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author | Justin Lecher <jlec@gentoo.org> | 2017-03-26 09:35:47 +0100 |
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committer | Justin Lecher <jlec@gentoo.org> | 2017-03-26 09:35:47 +0100 |
commit | 0371f3c41ab51fb064510b7beddcb02904a5181a (patch) | |
tree | b23ce6e27cc348235f3c6c5200597aaedeb8eade /sci-biology/gbrowse/gbrowse-2.39.ebuild | |
parent | Drop masked package - dev-python/pythonocc (diff) | |
download | sci-0371f3c41ab51fb064510b7beddcb02904a5181a.tar.gz sci-0371f3c41ab51fb064510b7beddcb02904a5181a.tar.bz2 sci-0371f3c41ab51fb064510b7beddcb02904a5181a.zip |
Drop masked package - sci-biology/gbrowse
Signed-off-by: Justin Lecher <jlec@gentoo.org>
Diffstat (limited to 'sci-biology/gbrowse/gbrowse-2.39.ebuild')
-rw-r--r-- | sci-biology/gbrowse/gbrowse-2.39.ebuild | 169 |
1 files changed, 0 insertions, 169 deletions
diff --git a/sci-biology/gbrowse/gbrowse-2.39.ebuild b/sci-biology/gbrowse/gbrowse-2.39.ebuild deleted file mode 100644 index ed43aae98..000000000 --- a/sci-biology/gbrowse/gbrowse-2.39.ebuild +++ /dev/null @@ -1,169 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils 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}/${MY_P}" - -# TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/Safe-World (not compatible w/perl-5.10) -# how about mod_fcgi and dev-libs/fcgi and mod_scgi? -DEPEND=" - >=virtual/perl-Module-Build-0.380.0 - >=dev-lang/perl-5.8.8:= - dev-perl/Capture-Tiny - >=sci-biology/bioperl-1.6.901 - >=dev-perl/GD-2.07 - dev-perl/IO-String - virtual/perl-Digest-MD5 - >=dev-perl/CGI-Session-4.03 - dev-perl/Statistics-Descriptive - >=dev-perl/Bio-Graphics-1.97 - >=dev-perl/JSON-2.510.0 - dev-perl/TermReadKey - dev-perl/libwww-perl - svg? ( dev-perl/GD-SVG ) - pdf? ( media-gfx/inkscape ) - mysql? ( dev-perl/DBD-mysql ) - postgres? ( dev-perl/DBD-Pg ) - sci-biology/ucsc-genome-browser" # that provides bigWig.h and jkweb.a, aka Jim Kent's src - -# TODO: based on the following message in apache/error_log the list of deps should be longer -# GBROWSE NOTICE: To enable PDF generation, please enter the directory "/home/httpd" and run the commands: "sudo mkdir .inkscape .gnome2" and "sudo chown apache .inkscape .gnome2". To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://127.0.0.1/gbrowse/cgi-bin/gbrowse_details/yeast?ref=chrII;start=90739;end=92028;name=YBL069W;class=Sequence;feature_id=881;db_id=annotations%3Adatabase - -RDEPEND="${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 - virtual/perl-Math-BigInt - virtual/perl-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 - sed -i 's/process_/bp_process_/g' INSTALL || die - epatch \ - "${FILESDIR}"/GBrowseInstall.pm-"${PV}".patch \ - "${FILESDIR}"/destdir.patch \ - "${FILESDIR}"/fix-PNG-export.patch \ - "${FILESDIR}"/symlink.patch \ - "${FILESDIR}"/gbrowse_metadb_config.pl.patch \ - "${FILESDIR}"/disable-gbrowse_metadb_config.pl.patch -} - -src_configure() { - # GBROWSE_ROOT is the root path in SRC_URI to be prepended - # /usr/share/webapps/gbrowse/2.03/htdocs/etc/gbrowse/GBrowse.conf - webapp_src_preinst - perl Makefile.PL \ - HTDOCS="${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 -} - -src_install() { - mydoc="Changes README TODO INSTALL" - perl-module_src_install - - # TODO: write our own readme - webapp_postinst_txt en "${S}"/INSTALL - webapp_src_install || die "Failed running webapp_src_install" - - # should create a /etc/init.d/ startup script based on this - # /var/tmp/portage/sci-biology/gbrowse-2.03/work/GBrowse-2.03/etc/init.d/gbrowse-slave - - chown -R apache.apache "${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}"##" "${S}"/blib/conf/GBrowse.conf* || die - sed -i 's#DBI:SQLite:'${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 update SQLite flatfiles of the live database." -} - -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 -} |