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Fix performance problems when using in-memory databases composed of m…

…ultiple GFF3 files. The fix is a hack that involves overwriting the Bio::DB::SeqFeature::Store::LoadHelper module!
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1 parent d76a19d commit 92846379434bcde45ebcbc73cf3022a8a10a7f81 @lstein lstein committed Jul 10, 2013
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@@ -9,6 +9,8 @@
* Clicking on the "Go" button when a filter plugin is selected opens up the configuration dialog.
* Added Juan Tena's split_wig.pl script, which is useful for uploading WIG files from genomes with lots
of scaffolds.
+ * Fix performance problems when using in-memory databases composed of multiple GFF3 files. The fix is
+ a hack that involves overwriting the Bio::DB::SeqFeature::Store::LoadHelper module!
2.54
* Version 2.53 introduced a bad bug into track configuration such
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@@ -442,7 +442,6 @@ 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
@@ -568,6 +567,7 @@ lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
lib/Bio/DB/SeqFeature/Store/Alias.pm
lib/Bio/DB/SeqFeature/Store/BedLoader.pm
+lib/Bio/DB/SeqFeature/Store/LoadHelper.pm
lib/Bio/DB/Tagger.pm
lib/Bio/DB/Tagger/mysql.pm
lib/Bio/DB/Tagger/Tag.pm
@@ -691,3 +691,5 @@ t/testdata/phylo_align/species.tre
t/testdata/phylo_align/volvox_alignment.conf
t/testdata/phylo_align/volvox_phyloalign.gff
t/testdata/TemplateCopy.pm
+META.yml
+META.json
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@@ -1,4 +1,4 @@
-# Note: this file was auto-generated by Module::Build::Compat version 0.3800
+# Note: this file was auto-generated by Module::Build::Compat version 0.4005
require 5.008;
unless (eval "use Module::Build::Compat 0.02; 1" ) {
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0 cgi-bin/das 100755 → 100644
No changes.
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0 cgi-bin/gbgff 100755 → 100644
No changes.
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0 cgi-bin/gbrowse 100755 → 100644
No changes.
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0 cgi-bin/gbrowse_details 100755 → 100644
No changes.
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0 cgi-bin/gbrowse_gmap 100755 → 100644
No changes.
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0 cgi-bin/gbrowse_img 100755 → 100644
No changes.
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0 cgi-bin/gbrowse_key_img 100755 → 100644
No changes.
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0 cgi-bin/gbrowse_login 100755 → 100644
No changes.
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0 cgi-bin/gbrowse_syn 100755 → 100644
No changes.
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@@ -61,17 +61,31 @@
<h3>Accelerated Demos</h3>
-If you have FastCGI and/or ModPerl installed, you will have access to
+If you have mod_fcgid, mod_fastcgi and/or ModPerl installed, you will have access to
an accelerated version of gbrowse at these URLs:
<ul>
- <li>FastCGI
+ <li>mod_fcgid
<ul>
<li><a href="/fgb2/gbrowse/yeast">http://your.host/fgb2/gbrowse/yeast</a></li>
<li><a href="/fgb2/gbrowse/yeast_advanced">http://your.host/fgb2/gbrowse/yeast_advanced</a></li>
<li><a href="/fgb2/gbrowse/yeast_renderfarm">http://your.host/fgb2/gbrowse/yeast_renderfarm</a></li>
</ul>
</li>
+ <li>mod_fastcgi
+ <ul>
+ <li><a href="/fast/gbrowse/yeast">http://your.host/fgb2/gbrowse/yeast</a></li>
+ <li><a href="/fast/gbrowse/yeast_advanced">http://your.host/fgb2/gbrowse/yeast_advanced</a></li>
+ <li><a href="/fast/gbrowse/yeast_renderfarm">http://your.host/fgb2/gbrowse/yeast_renderfarm</a></li>
+ </ul>
+ </li>
+ <li>mod_perl
+ <ul>
+ <li><a href="/mgb2/gbrowse/yeast">http://your.host/fgb2/gbrowse/yeast</a></li>
+ <li><a href="/mgb2/gbrowse/yeast_advanced">http://your.host/fgb2/gbrowse/yeast_advanced</a></li>
+ <li><a href="/mgb2/gbrowse/yeast_renderfarm">http://your.host/fgb2/gbrowse/yeast_renderfarm</a></li>
+ </ul>
+ </li>
</ul>
@@ -425,8 +425,8 @@ ScriptAlias "/gb2" "$cgibin"
</IfModule>
<IfModule mod_fastcgi.c>
- Alias /fgb2 "$cgibin"
- <Location /fgb2>
+ Alias /fast "$cgibin"
+ <Location /fast>
SetHandler fastcgi-script
</Location>
# Note: you may need to increase -idle-timeout if file uploads are timing out and returning server
@@ -2,7 +2,7 @@ package Bio::Graphics::Browser2;
# $Id$
# Globals and utilities for GBrowse and friends
-our $VERSION = '2.54';
+our $VERSION = '2.55';
use strict;
use warnings;

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