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fix database directory references in tutorial conf files

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1 parent 2fd4dc3 commit e6446277630e7e4d02162be51113907c1c7a82d3 @lstein lstein committed Jul 9, 2013
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1 MANIFEST
@@ -442,6 +442,7 @@ htdocs/tutorial/data_files/volvox_genes_simple.gff3
htdocs/tutorial/data_files/volvox_matches.gff3
htdocs/tutorial/data_files/volvox_microarray.gff3
htdocs/tutorial/data_files/volvox_microarray.wig
+htdocs/tutorial/data_files/track001.ctgA.1202327456.wig
htdocs/tutorial/data_files/volvox_phyloalign.fa
htdocs/tutorial/data_files/volvox_phyloalign.gff3
htdocs/tutorial/data_files/volvox_phyloalign_wigentries.gff3
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30 cgi-bin/gbrowse
@@ -1,14 +1,5 @@
#!/usr/bin/perl
-eval 'exec /usr/bin/perl -S $0 ${1+"$@"}'
- if 0; # not running under some shell
-
-eval 'exec /usr/bin/perl -S $0 ${1+"$@"}'
- if 0; # not running under some shell
-
-eval 'exec /usr/bin/perl -S $0 ${1+"$@"}'
- if 0; # not running under some shell
-
use strict;
use CGI;
use Bio::Graphics::Browser2;
@@ -20,17 +11,21 @@ my $fcgi = Bio::Graphics::Browser2::Render->fcgi_request;
my $init;
if ($fcgi) {
+
+ warn "[$$] FCGI mode started";
my $FCGI_DONE = 0;
- $SIG{USR1} = $SIG{PIPE} = $SIG{TERM} = sub {
- my $sig = shift;
- my $time = localtime;
- print STDERR "[$time] [notice] GBrowse FastCGI process caught sig$sig. Exiting... (pid $$)\n";
- $FCGI_DONE = 1;
- };
+# $SIG{USR1} = $SIG{PIPE} = $SIG{TERM} = sub {
+# my $sig = shift;
+# my $time = localtime;
+# print STDERR "[$time] [notice] GBrowse FastCGI process caught sig$sig. Exiting... (pid $$)\n";
+# $FCGI_DONE = 1;
+# };
my %sys_env = %ENV;
while (!$FCGI_DONE) {
+ warn "[$$] accepting...";
my $status = $fcgi->Accept;
+ warn "[$$] accepted, status = $status";
next unless $status >= 0;
%ENV = (%sys_env, %ENV);
my $globals = Bio::Graphics::Browser2->open_globals;
@@ -41,14 +36,17 @@ if ($fcgi) {
$render->run();
};
warn $@ if $@;
+ warn "[$$] destroying...";
$render->destroy;
+ warn "[$$] destroyed...";
}
my $pgrp = getpgrp();
+ warn "[$$] killing $pgrp";
kill TERM => -$pgrp;
} else {
- $SIG{TERM} = sub { warn "gbrowse going down..."; CORE::exit 0 };
+ $SIG{TERM} = sub { warn "[$$] gbrowse going down..."; CORE::exit 0 };
my $globals = Bio::Graphics::Browser2->open_globals;
Bio::Graphics::Browser2::Render::HTML->new($globals)->run();
}
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2 htdocs/tutorial/conf_files/elegans_core.conf
@@ -1,7 +1,7 @@
[GENERAL]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
- -dir "/var/www/gbrowse2/databases/elegans_core"
+ -dir "$DATABASES/elegans_core"
plugins = Aligner RestrictionAnnotator
View
2 htdocs/tutorial/conf_files/elegans_extra.conf
@@ -2,7 +2,7 @@
description = C. elegans Extra Annotations
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
- -dir "/var/www/gbrowse2/databases/elegans_extra"
+ -dir "$DATABASES/elegans_extra"
# options
drag and drop = 1
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2 htdocs/tutorial/conf_files/volvox.conf
@@ -1,7 +1,7 @@
[GENERAL]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
- -dir '/var/www/gbrowse2/databases/volvox'
+ -dir '$DATABASES/volvox'
# just the basic track dumper plugin
plugins = TrackDumper
View
2 htdocs/tutorial/conf_files/volvox_final.conf
@@ -1,7 +1,7 @@
[GENERAL]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
- -dir '/var/www/gbrowse2/databases/volvox'
+ -dir '$DATABASES/volvox'
plugins = Aligner RestrictionAnnotator TrackDumper
View
2 htdocs/tutorial/conf_files/volvox_final_withPhylo.conf
@@ -2,7 +2,7 @@
description = Volvox Example Database
db_adaptor = Bio::DB::GFF
db_args = -adaptor memory
- -dir '/var/www/gbrowse2/databases/volvox'
+ -dir '$DATABASES/volvox'
aggregators = match
BAC{left_end_read,right_end_read/BAC}
View
2 htdocs/tutorial/conf_files/volvox_halfway.conf
@@ -1,7 +1,7 @@
[GENERAL]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
- -dir '/var/www/gbrowse2/databases/volvox'
+ -dir '$DATABASES/volvox'
plugins = Aligner RestrictionAnnotator TrackDumper
View
2 htdocs/tutorial/conf_files/volvox_quarter.conf
@@ -1,7 +1,7 @@
[GENERAL]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
- -dir '/var/www/gbrowse2/databases/volvox'
+ -dir '$DATABASES/volvox'
plugins = Aligner RestrictionAnnotator TrackDumper
View
10 htdocs/tutorial/conf_files/volvox_refactored.conf
@@ -1,5 +1,5 @@
[GENERAL]
-databse = basic
+database = basic
plugins = Aligner RestrictionAnnotator BatchDumper TrackDumper
@@ -21,22 +21,22 @@ initial landmark = ctgA:5000..10000
[basic:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
- -dir '/var/www/gbrowse2/databases/volvox_basic'
+ -dir '$DATABASES/volvox_basic'
[genes:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
- -dir '/var/www/gbrowse2/databases/volvox_genes'
+ -dir '$DATABASES/volvox_genes'
[alignments:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
- -dir '/var/www/gbrowse2/databases/volvox_alignments'
+ -dir '$DATABASES/volvox_alignments'
[expression:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
- -dir '/var/www/gbrowse2/databases/volvox_expression'
+ -dir '$DATABASES/volvox_expression'
########################
# Default glyph settings
View
2 htdocs/tutorial/data_files/volvox_all.gff3
@@ -247,5 +247,5 @@ ctgA est EST_match 7000 7200 . + . ID=Match5;Name=agt767.5;Target=agt767.5 853 1
ctgA est EST_match 8000 9000 . - . ID=Match6;Name=agt767.3;Target=agt767.3 1 1001
-ctgA . microarray_oligo 1 50000 . . . Name=example;wigfile=/var/www/gbrowse2/databases/volvox/track001.ctgA.1202327456.wig
+ctgA . microarray_oligo 1 50000 . . . Name=example;wigfile=$DATABASES/volvox/track001.ctgA.1202327456.wig
ctgA example read 44401 45925 . + . Name=trace;trace=volvox_trace.scf
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2 htdocs/tutorial/data_files/volvox_microarray.gff3
@@ -1,3 +1,3 @@
##gff-version 3
-ctgA . microarray_oligo 1 50000 . . . Name=example;wigfile=/var/www/gbrowse2/databases/volvox/track001.ctgA.1202327456.wig
+ctgA . microarray_oligo 1 50000 . . . Name=example;wigfile=$DATABASES/volvox/track001.ctgA.1202327456.wig
View
2 lib/Bio/Graphics/Browser2/Action.pm
@@ -305,8 +305,6 @@ sub ACTION_add_tracks {
my $render = $self->render;
my @track_names = $q->param('track_names');
- warn "@track_names";
-
$render->init_database();
$render->init_plugins();
View
2 t/testdata/conf/languages/POSIX.pm
@@ -492,6 +492,8 @@ END
CONFIGURE_THIS_TRACK => '<b>Configure this track</b>',
+ POP_OUT => '<b>Pop out/in</b>',
+
DOWNLOAD_THIS_TRACK => '<b>Download this track</b>',
ABOUT_THIS_TRACK => '<b>About this track</b>',

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