1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/3c87628a9907/
changeset: 3c87628a9907
user: fubar
date: 2011-10-04 00:38:33
summary: Increase size limit for display of html files to 10000000 bytes - mirdeep2 creates very large html objects.
Size limit for display should probably be configurable.
affected #: 1 file (-1 bytes)
--- a/lib/galaxy/web/controllers/dataset.py Mon Oct 03 17:12:41 2011 -0400
+++ b/lib/galaxy/web/controllers/dataset.py Tue Oct 04 09:38:33 2011 +1100
@@ -376,6 +376,8 @@
raise paste.httpexceptions.HTTPNotFound( "File Not Found (%s)." % data.file_name )
max_peek_size = 1000000 # 1 MB
+ if isinstance(data.datatype, datatypes.images.Html):
+ max_peek_size = 10000000 # 10 MB for html
if not preview or isinstance(data.datatype, datatypes.images.Image) or os.stat( data.file_name ).st_size < max_peek_size:
return open( data.file_name )
else:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/aebbf6bdf5a6/
changeset: aebbf6bdf5a6
user: jgoecks
date: 2011-10-03 23:12:41
summary: Fix typos.
affected #: 1 file (-1 bytes)
--- a/tools/ngs_rna/cufflinks_wrapper.xml Mon Oct 03 15:10:21 2011 -0400
+++ b/tools/ngs_rna/cufflinks_wrapper.xml Mon Oct 03 17:12:41 2011 -0400
@@ -61,10 +61,10 @@
</param><when value="No"></when><when value="Use reference annotation">
- <param format="gff3,gtf" name="reference_annotation_file" type="data" label="Reference Aonnotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/>
+ <param format="gff3,gtf" name="reference_annotation_file" type="data" label="Reference Annotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/></when><when value="Use reference annotation guide">
- <param format="gff3,gtf" name="reference_annotation_guide_file" type="data" label="Reference Aonnotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/>
+ <param format="gff3,gtf" name="reference_annotation_guide_file" type="data" label="Reference Annotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/></when></conditional><conditional name="bias_correction">
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/0238b2b4b84e/
changeset: 0238b2b4b84e
user: jgoecks
date: 2011-10-03 19:34:32
summary: Trackster: fix display of reference data.
affected #: 1 file (-1 bytes)
--- a/static/scripts/trackster.js Mon Oct 03 11:11:16 2011 -0400
+++ b/static/scripts/trackster.js Mon Oct 03 13:34:32 2011 -0400
@@ -1157,12 +1157,13 @@
*/
add_drawable: function(drawable) {
DrawableCollection.prototype.add_drawable.call(this, drawable);
- if (drawable.init) { drawable.init(); }
+ drawable.init();
this.has_changes = true;
this.update_intro_div();
},
add_label_track: function (label_track) {
label_track.view = this;
+ label_track.init();
this.label_tracks.push(label_track);
},
/**
@@ -2196,6 +2197,7 @@
//
// Tracks with no dataset id are handled differently.
+ // FIXME: is this really necessary?
//
if (!track.dataset_id) {
return;
@@ -2728,6 +2730,10 @@
this.container_div.addClass( "label-track" );
};
extend(LabelTrack.prototype, Track.prototype, {
+ init: function() {
+ // Enable by default because there should always be data when drawing track.
+ this.enabled = true;
+ },
_draw: function() {
var view = this.view,
range = view.high - view.low,
@@ -2767,6 +2773,10 @@
this.tile_cache = new Cache(CACHED_TILES_LINE);
};
extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
+ init: function() {
+ // Enable by default because there should always be data when drawing track.
+ this.enabled = true;
+ },
/**
* Draw ReferenceTrack tile.
*/
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/61c45145fce6/
changeset: 61c45145fce6
user: dan
date: 2011-10-03 17:11:16
summary: Tweak validator for input bed file in SICER tool to work around workflow editor issue.
affected #: 1 file (-1 bytes)
--- a/tools/peak_calling/sicer_wrapper.xml Mon Oct 03 10:52:19 2011 -0400
+++ b/tools/peak_calling/sicer_wrapper.xml Mon Oct 03 11:11:16 2011 -0400
@@ -31,7 +31,7 @@
</requirements><inputs><param name="input_bed_file" type="data" format="bed" label="ChIP-Seq Tag File" >
- <validator type="expression" message="SICER is not available for the genome.">value.dbkey in [ 'mm8', 'mm9', 'hg18', 'hg19', 'dm2', 'dm3', 'sacCer1', 'pombe', 'rn4', 'tair8' ]</validator>
+ <validator type="expression" message="SICER is not available for the genome.">value is not None and value.dbkey in [ 'mm8', 'mm9', 'hg18', 'hg19', 'dm2', 'dm3', 'sacCer1', 'pombe', 'rn4', 'tair8' ]</validator></param><param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" optional="True"><!-- fix me, add filter to match dbkeys --><options>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/070c57978648/
changeset: 070c57978648
user: jgoecks
date: 2011-10-03 16:52:19
summary: Fix for getting reference data for a built-in genome build.
affected #: 1 file (-1 bytes)
--- a/lib/galaxy/web/controllers/tracks.py Mon Oct 03 10:40:36 2011 -0400
+++ b/lib/galaxy/web/controllers/tracks.py Mon Oct 03 10:52:19 2011 -0400
@@ -420,7 +420,7 @@
twobit_file_name = None
if dbkey in self.available_genomes:
# Built-in twobit.
- twobit_file_name = TwoBitFile( open( self.available_genomes[dbkey] ) )
+ twobit_file_name = self.available_genomes[dbkey]
else:
# From custom build.
# TODO: how to make this work for shared visualizations?
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.