browser" # that provides bigWig.h and jkweb.a, aka Jim Kent's src + +# TODO: based on the following message in apache/error_log the list of deps should be longer +# GBROWSE NOTICE: To enable PDF generation, please enter the directory "/home/httpd" and run the commands: "sudo mkdir .inkscape .gnome2" and "sudo chown apache .inkscape .gnome2". To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://127.0.0.1/gbrowse/cgi-bin/gbrowse_details/yeast?ref=chrII;start=90739;end=92028;name=YBL069W;class=Sequence;feature_id=881;db_id=annotations%3Adatabase + +RDEPEND="${DEPEND} + >=www-servers/apache-2.0.47 + fastcgi? ( dev-libs/fcgi ) + 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 + postgres? ( >=dev-perl/Bio-DB-Das-Chado-0.32 ) + >=dev-perl/Bio-SamTools-1.29 + >=dev-perl/Bio-BigFile-1.06 + )" + +src_prepare() { + sed -i 's/return unless -t STDIN/return/' install_util/GBrowseInstall.pm || die "Failed to kill the interactive behavior of install_util/GBrowseInstall.pm" + sed -i 's/process_/bp_process_/g' INSTALL || die "Failed to prepend bp_ prefix to INSTALL file" + epatch "${FILESDIR}"/GBrowseInstall.pm-"${PV}".patch || die "Failed to apply GBrowseInstall.pm-"${PV}".patch" + epatch "${FILESDIR}"/destdir.patch || die "Failed to apply destdir.patch" + epatch "${FILESDIR}"/fix-PNG-export.patch || die "Failed to apply fix-PNG-export.patch" + epatch "${FILESDIR}"/symlink.patch || die "Failed to apply symlink.patch" + epatch "${FILESDIR}"/gbrowse_metadb_config.pl.patch || die "Failed to apply gbrowse_metadb_config.pl.patch" + epatch "${FILESDIR}"/disable-gbrowse_metadb_config.pl.patch || die "Failed to apply disable-gbrowse_metadb_config.pl.patch" + for f in conf/synteny/wild_rice_synteny.conf conf/synteny/rice_synteny.conf conf/GBrowse.conf \ + htdocs/tutorial/tutorial.html htdocs/index.html lib/Bio/Graphics/Browser2/Action.pm \ + Changes; do + sed -i 's#/var/lib/gbrowse2#/var/db/gbrowse2#' $f || die "Failed to rewrite /var/lib/gbrowse2 to /var/db/gbrowse2 in $f" + done + for f in htdocs/index.html; do + sed -i 's#/usr/lib/cgi-bin/gb2#/usr/share/webapps/gbrowse/"${PV}"/htdocs/cgi-bin#' $f || die "Failed to rewrite /usr/lib/cgi-bin/gb2 to /usr/share/webapps/gbrowse/"${PV}"/htdocs/cgi-bin in $f" + done +} + +src_configure() { + # GBROWSE_ROOT is the root path in SRC_URI to be prepended + # /usr/share/webapps/gbrowse/2.03/htdocs/etc/gbrowse/GBrowse.conf + webapp_src_preinst + perl Makefile.PL \ + HTDOCS="${MY_HTDOCSDIR}" \ + CGIBIN="${MY_HTDOCSDIR}"/cgi-bin \ + CONF="${MY_HTDOCSDIR}"/etc/gbrowse \ + PACKAGE_DIR="${D}" \ + INSTALLDIRS=vendor \ + GBROWSE_ROOT="gbrowse" \ + DESTDIR="${D}" \ + DATABASES="/var/db/gbrowse2/databases" \ + PERSISTENT="/var/db/gbrowse2" \ + TMP="/var/tmp/gbrowse2" \ + INSTALLETC="n" \ + INSTALLCONF="n" \ + WWWUSER="apache" \ + DO_XS=1 \ + NONROOT=1 \ + || die +} + +src_install() { + mydoc="Changes README TODO INSTALL" + perl-module_src_install + + # TODO: write our own readme + webapp_postinst_txt en "${S}"/INSTALL + webapp_src_install || die "Failed running webapp_src_install" + + # should create a /etc/init.d/ startup script based on this + # /var/tmp/portage/sci-biology/gbrowse-2.03/work/GBrowse-2.03/etc/init.d/gbrowse-slave + + mkdir -p "${D}"/var/tmp/gbrowse2/images + chown -R apache.apache "${D}"/var/tmp/gbrowse2 + + # mkdir -p "${D}"/var/www/localhost/htdocs/gbrowse || die + # ln -s "${D}"/var/tmp/gbrowse2/images "${D}"/usr/share/webapps/gbrowse/"${PV}"/htdocs/i || die + + # whole "${D}"/var/db/gbrowse2 has to be owned by apache.apache otherwise: + # 1. you hit an error that /var/db/gbrowse2/sessions/cgisess.db.lck + # [no, it is not enough chown -R apache.apache /var/db/gbrowse2/sessions, the parent dir has to be apapche.apache as well] + # 2. even if you set /var/db/gbrowse2 to apache.apache still it is not enough, you will get + # [Tue Jan 17 14:59:40 2012] [error] [client 127.0.0.1] Use of uninitialized value $label in lc at /usr/lib/perl5/vendor_perl/5.12.4/i686-linux-thread-multi/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm line 34., referer: http://127.0.0.1/gbrowse/cgi-bin/gbrowse/yeast/ + + mkdir -p "${D}"/var/db/gbrowse2 + mkdir -p "${D}"/var/db/gbrowse2/databases + mkdir -p "${D}"/var/db/gbrowse2/sessions "${D}"/var/db/gbrowse2/userdata + chown -R apache.apache "${D}"/var/db/gbrowse2 # it has to be owned by apache.apache otherwise /var/db/gbrowse2/sessions/cgisess.db.lck cannot be created although /var/db/gbrowse2/sessions is owner by apache.apache + + einfo "Dropping trailing 'databases' from db_variable in conf/GBrowse.conf" + sed -i 's#/var/db/gbrowse2/databases#/var/db/gbrowse2#' conf/GBrowse.conf || die "Failed to dropping trailing 'databases' from db_variable in conf/GBrowse.conf" + + 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 do" + einfo "cp -i ${FILESDIR}/gbrowse.conf.vhosts.d /etc/apache2/vhosts.d/gbrowse.conf" + + sed -i "s#"${D}"##g" "${S}"/install_util/GBrowseInstall.pm || die + sed -i "s#"${D}"##" "${S}"/blib/conf/GBrowse.conf* + sed -i 's#DBI:SQLite:'${D}'/var/lib/gbrowse2/databases/#DBI:SQLite:/var/db/gbrowse2/databases/#' "${S}"/install_util/GBrowseInstall.pm || die +} + +pkg_postinst() { + webapp_pkg_postinst || die "webapp_pkg_postinst failed" + + einfo "Please run gbrowse_metadb_config.pl to update SQLite flatfiles of the live database." + einfo "d='/usr/share/webapps/gbrowse/${PV}/htdocs/etc/gbrowse'; for f in \$d/*.conf.new; do \ " + einfo " mv -i \$f \$d/\`basename \$f .new\`; done" + + einfo "Fix also the other copy of the file:" + einfo "d='/var/www/localhost/htdocs/gbrowse/etc/gbrowse'; for f in \$d/*.conf.new; do \ " + einfo " mv -i \$f \$d/\`basename \$f .new\`; done" +} + +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 +} |