* [gentoo-commits] proj/sci:master commit in: sci-biology/gbrowse/files/, sci-biology/gbrowse/
@ 2011-07-30 15:43 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2011-07-30 15:43 UTC (permalink / raw
To: gentoo-commits
commit: f67b7b7711a847bed69fcec066f3aa4d3b42427d
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Jul 30 15:43:31 2011 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Jul 30 15:43:31 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f67b7b77
sci-biology/gbrowse: add missing brackets cause a perl error while exporting a PNG image
(Portage version: 2.1.10.7/git/Linux i686, unsigned Manifest commit)
---
sci-biology/gbrowse/ChangeLog | 5 +++++
sci-biology/gbrowse/files/fix-PNG-export.patch | 11 +++++++++++
sci-biology/gbrowse/gbrowse-2.39.ebuild | 3 ++-
3 files changed, 18 insertions(+), 1 deletions(-)
diff --git a/sci-biology/gbrowse/ChangeLog b/sci-biology/gbrowse/ChangeLog
index 5c2bd3e..a55fdce 100644
--- a/sci-biology/gbrowse/ChangeLog
+++ b/sci-biology/gbrowse/ChangeLog
@@ -3,6 +3,11 @@
# $Header: /var/cvsroot/gentoo-x86/sci-biology/generic-genome-browser/ChangeLog,v 1.10 2007/07/29 17:07:38 phreak Exp $
30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ gbrowse-2.39.ebuild, +files/fix-PNG-export.patch:
+ sci-biology/gbrowse: add missing brackets cause a perl error while exporting
+ a PNG image gbrowse-2.39.ebuild files/fix-PNG-export.patch
+
+ 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
gbrowse-2.39.ebuild, +files/destdir.patch:
added support for --destdir, patch sent to upstream gbrowse-2.39.ebuild
diff --git a/sci-biology/gbrowse/files/fix-PNG-export.patch b/sci-biology/gbrowse/files/fix-PNG-export.patch
new file mode 100644
index 0000000..469f752
--- /dev/null
+++ b/sci-biology/gbrowse/files/fix-PNG-export.patch
@@ -0,0 +1,11 @@
+--- lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm.ori 2011-07-30 17:14:28.000000000 +0200
++++ lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm 2011-07-30 17:13:13.000000000 +0200
+@@ -30,7 +30,7 @@
+ sub setting {
+ my $self = shift;
+ my ($label,$option,@rest) = @_ >= 2 ? @_ : ('general',@_);
+- $label = 'general' if lc $label eq 'general'; # buglet
++ $label = 'general' if lc($label) eq 'general'; # buglet
+ $self->SUPER::setting($label,$option,@rest);
+ }
+
diff --git a/sci-biology/gbrowse/gbrowse-2.39.ebuild b/sci-biology/gbrowse/gbrowse-2.39.ebuild
index 35af68f..c0bcf25 100644
--- a/sci-biology/gbrowse/gbrowse-2.39.ebuild
+++ b/sci-biology/gbrowse/gbrowse-2.39.ebuild
@@ -90,7 +90,8 @@ src_prepare() {
sed -i 's/return unless -t STDIN/return/' install_util/GBrowseInstall.pm || die
sed -i 's/process_/bp_process_/g' INSTALL || die
epatch "${FILESDIR}"/GBrowseInstall.pm-"${PV}".patch || die "Failed to apply GBrowseInstall.pm-"${PV}".patch"
- epatch "${FILESDIR}"/destdir.patch || die "Failed to apply destdir.patch "
+ epatch "${FILESDIR}"/destdir.patch || die "Failed to apply destdir.patch"
+ epatch "${FILESDIR}"/fix-PNG-export.patch || die "Failed to apply fix-PNG-export.patch"
}
src_configure() {
^ permalink raw reply related [flat|nested] 8+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/gbrowse/files/, sci-biology/gbrowse/
@ 2012-01-17 18:11 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2012-01-17 18:11 UTC (permalink / raw
To: gentoo-commits
commit: bfc8451b06a8727456543751d139d29706473c03
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 17 18:11:07 2012 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 17 18:11:07 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bfc8451b
version bump and some fixes so that it works with webappconfig again?
(Portage version: 2.1.10.44/git/Linux i686, unsigned Manifest commit)
---
sci-biology/gbrowse/ChangeLog | 6 +
.../gbrowse/files/GBrowseInstall.pm-2.45.patch | 32 +++
sci-biology/gbrowse/gbrowse-2.45.ebuild | 199 ++++++++++++++++++++
3 files changed, 237 insertions(+), 0 deletions(-)
diff --git a/sci-biology/gbrowse/ChangeLog b/sci-biology/gbrowse/ChangeLog
index c63914a..41e2334 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/files/GBrowseInstall.pm-2.45.patch b/sci-biology/gbrowse/files/GBrowseInstall.pm-2.45.patch
new file mode 100644
index 0000000..e91fe16
--- /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 0000000..f914844
--- /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
+}
^ permalink raw reply related [flat|nested] 8+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/gbrowse/files/, sci-biology/gbrowse/
@ 2011-07-30 19:22 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2011-07-30 19:22 UTC (permalink / raw
To: gentoo-commits
commit: 85b7bd86f5737125ae7d6eeee78080bd8169dc0c
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Jul 30 19:22:30 2011 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Jul 30 19:22:30 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=85b7bd86
Make sure portage does not run gbrowse_metadb_config.pl otherwise sandbox violation occurs when modifying /var/www/gbrowse2/databases/users.sqlite* file, maybe we could copy these during src_install to the {}, fix there and copy back to live filesystem? Improve error handling in gbrowse_metadb_config.pl. Fix symlink creation during install procedure.
(Portage version: 2.1.10.7/git/Linux i686, unsigned Manifest commit)
---
sci-biology/gbrowse/ChangeLog | 14 +++++
.../files/disable-gbrowse_metadb_config.pl.patch | 19 +++++++
.../gbrowse/files/gbrowse_metadb_config.pl.patch | 55 ++++++++++++++++++++
sci-biology/gbrowse/files/symlink.patch | 11 ++++
sci-biology/gbrowse/gbrowse-2.39.ebuild | 9 ++-
5 files changed, 105 insertions(+), 3 deletions(-)
diff --git a/sci-biology/gbrowse/ChangeLog b/sci-biology/gbrowse/ChangeLog
index a55fdce..b64e880 100644
--- a/sci-biology/gbrowse/ChangeLog
+++ b/sci-biology/gbrowse/ChangeLog
@@ -3,6 +3,20 @@
# $Header: /var/cvsroot/gentoo-x86/sci-biology/generic-genome-browser/ChangeLog,v 1.10 2007/07/29 17:07:38 phreak Exp $
30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ gbrowse-2.39.ebuild, +files/disable-gbrowse_metadb_config.pl.patch,
+ +files/gbrowse_metadb_config.pl.patch, +files/symlink.patch:
+ Make sure portage does not run gbrowse_metadb_config.pl otherwise sandbox
+ violation occurs when modifying /var/www/gbrowse2/databases/users.sqlite*
+ file, maybe we could copy these during src_install to the {}, fix there and
+ copy back to live filesystem? Improve error handling in
+ gbrowse_metadb_config.pl. Fix symlink creation during install procedure.
+ gbrowse-2.39.ebuild files/GBrowseInstall.pm-2.39.patch files/destdir.patch
+ files/disable-gbrowse_metadb_config.pl.patch files/fix-PNG-export.patch
+ files/gbrowse-slave.default files/gbrowse-slave.init.d
+ files/gbrowse.conf.vhosts.d files/gbrowse_metadb_config.pl.patch
+ files/symlink.patch
+
+ 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
gbrowse-2.39.ebuild, +files/fix-PNG-export.patch:
sci-biology/gbrowse: add missing brackets cause a perl error while exporting
a PNG image gbrowse-2.39.ebuild files/fix-PNG-export.patch
diff --git a/sci-biology/gbrowse/files/disable-gbrowse_metadb_config.pl.patch b/sci-biology/gbrowse/files/disable-gbrowse_metadb_config.pl.patch
new file mode 100644
index 0000000..1e96bb8
--- /dev/null
+++ b/sci-biology/gbrowse/files/disable-gbrowse_metadb_config.pl.patch
@@ -0,0 +1,19 @@
+--- install_util/GBrowseInstall.pm.ori 2011-07-30 20:42:02.000000000 +0200
++++ install_util/GBrowseInstall.pm 2011-07-30 20:42:19.000000000 +0200
+@@ -486,11 +486,11 @@
+ 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;
++# 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;
+ system 'sudo','chown','-R',"$uid.$gid",$destdir.$sessions,$destdir.$userdata;
+
+ # if (Module::Build->y_n(
diff --git a/sci-biology/gbrowse/files/gbrowse_metadb_config.pl.patch b/sci-biology/gbrowse/files/gbrowse_metadb_config.pl.patch
new file mode 100644
index 0000000..0f7d5d3
--- /dev/null
+++ b/sci-biology/gbrowse/files/gbrowse_metadb_config.pl.patch
@@ -0,0 +1,55 @@
+--- bin/gbrowse_metadb_config.pl.ori 2011-07-30 19:57:33.000000000 +0200
++++ bin/gbrowse_metadb_config.pl 2011-07-30 20:04:51.000000000 +0200
+@@ -703,9 +703,9 @@
+ local $database->{AutoCommit} = 0;
+ local $database->{RaiseError} = 1;
+ eval {
+- $database->do("delete from $table");
+- $database->do("insert into $table (schema_version) values ($version)");
+- $database->commit();
++ $database->do("delete from $table") or warn "delete from $table failed with: $database->errstr";
++ $database->do("insert into $table (schema_version) values ($version)") or warn "insert into $table (schema_version) values ($version) failed with: $database->errstr";
++ $database->commit() or warn "commitfailed with: $database->errstr";
+ };
+ if ($@) {
+ warn "update failed due to $@. Rolling back";
+@@ -768,11 +768,11 @@
+ $insert_user->finish;
+ # rename the current users table
+ $database->do('drop table users')
+- or die "Couldn't drop old users table";
++ or die "Couldn't drop old users table: $database->errstr";
+ $database->do('alter table users_new rename to users')
+- or die "Couldn't rename new users table";
++ or die "Couldn't rename new users table: $database->errstr";
+ $database->do('create index index_session on session(username)')
+- or die "Couldn't index sessions table";
++ or die "Couldn't index sessions table: $database->errstr";
+
+ # now do the uploads table
+ # this upgrades to latest version 0
+@@ -808,9 +808,9 @@
+ $insert->finish();
+
+ $database->do('drop table uploads')
+- or die "Couldn't drop old uploads table";
++ or die "Couldn't drop old uploads table: $database->errstr";
+ $database->do('alter table uploads_new rename to uploads')
+- or die "Couldn't rename new uploads table";
++ or die "Couldn't rename new uploads table: $database->errstr";
+
+ # now do the openid_users table
+ # this creates the new one
+@@ -916,10 +916,10 @@
+ $select->finish;
+ $insert->finish;
+ $database->do('drop table users')
+- or die "Couldn't drop old users table";
++ or die "Couldn't drop old users table: $database->errstr";
+
+ $database->do('alter table users_new rename to users')
+- or die "Couldn't rename new users table";
++ or die "Couldn't rename new users table: $database->errstr";
+ $database->commit();
+ };
+
diff --git a/sci-biology/gbrowse/files/symlink.patch b/sci-biology/gbrowse/files/symlink.patch
new file mode 100644
index 0000000..e6df771
--- /dev/null
+++ b/sci-biology/gbrowse/files/symlink.patch
@@ -0,0 +1,11 @@
+--- install_util/GBrowseInstall.pm.ori 2011-07-30 19:41:55.000000000 +0200
++++ install_util/GBrowseInstall.pm 2011-07-30 19:42:31.000000000 +0200
+@@ -465,7 +465,7 @@
+ chown $uid,-1,$destdir.$htdocs;
+ {
+ local $> = $uid;
+- symlink($images,$htdocs_i); # so symlinkifowner match works!
++ symlink($images,$destdir.$htdocs_i) or warn "symlink($images,$destdir.$htdocs_i) failed: $!\n"; # so symlinkifowner match works!
+ }
+ chown $>,-1,$destdir.$self->install_path->{htdocs};
+
diff --git a/sci-biology/gbrowse/gbrowse-2.39.ebuild b/sci-biology/gbrowse/gbrowse-2.39.ebuild
index c0bcf25..d4cee63 100644
--- a/sci-biology/gbrowse/gbrowse-2.39.ebuild
+++ b/sci-biology/gbrowse/gbrowse-2.39.ebuild
@@ -28,7 +28,7 @@ SRC_URI="
LICENSE="Artistic"
# webapp ebuilds do not set SLOT
KEYWORDS="~x86 ~amd64"
-IUSE="cgi fastcgi minimal mysql postgres svg test" # lwp moby scf
+IUSE="cgi fastcgi minimal mysql pdf postgres svg test" # lwp moby scf
S="${WORKDIR}/${MY_P}"
@@ -48,6 +48,7 @@ DEPEND="
>=dev-perl/JSON-2.510.0
dev-perl/libwww-perl
svg? ( dev-perl/GD-SVG )
+ pdf? ( media-gfx/inkscape )
mysql? ( dev-perl/DBD-mysql )
postgres? ( dev-perl/DBD-Pg )
sci-biology/ucsc-genome-browser" # that provides bigWig.h and jkweb.a, aka Jim Kent's src
@@ -92,6 +93,9 @@ src_prepare() {
epatch "${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 "${FILESDIR}"/disable-gbrowse_metadb_config.pl.patch || die "Failed to apply disable-gbrowse_metadb_config.pl.patch"
}
src_configure() {
@@ -145,8 +149,7 @@ src_install() {
pkg_postinst() {
webapp_pkg_postinst || die "webapp_pkg_postinst failed"
- einfo "Please run gbrowse_metadb_config.pl to update SQlite flatfiles or the live database"
- einfo "This was disabled by "${FILESDIR}"/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm.patch"
+ einfo "Please run gbrowse_metadb_config.pl to update SQLite flatfiles of the live database."
}
src_test() {
^ permalink raw reply related [flat|nested] 8+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/gbrowse/files/, sci-biology/gbrowse/
@ 2011-07-30 14:45 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2011-07-30 14:45 UTC (permalink / raw
To: gentoo-commits
commit: fa7a65b1a985d0cd4c830b8cac8e63ce2e576c28
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Jul 30 14:45:25 2011 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Jul 30 14:45:25 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=fa7a65b1
sci-biology/gbrowse: added support for --destdir, patch sent to upstream
(Portage version: 2.1.10.7/git/Linux i686, unsigned Manifest commit)
---
sci-biology/gbrowse/ChangeLog | 8 +++
sci-biology/gbrowse/files/destdir.patch | 92 +++++++++++++++++++++++++++++++
sci-biology/gbrowse/gbrowse-2.39.ebuild | 3 +-
3 files changed, 102 insertions(+), 1 deletions(-)
diff --git a/sci-biology/gbrowse/ChangeLog b/sci-biology/gbrowse/ChangeLog
index b8780b1..5c2bd3e 100644
--- a/sci-biology/gbrowse/ChangeLog
+++ b/sci-biology/gbrowse/ChangeLog
@@ -3,6 +3,14 @@
# $Header: /var/cvsroot/gentoo-x86/sci-biology/generic-genome-browser/ChangeLog,v 1.10 2007/07/29 17:07:38 phreak Exp $
30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ gbrowse-2.39.ebuild, +files/destdir.patch:
+ added support for --destdir, patch sent to upstream gbrowse-2.39.ebuild
+
+ 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ gbrowse-2.39.ebuild, +files/destdir.patch:
+ added support for --destdir, patch sent to upstream
+
+ 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
-gbrowse-2.38.ebuild, -files/GBrowseInstall.pm-2.38.patch,
+gbrowse-2.39.ebuild, +files/GBrowseInstall.pm-2.39.patch:
version bump but still need to rewrite upstream's install procedure to
diff --git a/sci-biology/gbrowse/files/destdir.patch b/sci-biology/gbrowse/files/destdir.patch
new file mode 100644
index 0000000..655158c
--- /dev/null
+++ b/sci-biology/gbrowse/files/destdir.patch
@@ -0,0 +1,92 @@
+--- install_util/GBrowseInstall.pm.ori 2011-07-30 16:06:18.000000000 +0200
++++ install_util/GBrowseInstall.pm 2011-07-30 16:06:28.000000000 +0200
+@@ -419,6 +419,7 @@
+ sub ACTION_install {
+ my $self = shift;
+ my $prefix = $self->install_base || $self->prefix || '';
++ my $destdir = $self->destdir || '';
+ GBrowseGuessDirectories->prefix($prefix);
+
+ $self->depends_on('config_data');
+@@ -445,7 +446,7 @@
+
+ # fix some directories so that www user can write into them
+ my $tmp = $self->config_data('tmp') || GBrowseGuessDirectories->tmp;
+- mkpath($tmp);
++ mkpath($destdir.$tmp);
+ my ($uid,$gid) = (getpwnam($user))[2,3];
+
+ # taint check issues
+@@ -454,29 +455,29 @@
+ $gid =~ /^(\d+)$/;
+ $gid = $1;
+
+- unless (chown $uid,$gid,$tmp) {
++ unless (chown $uid,$gid,$destdir.$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;
++ chown $uid,-1,$destdir.$htdocs;
+ {
+ local $> = $uid;
+ symlink($images,$htdocs_i); # so symlinkifowner match works!
+ }
+- chown $>,-1,$self->install_path->{htdocs};
++ chown $>,-1,$destdir.$self->install_path->{htdocs};
+
+ my $persistent = $self->install_path->{'persistent'};
+ my $sessions = File::Spec->catfile($persistent,'sessions');
+ my $userdata = File::Spec->catfile($persistent,'userdata');
+- mkpath([$sessions,$userdata],0711);
++ mkpath([$destdir.$sessions,$destdir.$userdata],0711);
+
+ 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($destdir.File::Spec->catfile($databases,'').'*')) {
++ $self->ownership_warning($destdir.$databases,$user);
+ }
+
+ # chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave');
+@@ -490,7 +491,7 @@
+ my $perl = $self->perl;
+ my @inc = map{"-I$_"} split ':',$self->added_to_INC;
+ system $perl,@inc,$metadb_script;
+- system 'sudo','chown','-R',"$uid.$gid",$sessions,$userdata;
++ system 'sudo','chown','-R',"$uid.$gid",$destdir.$sessions,$destdir.$userdata;
+
+ # if (Module::Build->y_n(
+ # "It is recommended that you restart Apache. Shall I try this for you?",'y'
+@@ -600,6 +601,7 @@
+ my $self = shift;
+
+ my $prefix = $self->install_base || $self->prefix || '';
++ my $destdir = $self->destdir || '';
+ GBrowseGuessDirectories->prefix($prefix);
+ my $install_path = GBrowseGuessDirectories->etc;
+
+@@ -647,7 +649,7 @@
+ if ($self->config_data('installconf') =~ /^[yY]/ && !-e "${includes}/$file") {
+ warn "Creating include file for Apache config: $target\n";
+ my $dir = dirname($target);
+- mkpath([$dir]);
++ mkpath([$destdir.$dir]);
+ if (my $f = IO::File->new("blib${includes}/$file",'>')) {
+ $f->print($self->apache_conf);
+ $f->close;
+@@ -935,8 +937,9 @@
+ sub ownership_warning {
+ my $self = shift;
+ my ($path,$owner) = @_;
++ my $destdir = $self->destdir || '';
+ warn "*** WARNING: Using sudo to change ownership of $path to '$owner'. You may be prompted for your login password ***\n";
+- system "sudo chown -R $owner $path";
++ system "sudo chown -R $owner $destdir.$path";
+ }
+
+ sub cgiurl {
diff --git a/sci-biology/gbrowse/gbrowse-2.39.ebuild b/sci-biology/gbrowse/gbrowse-2.39.ebuild
index 426ee4b..0acd25a 100644
--- a/sci-biology/gbrowse/gbrowse-2.39.ebuild
+++ b/sci-biology/gbrowse/gbrowse-2.39.ebuild
@@ -89,7 +89,8 @@ RDEPEND="${DEPEND}
src_prepare() {
sed -i 's/return unless -t STDIN/return/' install_util/GBrowseInstall.pm || die
sed -i 's/process_/bp_process_/g' INSTALL || die
- epatch "${FILESDIR}"/GBrowseInstall.pm-"${PV}".patch || die "Failed to patch"
+ epatch "${FILESDIR}"/GBrowseInstall.pm-"${PV}".patch || die "Failed to apply GBrowseInstall.pm-"${PV}".patch"
+ epatch "${FILESDIR}"/destdir.patch || die "Failed to apply destdir.patch "
}
src_configure() {
^ permalink raw reply related [flat|nested] 8+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/gbrowse/files/, sci-biology/gbrowse/
@ 2011-07-30 10:46 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2011-07-30 10:46 UTC (permalink / raw
To: gentoo-commits
commit: 9f07546c0a41c51798aeca2c26010741db03535c
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Jul 30 10:40:38 2011 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Jul 30 10:40:38 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9f07546c
version bump but still need to rewrite upstream's install procedure to prevent 'mkdir /var/lib/gbrowse2' from happening
(Portage version: 2.1.10.7/git/Linux i686, unsigned Manifest commit)
---
sci-biology/gbrowse/ChangeLog | 14 ++++++++++++
....pm-2.38.patch => GBrowseInstall.pm-2.39.patch} | 0
.../{gbrowse-2.38.ebuild => gbrowse-2.39.ebuild} | 22 ++++++++++----------
3 files changed, 25 insertions(+), 11 deletions(-)
diff --git a/sci-biology/gbrowse/ChangeLog b/sci-biology/gbrowse/ChangeLog
index eaa41a4..b8780b1 100644
--- a/sci-biology/gbrowse/ChangeLog
+++ b/sci-biology/gbrowse/ChangeLog
@@ -2,6 +2,20 @@
# 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 $
+ 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ -gbrowse-2.38.ebuild, -files/GBrowseInstall.pm-2.38.patch,
+ +gbrowse-2.39.ebuild, +files/GBrowseInstall.pm-2.39.patch:
+ version bump but still need to rewrite upstream's install procedure to
+ prevent 'mkdir /var/lib/gbrowse2' from happening
+
+*gbrowse-2.39 (30 Jul 2011)
+
+ 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ -gbrowse-2.38.ebuild, -files/GBrowseInstall.pm-2.38.patch,
+ +gbrowse-2.39.ebuild, +files/GBrowseInstall.pm-2.39.patch:
+ version bump but still need to rewrite upstream's install procedure to
+ prevent 'mkdir /var/lib/gbrowse2' from happening
+
08 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
gbrowse-2.38.ebuild:
Added dependency on >=perl-gcpan/Text-ParseWords-3.27, documented requirement
diff --git a/sci-biology/gbrowse/files/GBrowseInstall.pm-2.38.patch b/sci-biology/gbrowse/files/GBrowseInstall.pm-2.39.patch
similarity index 100%
rename from sci-biology/gbrowse/files/GBrowseInstall.pm-2.38.patch
rename to sci-biology/gbrowse/files/GBrowseInstall.pm-2.39.patch
diff --git a/sci-biology/gbrowse/gbrowse-2.38.ebuild b/sci-biology/gbrowse/gbrowse-2.39.ebuild
similarity index 92%
rename from sci-biology/gbrowse/gbrowse-2.38.ebuild
rename to sci-biology/gbrowse/gbrowse-2.39.ebuild
index ea981ca..426ee4b 100644
--- a/sci-biology/gbrowse/gbrowse-2.38.ebuild
+++ b/sci-biology/gbrowse/gbrowse-2.39.ebuild
@@ -28,17 +28,17 @@ SRC_URI="
LICENSE="Artistic"
# webapp ebuilds do not set SLOT
KEYWORDS="~x86 ~amd64"
-IUSE="-minimal svg test" # lwp moby scf
+IUSE="cgi fastcgi minimal mysql 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)
-# TODO: make sure www-servers/apache +cgi
+# how about mod_fcgi and dev-libs/fcgi and mod_scgi?
DEPEND="
>=perl-core/Module-Build-0.380.0
>=dev-lang/perl-5.8.8
dev-perl/Capture-Tiny
- >=sci-biology/bioperl-1.6
+ >=sci-biology/bioperl-1.6.901
>=dev-perl/GD-2.07
dev-perl/IO-String
virtual/perl-Digest-MD5
@@ -47,20 +47,17 @@ DEPEND="
>=dev-perl/Bio-Graphics-1.97
>=dev-perl/JSON-2.510.0
dev-perl/libwww-perl
- svg? ( dev-perl/GD-SVG )"
+ svg? ( dev-perl/GD-SVG )
+ 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
-# TODO: implement ebuild checks for these version of packages
-# ! Bio::Root::Version (1.006001) is installed, but we need version >= 1.0069
-# * Bio::DB::BigFile is not installed
-# * Bio::DB::Sam is not installed, install http://cpansearch.perl.org/src/LDS/Bio-SamTools-1.29
-# * DBD::Pg is not installed
-# >=perl-gcpan/Text-ParseWords-3.27
-
RDEPEND="${DEPEND}
>=www-servers/apache-2.0.47
+ fastcgi? ( dev-libs/fcgi )
www-apache/mod_fastcgi
dev-perl/DBI
|| ( dev-perl/DBD-Pg dev-perl/DBD-mysql )
@@ -84,6 +81,9 @@ RDEPEND="${DEPEND}
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() {
^ permalink raw reply related [flat|nested] 8+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/gbrowse/files/, sci-biology/gbrowse/
@ 2011-06-28 17:15 Justin Lecher
0 siblings, 0 replies; 8+ messages in thread
From: Justin Lecher @ 2011-06-28 17:15 UTC (permalink / raw
To: gentoo-commits
commit: a50c105c259094c0b358fb024a326dccc3751247
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 26 08:02:44 2011 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jun 26 08:02:44 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a50c105c
Version Bump
(Portage version: 2.2.0_alpha41/git/Linux x86_64, signed Manifest commit with key 70EB7916)
---
sci-biology/gbrowse/ChangeLog | 9 +
.../gbrowse/files/GBrowseInstall.pm-2.26.patch | 72 --------
....pm-2.33.patch => GBrowseInstall.pm-2.38.patch} | 0
...-disable-gbrowse_metadb_config.pl.pm-2.26.patch | 21 ---
sci-biology/gbrowse/gbrowse-2.26.ebuild | 170 --------------------
.../{gbrowse-2.33.ebuild => gbrowse-2.38.ebuild} | 0
6 files changed, 9 insertions(+), 263 deletions(-)
diff --git a/sci-biology/gbrowse/ChangeLog b/sci-biology/gbrowse/ChangeLog
index b66d69a..e36ad47 100644
--- a/sci-biology/gbrowse/ChangeLog
+++ b/sci-biology/gbrowse/ChangeLog
@@ -2,6 +2,15 @@
# 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
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 4c17f8d..0000000
--- 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
similarity index 100%
rename from sci-biology/gbrowse/files/GBrowseInstall.pm-2.33.patch
rename to 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 0dde704..0000000
--- 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-2.26.ebuild b/sci-biology/gbrowse/gbrowse-2.26.ebuild
deleted file mode 100644
index 363d18d..0000000
--- a/sci-biology/gbrowse/gbrowse-2.26.ebuild
+++ /dev/null
@@ -1,170 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-EAPI="2"
-
-inherit perl-module webapp
-
-MY_P="GBrowse-${PV}"
-
-DESCRIPTION="Display of genomic annotations on interactive web pages"
-HOMEPAGE="http://gmod.org/"
-SRC_URI="
- mirror://sourceforge/gmod/${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
similarity index 100%
rename from sci-biology/gbrowse/gbrowse-2.33.ebuild
rename to sci-biology/gbrowse/gbrowse-2.38.ebuild
^ permalink raw reply related [flat|nested] 8+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/gbrowse/files/, sci-biology/gbrowse/
@ 2011-05-11 8:59 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2011-05-11 8:59 UTC (permalink / raw
To: gentoo-commits
commit: 46b6d2ba846a0e8ea47e0de6da3946d673aa7c79
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed May 11 08:58:07 2011 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed May 11 08:58:07 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=46b6d2ba
sci-biology/gbrowse-2.26: fixed sanbox violation but webap-config bug pops up afterwards (happens later during install)
(Portage version: 2.1.9.43/git/Linux i686, unsigned Manifest commit)
---
...stall.pm.patch => GBrowseInstall.pm-2.26.patch} | 12 ++++----
.../gbrowse/files/GBrowseInstall.pm-2.33.patch | 32 ++++++++++++++++++++
...-disable-gbrowse_metadb_config.pl.pm-2.26.patch | 21 +++++++++++++
sci-biology/gbrowse/gbrowse-2.26.ebuild | 30 +++++++++++++++---
.../{gbrowse-2.26.ebuild => gbrowse-2.33.ebuild} | 19 +++++++++--
5 files changed, 99 insertions(+), 15 deletions(-)
diff --git a/sci-biology/gbrowse/files/GBrowseInstall.pm.patch b/sci-biology/gbrowse/files/GBrowseInstall.pm-2.26.patch
similarity index 81%
rename from sci-biology/gbrowse/files/GBrowseInstall.pm.patch
rename to sci-biology/gbrowse/files/GBrowseInstall.pm-2.26.patch
index 863930e..4c17f8d 100644
--- a/sci-biology/gbrowse/files/GBrowseInstall.pm.patch
+++ b/sci-biology/gbrowse/files/GBrowseInstall.pm-2.26.patch
@@ -1,5 +1,5 @@
---- GBrowse-2.26/install_util/GBrowseInstall.pm.ori 2010-11-27 12:01:58.000000000 +0100
-+++ GBrowse-2.26/install_util/GBrowseInstall.pm 2010-11-27 12:02:15.000000000 +0100
+--- 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);
}
@@ -11,8 +11,8 @@
my $base = basename($self->install_path->{htdocs});
---- GBrowse-2.26/install_util/GBrowseInstall.pm.ori 2011-02-14 13:39:46.000000000 +0100
-+++ GBrowse-2.26/install_util/GBrowseInstall.pm 2011-02-14 13:41:50.000000000 +0100
+--- 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 = $1;
@@ -51,8 +51,8 @@
# chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave');
# $self->fix_selinux;
---- GBrowse-2.26/install_util/GBrowseInstall.pm.ori 2011-02-14 13:50:41.000000000 +0100
-+++ GBrowse-2.26/install_util/GBrowseInstall.pm 2011-02-14 13:51:46.000000000 +0100
+--- install_util/GBrowseInstall.pm.ori 2011-02-14 13:50:41.000000000 +0100
++++ install_util/GBrowseInstall.pm 2011-02-14 13:51:46.000000000 +0100
@@ -470,11 +470,11 @@
my @inc = map{"-I$_"} split ':',$self->added_to_INC;
system $perl,@inc,$metadb_script;
diff --git a/sci-biology/gbrowse/files/GBrowseInstall.pm-2.33.patch b/sci-biology/gbrowse/files/GBrowseInstall.pm-2.33.patch
new file mode 100644
index 0000000..e91fe16
--- /dev/null
+++ b/sci-biology/gbrowse/files/GBrowseInstall.pm-2.33.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/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
new file mode 100644
index 0000000..0dde704
--- /dev/null
+++ b/sci-biology/gbrowse/files/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm-2.26.patch
@@ -0,0 +1,21 @@
+--- 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-2.26.ebuild b/sci-biology/gbrowse/gbrowse-2.26.ebuild
index b525bcc..89000cf 100644
--- a/sci-biology/gbrowse/gbrowse-2.26.ebuild
+++ b/sci-biology/gbrowse/gbrowse-2.26.ebuild
@@ -50,7 +50,6 @@ DEPEND=">=dev-lang/perl-5.8.8
# * Bio::DB::Sam is not installed
# * DBD::Pg is not installed
-
RDEPEND="${DEPEND}
>=www-servers/apache-2.0.47
www-apache/mod_fastcgi
@@ -81,12 +80,17 @@ RDEPEND="${DEPEND}
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 "${FILESDIR}"/GBrowseInstall.pm.patch || die "Failed to patch"
+ epatch "${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}" \
@@ -104,6 +108,12 @@ src_configure() {
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() {
@@ -111,25 +121,35 @@ src_install() {
perl-module_src_install
# TODO: write our own readme
- webapp_postinst_txt en "${S}"/INSTALL
- webapp_src_install || die "Failed running webapp_src_install"
+ webapp_src_preinst
+ webapp_postinst_txt en "${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() {
diff --git a/sci-biology/gbrowse/gbrowse-2.26.ebuild b/sci-biology/gbrowse/gbrowse-2.33.ebuild
similarity index 86%
copy from sci-biology/gbrowse/gbrowse-2.26.ebuild
copy to sci-biology/gbrowse/gbrowse-2.33.ebuild
index b525bcc..e2bcfc3 100644
--- a/sci-biology/gbrowse/gbrowse-2.26.ebuild
+++ b/sci-biology/gbrowse/gbrowse-2.33.ebuild
@@ -9,7 +9,9 @@ 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
+# 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
@@ -30,7 +32,9 @@ 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
+DEPEND="
+ >=perl-core/Module-Build-0.380.0
+ >=dev-lang/perl-5.8.8
dev-perl/Capture-Tiny
>=sci-biology/bioperl-1.6
>=dev-perl/GD-2.07
@@ -39,7 +43,7 @@ DEPEND=">=dev-lang/perl-5.8.8
>=dev-perl/CGI-Session-4.03
dev-perl/Statistics-Descriptive
>=dev-perl/Bio-Graphics-1.97
- dev-perl/JSON
+ >=dev-perl/JSON-2.510.0
dev-perl/libwww-perl
svg? ( dev-perl/GD-SVG )"
@@ -81,7 +85,7 @@ RDEPEND="${DEPEND}
src_prepare() {
sed -i 's/return unless -t STDIN/return/' install_util/GBrowseInstall.pm || die
sed -i 's/process_/bp_process_/g' INSTALL || die
- epatch "${FILESDIR}"/GBrowseInstall.pm.patch || die "Failed to patch"
+ epatch "${FILESDIR}"/GBrowseInstall.pm-"${PV}".patch || die "Failed to patch"
}
src_configure() {
@@ -126,10 +130,17 @@ src_install() {
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() {
^ permalink raw reply related [flat|nested] 8+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/gbrowse/files/, sci-biology/gbrowse/
@ 2011-02-14 15:48 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2011-02-14 15:48 UTC (permalink / raw
To: gentoo-commits
commit: 2cd3f93dfd0672f228900dd9584f57f573fbdc46
Author: Martin Mokrejs <mmokrejs <AT> gentoo <DOT> org>
AuthorDate: Mon Feb 14 15:30:31 2011 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Feb 14 15:30:31 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2cd3f93d
sci-biology/gbrowse: version bump, more DEPS added, tiny webappconfig improvement
(Portage version: 2.1.9.28/git/Linux i686, unsigned Manifest commit)
---
sci-biology/gbrowse/files/GBrowseInstall.pm.patch | 63 +++++++++++++++++++-
.../{gbrowse-2.03.ebuild => gbrowse-2.26.ebuild} | 16 +++++-
2 files changed, 76 insertions(+), 3 deletions(-)
diff --git a/sci-biology/gbrowse/files/GBrowseInstall.pm.patch b/sci-biology/gbrowse/files/GBrowseInstall.pm.patch
index e6163a7..863930e 100644
--- a/sci-biology/gbrowse/files/GBrowseInstall.pm.patch
+++ b/sci-biology/gbrowse/files/GBrowseInstall.pm.patch
@@ -1,5 +1,5 @@
---- GBrowse-2.03/install_util/GBrowseInstall.pm.ori 2010-11-27 12:01:58.000000000 +0100
-+++ GBrowse-2.03/install_util/GBrowseInstall.pm 2010-11-27 12:02:15.000000000 +0100
+--- GBrowse-2.26/install_util/GBrowseInstall.pm.ori 2010-11-27 12:01:58.000000000 +0100
++++ GBrowse-2.26/install_util/GBrowseInstall.pm 2010-11-27 12:02:15.000000000 +0100
@@ -436,8 +436,8 @@
$self->ownership_warning($databases,$user);
}
@@ -11,3 +11,62 @@
my $base = basename($self->install_path->{htdocs});
+--- GBrowse-2.26/install_util/GBrowseInstall.pm.ori 2011-02-14 13:39:46.000000000 +0100
++++ GBrowse-2.26/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');
+ # $self->fix_selinux;
+--- GBrowse-2.26/install_util/GBrowseInstall.pm.ori 2011-02-14 13:50:41.000000000 +0100
++++ GBrowse-2.26/install_util/GBrowseInstall.pm 2011-02-14 13:51:46.000000000 +0100
+@@ -470,11 +470,11 @@
+ my @inc = map{"-I$_"} 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/$base for demo and documentation.\n";
diff --git a/sci-biology/gbrowse/gbrowse-2.03.ebuild b/sci-biology/gbrowse/gbrowse-2.26.ebuild
similarity index 93%
rename from sci-biology/gbrowse/gbrowse-2.03.ebuild
rename to sci-biology/gbrowse/gbrowse-2.26.ebuild
index 9fc872b..b525bcc 100644
--- a/sci-biology/gbrowse/gbrowse-2.03.ebuild
+++ b/sci-biology/gbrowse/gbrowse-2.26.ebuild
@@ -31,6 +31,7 @@ S="${WORKDIR}/${MY_P}"
# TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/Safe-World (not compatible w/perl-5.10)
# TODO: make sure www-servers/apache +cgi
DEPEND=">=dev-lang/perl-5.8.8
+ dev-perl/Capture-Tiny
>=sci-biology/bioperl-1.6
>=dev-perl/GD-2.07
dev-perl/IO-String
@@ -45,6 +46,11 @@ DEPEND=">=dev-lang/perl-5.8.8
# TODO: based on the following message in apache/error_log the list of deps should be longer
# GBROWSE NOTICE: To enable PDF generation, please enter the directory "/home/httpd" and run the commands: "sudo mkdir .inkscape .gnome2" and "sudo chown apache .inkscape .gnome2". To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://127.0.0.1/gbrowse/cgi-bin/gbrowse_details/yeast?ref=chrII;start=90739;end=92028;name=YBL069W;class=Sequence;feature_id=881;db_id=annotations%3Adatabase
+# * Bio::DB::BigFile is not installed
+# * Bio::DB::Sam is not installed
+# * DBD::Pg is not installed
+
+
RDEPEND="${DEPEND}
>=www-servers/apache-2.0.47
www-apache/mod_fastcgi
@@ -54,6 +60,8 @@ RDEPEND="${DEPEND}
dev-perl/File-NFSLock
dev-perl/FCGI
perl-core/Math-BigInt
+ perl-core/Math-BigInt-FastCalc
+ dev-perl/Math-BigInt-GMP
dev-perl/Digest-SHA1
dev-perl/Crypt-SSLeay
dev-perl/Net-SMTP-SSL
@@ -67,6 +75,7 @@ RDEPEND="${DEPEND}
dev-perl/XML-Writer
dev-perl/XML-Parser
dev-perl/Bio-Das
+ dev-perl/Text-Shellwords
)"
src_prepare() {
@@ -93,6 +102,7 @@ src_configure() {
INSTALLCONF="n" \
WWWUSER="apache" \
DO_XS=1 \
+ NONROOT=1 \
|| die
}
@@ -102,7 +112,7 @@ src_install() {
# TODO: write our own readme
webapp_postinst_txt en "${S}"/INSTALL
- webapp_src_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
@@ -118,6 +128,10 @@ src_install() {
einfo "Make sure you compiled apache with +cgi and copy ${FILESDIR}/gbrowse.conf.vhosts.d to /etc/apache2/vhosts.d/"
}
+pkg_postinst() {
+ webapp_pkg_postinst || die "webapp_pkg_postinst failed"
+}
+
src_test() {
mysql -uroot -p password -e 'create database yeast'
mysql -uroot -p password -e 'grant all privileges on yeast.* to gbrowse@localhost'
^ permalink raw reply related [flat|nested] 8+ messages in thread
end of thread, other threads:[~2012-01-17 18:11 UTC | newest]
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2012-01-17 18:11 Martin Mokrejs
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