From: "Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>
To: gentoo-commits@lists.gentoo.org
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/gbrowse/files/, sci-biology/gbrowse/
Date: Wed, 11 May 2011 08:59:31 +0000 (UTC) [thread overview]
Message-ID: <46b6d2ba846a0e8ea47e0de6da3946d673aa7c79.mmokrejs@gentoo> (raw)
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() {
next reply other threads:[~2011-05-11 8:59 UTC|newest]
Thread overview: 8+ messages / expand[flat|nested] mbox.gz Atom feed top
2011-05-11 8:59 Martin Mokrejs [this message]
-- strict thread matches above, loose matches on Subject: below --
2012-01-17 18:11 [gentoo-commits] proj/sci:master commit in: sci-biology/gbrowse/files/, sci-biology/gbrowse/ Martin Mokrejs
2011-07-30 19:22 Martin Mokrejs
2011-07-30 15:43 Martin Mokrejs
2011-07-30 14:45 Martin Mokrejs
2011-07-30 10:46 Martin Mokrejs
2011-06-28 17:15 Justin Lecher
2011-02-14 15:48 Martin Mokrejs
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