1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/4033d81b3311/
changeset: 4033d81b3311
user: greg
date: 2012-12-14 22:37:42
summary: Missed an import.
affected #: 1 file
diff -r f14ca41c8cf34779d0b89979320488ebe04eb943 -r 4033d81b3311e105f79377cfe64df5861851f5d1 lib/galaxy/tool_shed/tool_dependencies/install_util.py
--- a/lib/galaxy/tool_shed/tool_dependencies/install_util.py
+++ b/lib/galaxy/tool_shed/tool_dependencies/install_util.py
@@ -1,7 +1,7 @@
import sys, os, subprocess, tempfile
import common_util
import fabric_util
-from galaxy.tool_shed.encoding_util import tool_shed_encode
+from galaxy.tool_shed.encoding_util import encoding_sep, tool_shed_encode, tool_shed_decode
from galaxy.model.orm import and_
from galaxy import eggs
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/33d4ab5cc642/
changeset: 33d4ab5cc642
user: carlfeberhard
date: 2012-12-14 21:41:51
summary: history panel: do not render body html until hda is expanded
affected #: 1 file
diff -r f45730d9e8904783f5f8a29cf2a2a0c93e5a2047 -r 33d4ab5cc642f2bdc5ad8670abf4400063bb8415 static/scripts/mvc/dataset/hda-base.js
--- a/static/scripts/mvc/dataset/hda-base.js
+++ b/static/scripts/mvc/dataset/hda-base.js
@@ -77,6 +77,7 @@
itemWrapper.append( this._render_warnings() );
itemWrapper.append( this._render_titleBar() );
+
this.body = $( this._render_body() );
itemWrapper.append( this.body );
@@ -321,18 +322,31 @@
},
// ......................................................................... state body renderers
- /** Render the (expanded) body of an HDA, dispatching to other functions based on the HDA state
+ /** Render the enclosing div of the hda body and, if expanded, the html in the body
* @returns {jQuery} rendered DOM
*/
//TODO: only render these on expansion (or already expanded)
_render_body : function(){
- //this.log( this + '_render_body' );
-
var body = $( '<div/>' )
.attr( 'id', 'info-' + this.model.get( 'id' ) )
.addClass( 'historyItemBody' )
- .attr( 'style', 'display: block' );
+ .attr( 'style', 'display: none' );
+ if( this.expanded ){
+ // only render the body html if it's being shown
+ this._render_body_html( body );
+ body.show();
+ }
+ return body;
+ },
+
+ /** Render the (expanded) body of an HDA, dispatching to other functions based on the HDA state
+ * @param {jQuery} body the body element to append the html to
+ */
+ //TODO: only render these on expansion (or already expanded)
+ _render_body_html : function( body ){
+ //this.log( this + '_render_body' );
+ body.html( '' );
//TODO: not a fan of this dispatch
switch( this.model.get( 'state' ) ){
case HistoryDatasetAssociation.STATES.NEW :
@@ -375,13 +389,6 @@
body.append( $( '<div>Error: unknown dataset state "' + this.model.get( 'state' ) + '".</div>' ) );
}
body.append( '<div style="clear: both"></div>' );
-
- if( this.expanded ){
- body.show();
- } else {
- body.hide();
- }
- return body;
},
/** Render inaccessible, not-owned by curr user.
@@ -514,17 +521,17 @@
* @fires body-collapsed when a body has been collapsed
*/
toggleBodyVisibility : function( event, expanded ){
- var hdaView = this,
- $body = this.$el.find( '.historyItemBody' );
- expanded = ( expanded === undefined )?( !$body.is( ':visible' ) ):( expanded );
+ var hdaView = this;
+ this.expanded = ( expanded === undefined )?( !this.body.is( ':visible' ) ):( expanded );
//this.log( 'toggleBodyVisibility, expanded:', expanded, '$body:', $body );
- if( expanded ){
- $body.slideDown( 'fast', function(){
+ if( this.expanded ){
+ hdaView._render_body_html( hdaView.body );
+ this.body.slideDown( 'fast', function(){
hdaView.trigger( 'body-expanded', hdaView.model.get( 'id' ) );
});
} else {
- $body.slideUp( 'fast', function(){
+ this.body.slideUp( 'fast', function(){
hdaView.trigger( 'body-collapsed', hdaView.model.get( 'id' ) );
});
}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/f45730d9e890/
changeset: f45730d9e890
user: carlfeberhard
date: 2012-12-14 20:53:41
summary: Make hda name text selectable
affected #: 1 file
diff -r 4b4ea995233684e49259a8126257a2d226b8a026 -r f45730d9e8904783f5f8a29cf2a2a0c93e5a2047 templates/root/alternate_history.mako
--- a/templates/root/alternate_history.mako
+++ b/templates/root/alternate_history.mako
@@ -537,9 +537,6 @@
.historyItemTitle {
text-decoration: underline;
cursor: pointer;
- -webkit-user-select: none;
- -moz-user-select: none;
- -khtml-user-select: none;
}
.historyItemTitle:hover {
text-decoration: underline;
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/4b4ea9952336/
changeset: 4b4ea9952336
user: jgoecks
date: 2012-12-14 19:10:39
summary: Remove deprecated parameters from Tophat2 wrapper.
affected #: 2 files
diff -r 52ecc79edd361051da70e81d63cb670a3a265dc7 -r 4b4ea995233684e49259a8126257a2d226b8a026 tools/ngs_rna/tophat2_wrapper.py
--- a/tools/ngs_rna/tophat2_wrapper.py
+++ b/tools/ngs_rna/tophat2_wrapper.py
@@ -20,8 +20,6 @@
where each end is 50bp, you should set -r to be 200. There is no default, \
and this parameter is required for paired end runs.')
parser.add_option( '', '--mate-std-dev', dest='mate_std_dev', help='Standard deviation of distribution on inner distances between male pairs.' )
- parser.add_option( '-n', '--transcriptome-mismatches', dest='transcriptome_mismatches' )
- parser.add_option( '', '--genome-read-mismatches', dest='genome_read_mismatches' )
parser.add_option( '', '--read-mismatches', dest='read_mismatches' )
parser.add_option( '', '--bowtie-n', action="store_true", dest='bowtie_n' )
parser.add_option( '', '--report-discordant-pair-alignments', action="store_true", dest='report_discordant_pairs' )
@@ -171,10 +169,6 @@
# need to warn user of this fact
#sys.stdout.write( "Max insertion length and max deletion length options don't work in Tophat v1.2.0\n" )
- if options.transcriptome_mismatches:
- opts += ' --transcriptome-mismatches %i' % int( options.transcriptome_mismatches )
- if options.genome_read_mismatches:
- opts += ' --genome-read-mismatches %i' % int( options.genome_read_mismatches )
if options.read_mismatches:
opts += ' --read-mismatches %i' % int( options.read_mismatches )
if options.bowtie_n:
diff -r 52ecc79edd361051da70e81d63cb670a3a265dc7 -r 4b4ea995233684e49259a8126257a2d226b8a026 tools/ngs_rna/tophat2_wrapper.xml
--- a/tools/ngs_rna/tophat2_wrapper.xml
+++ b/tools/ngs_rna/tophat2_wrapper.xml
@@ -45,8 +45,6 @@
## Set params.
--settings=$params.settingsType
#if $params.settingsType == "full":
- -n $params.transcriptome_mismatches
- --genome-read-mismatches $params.genome_read_mismatches
--read-mismatches $params.read_mismatches
#if str($params.bowtie_n) == "Yes":
--bowtie-n
@@ -167,8 +165,6 @@
<option value="fr-firststrand">FR First Strand</option><option value="fr-secondstrand">FR Second Strand</option></param>
- <param name="transcriptome_mismatches" type="integer" value="2" label="Transcriptome mismatches" help="Maximum number of mismatches allowed when reads are aligned to the transcriptome. When Bowtie2 is used, this number is also used to decide whether or not to further re-align some of the transcriptome-mapped reads to the genome. If the alignment score of the best alignment among multiple candidates for a read is lower than 'bowtie2-min-score', which is internally defined as (max_penalty - 1) * max_mismatches, then the reads will be kept for re-alignment through the rest of the pipeline. You can specify max_penalty via '--b2-mp' option." />
- <param name="genome_read_mismatches" type="integer" value="2" label="Genome read mismatches" help="When whole reads are first mapped on the genome, this many mismatches in each read alignment are allowed. The default is 2. This number is also used to decide whether to further re-align some of the reads (by splitting them into segments) with a similar scoring threshold scheme as described for the --transcriptome-mismatches option above." /><param name="read_mismatches" type="integer" value="2" label="Final read mismatches" help="Final read alignments having more than these many mismatches are discarded." /><param name="bowtie_n" type="select" label="Use bowtie -n mode"><option selected="true" value="No">No</option>
@@ -425,8 +421,6 @@
<param name="ownFile" value="tophat_in1.fasta"/><param name="settingsType" value="full"/><param name="library_type" value="FR Unstranded"/>
- <param name="transcriptome_mismatches" value="2"/>
- <param name="genome_read_mismatches" value="2"/><param name="read_mismatches" value="2"/><param name="bowtie_n" value="No"/><param name="anchor_length" value="8"/>
@@ -478,8 +472,6 @@
<param name="mate_inner_distance" value="20"/><param name="settingsType" value="full"/><param name="library_type" value="FR Unstranded"/>
- <param name="transcriptome_mismatches" value="3"/>
- <param name="genome_read_mismatches" value="4"/><param name="read_mismatches" value="5"/><param name="bowtie_n" value="Yes"/><param name="mate_std_dev" value="20"/>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/4929a37823b5/
changeset: 4929a37823b5
user: carlfeberhard
date: 2012-12-14 17:05:43
summary: api/histories, show: remove get_api_value for each dataset in get_dataset_state_summaries
affected #: 1 file
diff -r 742aac57ec941aa89ac7ca07548bf531127bc31b -r 4929a37823b5454178bf811b6b65f2216c7ac4c3 lib/galaxy/webapps/galaxy/api/histories.py
--- a/lib/galaxy/webapps/galaxy/api/histories.py
+++ b/lib/galaxy/webapps/galaxy/api/histories.py
@@ -75,14 +75,10 @@
# cycle through datasets saving each ds' state
for dataset in datasets:
- dataset_dict = dataset.get_api_value( view='element' )
- item_state = dataset_dict[ 'state' ]
-
- if not dataset_dict['deleted']:
+ item_state = dataset.state
+ if not dataset.deleted:
state_counts[ item_state ] = state_counts[ item_state ] + 1
-
- state_ids[ item_state ].append( trans.security.encode_id( dataset_dict[ 'id' ] ) )
-
+ state_ids[ item_state ].append( trans.security.encode_id( dataset.id ) )
return ( state_counts, state_ids )
# try to load the history, by most_recently_used or the given id
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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