fix database directory references in tutorial conf files

GMOD · Jul 9, 2013 · e644627 · e644627
1 parent 2fd4dc3
commit e644627
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Showing 14 changed files with 31 additions and 32 deletions.
diff --git a/MANIFEST b/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

diff --git a/cgi-bin/gbrowse b/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();
 }

diff --git a/htdocs/tutorial/conf_files/elegans_core.conf b/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
 

diff --git a/htdocs/tutorial/conf_files/elegans_extra.conf b/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

diff --git a/htdocs/tutorial/conf_files/volvox.conf b/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

diff --git a/htdocs/tutorial/conf_files/volvox_final.conf b/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
 

diff --git a/htdocs/tutorial/conf_files/volvox_final_withPhylo.conf b/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}

diff --git a/htdocs/tutorial/conf_files/volvox_halfway.conf b/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
 

diff --git a/htdocs/tutorial/conf_files/volvox_quarter.conf b/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
 

diff --git a/htdocs/tutorial/conf_files/volvox_refactored.conf b/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

diff --git a/htdocs/tutorial/data_files/volvox_all.gff3 b/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
diff --git a/htdocs/tutorial/data_files/volvox_microarray.gff3 b/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
diff --git a/lib/Bio/Graphics/Browser2/Action.pm b/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();
 

diff --git a/t/testdata/conf/languages/POSIX.pm b/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>',