1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/0d6653d29222/
changeset: 0d6653d29222
user: inithello
date: 2012-12-18 21:31:46
summary: Fix for reinstalling repository with tool dependencies when tool_dependency_dir is not set.
affected #: 1 file
diff -r 829ee499d6953c1b6efb957d93918b4d3f3ac1a4 -r 0d6653d29222880e3ade27bd055569ccebc7234e lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -1511,6 +1511,7 @@
@web.expose
@web.require_admin
def reselect_tool_panel_section( self, trans, **kwd ):
+ message = ''
repository_id = kwd[ 'id' ]
tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id )
metadata = tool_shed_repository.metadata
@@ -1551,14 +1552,14 @@
tool_panel_section_select_field = build_tool_panel_section_select_field( trans )
no_changes_check_box = CheckboxField( 'no_changes', checked=True )
if original_section_name:
- message = "The tools contained in your <b>%s</b> repository were last loaded into the tool panel section <b>%s</b>. " \
+ message += "The tools contained in your <b>%s</b> repository were last loaded into the tool panel section <b>%s</b>. " \
% ( tool_shed_repository.name, original_section_name )
message += "Uncheck the <b>No changes</b> check box and select a different tool panel section to load the tools in a "
- message += "different section in the tool panel."
+ message += "different section in the tool panel. "
status = 'warning'
else:
- message = "The tools contained in your <b>%s</b> repository were last loaded into the tool panel outside of any sections. " % tool_shed_repository.name
- message += "Uncheck the <b>No changes</b> check box and select a tool panel section to load the tools into that section."
+ message += "The tools contained in your <b>%s</b> repository were last loaded into the tool panel outside of any sections. " % tool_shed_repository.name
+ message += "Uncheck the <b>No changes</b> check box and select a tool panel section to load the tools into that section. "
status = 'warning'
if metadata and 'readme_files' in metadata:
url = suc.url_join( tool_shed_url,
@@ -1582,9 +1583,9 @@
install_repository_dependencies_check_box = CheckboxField( 'install_repository_dependencies', checked=True )
# Handle tool dependencies check box.
if trans.app.config.tool_dependency_dir is None:
- if includes_tool_dependencies:
- message = "Tool dependencies defined in this repository can be automatically installed if you set the value of your <b>tool_dependency_dir</b> "
- message += "setting in your Galaxy config file (universe_wsgi.ini) and restart your Galaxy server before installing the repository."
+ if tool_shed_repository.includes_tool_dependencies:
+ message += "Tool dependencies defined in this repository can be automatically installed if you set the value of your <b>tool_dependency_dir</b> "
+ message += "setting in your Galaxy config file (universe_wsgi.ini) and restart your Galaxy server before installing the repository. "
status = "warning"
install_tool_dependencies_check_box_checked = False
else:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/454638eb2434/
changeset: 454638eb2434
user: carlfeberhard
date: 2012-12-18 19:53:55
summary: history panel: fix to js behaviors on late-rendered hda bodies
affected #: 2 files
diff -r c961f5647673a8cbe5f0f7275b82513e2067afc9 -r 454638eb2434c827350b2c8dadbc04760ffa11b6 static/scripts/mvc/dataset/hda-base.js
--- a/static/scripts/mvc/dataset/hda-base.js
+++ b/static/scripts/mvc/dataset/hda-base.js
@@ -78,16 +78,12 @@
itemWrapper.append( this._render_warnings() );
itemWrapper.append( this._render_titleBar() );
+ //NOTE: only sets behaviors on title and warnings - body will set up it's own
+ this._setUpBehaviors( itemWrapper );
+
this.body = $( this._render_body() );
itemWrapper.append( this.body );
- //TODO: move to own function: setUpBehaviours
- // we can potentially skip this step and call popupmenu directly on the download button
- make_popup_menus( itemWrapper );
-
- // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.)
- itemWrapper.find( '.tooltip' ).tooltip({ placement : 'bottom' });
-
// transition...
this.$el.fadeOut( 'fast', function(){
view.$el.children().remove();
@@ -155,6 +151,17 @@
});
},
+ /** set up js behaviors, event handlers for elements within the given container
+ * @param {jQuery} $container jq object that contains the elements to process (defaults to this.$el)
+ */
+ _setUpBehaviors : function( $container ){
+ $container = $container || this.$el;
+ // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.)
+ //TODO: we can potentially skip this step and call popupmenu directly on the download button
+ make_popup_menus( $container );
+ $container.find( '.tooltip' ).tooltip({ placement : 'bottom' });
+ },
+
// ................................................................................ RENDER titlebar
/** Render any hda warnings including: is deleted, is purged, is hidden.
* (including links to further actions (undelete, etc.))
@@ -389,6 +396,7 @@
body.append( $( '<div>Error: unknown dataset state "' + this.model.get( 'state' ) + '".</div>' ) );
}
body.append( '<div style="clear: both"></div>' );
+ this._setUpBehaviors( body );
},
/** Render inaccessible, not-owned by curr user.
diff -r c961f5647673a8cbe5f0f7275b82513e2067afc9 -r 454638eb2434c827350b2c8dadbc04760ffa11b6 static/scripts/mvc/dataset/hda-model.js
--- a/static/scripts/mvc/dataset/hda-model.js
+++ b/static/scripts/mvc/dataset/hda-model.js
@@ -220,7 +220,15 @@
* @returns array of encoded ids
*/
ids : function(){
- return this.map( function( item ){ return item.id; });
+ return this.map( function( hda ){ return hda.id; });
+ },
+
+ /** Get the hda with the given hid
+ * @param {Int} hid the hid to search for
+ * @returns {HistoryDatasetAssociation} the hda with the given hid or undefined if not found
+ */
+ getByHid : function( hid ){
+ return _.first( this.filter( function( hda ){ return hda.get( 'hid' ) === hid; }) );
},
/** If the given hid is in the collection, return it's index. If not, return the insertion point it would need.
https://bitbucket.org/galaxy/galaxy-central/changeset/eb3962726462/
changeset: eb3962726462
user: carlfeberhard
date: 2012-12-18 20:37:54
summary: merge staging:454638eb2434 to central
affected #: 2 files
diff -r 715063d652abc9dc3197617012763284143e7ab2 -r eb39627264622db4805927d0d0f35972067a58b7 static/scripts/mvc/dataset/hda-base.js
--- a/static/scripts/mvc/dataset/hda-base.js
+++ b/static/scripts/mvc/dataset/hda-base.js
@@ -78,16 +78,12 @@
itemWrapper.append( this._render_warnings() );
itemWrapper.append( this._render_titleBar() );
+ //NOTE: only sets behaviors on title and warnings - body will set up it's own
+ this._setUpBehaviors( itemWrapper );
+
this.body = $( this._render_body() );
itemWrapper.append( this.body );
- //TODO: move to own function: setUpBehaviours
- // we can potentially skip this step and call popupmenu directly on the download button
- make_popup_menus( itemWrapper );
-
- // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.)
- itemWrapper.find( '.tooltip' ).tooltip({ placement : 'bottom' });
-
// transition...
this.$el.fadeOut( 'fast', function(){
view.$el.children().remove();
@@ -155,6 +151,17 @@
});
},
+ /** set up js behaviors, event handlers for elements within the given container
+ * @param {jQuery} $container jq object that contains the elements to process (defaults to this.$el)
+ */
+ _setUpBehaviors : function( $container ){
+ $container = $container || this.$el;
+ // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.)
+ //TODO: we can potentially skip this step and call popupmenu directly on the download button
+ make_popup_menus( $container );
+ $container.find( '.tooltip' ).tooltip({ placement : 'bottom' });
+ },
+
// ................................................................................ RENDER titlebar
/** Render any hda warnings including: is deleted, is purged, is hidden.
* (including links to further actions (undelete, etc.))
@@ -389,6 +396,7 @@
body.append( $( '<div>Error: unknown dataset state "' + this.model.get( 'state' ) + '".</div>' ) );
}
body.append( '<div style="clear: both"></div>' );
+ this._setUpBehaviors( body );
},
/** Render inaccessible, not-owned by curr user.
diff -r 715063d652abc9dc3197617012763284143e7ab2 -r eb39627264622db4805927d0d0f35972067a58b7 static/scripts/mvc/dataset/hda-model.js
--- a/static/scripts/mvc/dataset/hda-model.js
+++ b/static/scripts/mvc/dataset/hda-model.js
@@ -220,7 +220,15 @@
* @returns array of encoded ids
*/
ids : function(){
- return this.map( function( item ){ return item.id; });
+ return this.map( function( hda ){ return hda.id; });
+ },
+
+ /** Get the hda with the given hid
+ * @param {Int} hid the hid to search for
+ * @returns {HistoryDatasetAssociation} the hda with the given hid or undefined if not found
+ */
+ getByHid : function( hid ){
+ return _.first( this.filter( function( hda ){ return hda.get( 'hid' ) === hid; }) );
},
/** If the given hid is in the collection, return it's index. If not, return the insertion point it would need.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/29957b479e5d/
changeset: 29957b479e5d
user: jgoecks
date: 2012-12-18 19:35:56
summary: Bowtie2 wrapper: move read group parameters out of full parameter settings and into own group.
affected #: 1 file
diff -r e6030730bb85b532534f7229c79751efadcd1eb7 -r 29957b479e5d1e376a2b47dfdf7bd76dcd980fc6 tools/sr_mapping/bowtie2_wrapper.xml
--- a/tools/sr_mapping/bowtie2_wrapper.xml
+++ b/tools/sr_mapping/bowtie2_wrapper.xml
@@ -46,11 +46,11 @@
#end if
## Read group information.
- #if $params.readGroup.specReadGroup == "yes"
- --rgid="$params.readGroup.rgid"
- --rglb="$params.readGroup.rglb"
- --rgpl="$params.readGroup.rgpl"
- --rgsm="$params.readGroup.rgsm"
+ #if $readGroup.specReadGroup == "yes"
+ --rgid="$readGroup.rgid"
+ --rglb="$readGroup.rglb"
+ --rgpl="$readGroup.rgpl"
+ --rgsm="$readGroup.rgsm"
#end if
</command><inputs>
@@ -114,21 +114,21 @@
</when><when value="No" /></conditional>
- <conditional name="readGroup">
- <param name="specReadGroup" type="select" label="Specify the read group for this file?">
- <option value="yes">Yes</option>
- <option value="no" selected="True">No</option>
- </param>
- <when value="yes">
- <param name="rgid" type="text" size="25" label="Read group identifier (ID). Each @RG line must have a unique ID. The value of ID is used in the RG tags of alignment records. Must be unique among all read groups in header section." help="Required if RG specified. Read group IDs may be modified when merging SAM files in order to handle collisions." />
- <param name="rglb" type="text" size="25" label="Library name (LB)" help="Required if RG specified" />
- <param name="rgpl" type="text" size="25" label="Platform/technology used to produce the reads (PL)" help="Required if RG specified. Valid values : CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT and PACBIO" />
- <param name="rgsm" type="text" size="25" label="Sample (SM)" help="Required if RG specified. Use pool name where a pool is being sequenced" />
- </when>
- <when value="no" />
- </conditional></when><!-- full --></conditional><!-- params -->
+ <conditional name="readGroup">
+ <param name="specReadGroup" type="select" label="Specify the read group for this file?">
+ <option value="yes">Yes</option>
+ <option value="no" selected="True">No</option>
+ </param>
+ <when value="yes">
+ <param name="rgid" type="text" size="25" label="Read group identifier (ID). Each @RG line must have a unique ID. The value of ID is used in the RG tags of alignment records. Must be unique among all read groups in header section." help="Required if RG specified. Read group IDs may be modified when merging SAM files in order to handle collisions." />
+ <param name="rglb" type="text" size="25" label="Library name (LB)" help="Required if RG specified" />
+ <param name="rgpl" type="text" size="25" label="Platform/technology used to produce the reads (PL)" help="Required if RG specified. Valid values : CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT and PACBIO" />
+ <param name="rgsm" type="text" size="25" label="Sample (SM)" help="Required if RG specified. Use pool name where a pool is being sequenced" />
+ </when>
+ <when value="no" />
+ </conditional><!-- readGroup --></inputs><outputs>
https://bitbucket.org/galaxy/galaxy-central/changeset/715063d652ab/
changeset: 715063d652ab
user: jgoecks
date: 2012-12-18 20:02:12
summary: Add simple read group options to Tophat2 wrapper.
affected #: 2 files
diff -r 29957b479e5d1e376a2b47dfdf7bd76dcd980fc6 -r 715063d652abc9dc3197617012763284143e7ab2 tools/ngs_rna/tophat2_wrapper.py
--- a/tools/ngs_rna/tophat2_wrapper.py
+++ b/tools/ngs_rna/tophat2_wrapper.py
@@ -83,6 +83,12 @@
parser.add_option( '', '--single-paired', dest='single_paired', help='' )
parser.add_option( '', '--settings', dest='settings', help='' )
+ # Read group options.
+ parser.add_option( '', '--rgid', dest='rgid', help='Read group identifier' )
+ parser.add_option( '', '--rglb', dest='rglb', help='Library name' )
+ parser.add_option( '', '--rgpl', dest='rgpl', help='Platform/technology used to produce the reads' )
+ parser.add_option( '', '--rgsm', dest='rgsm', help='Sample' )
+
(options, args) = parser.parse_args()
# Color or base space
@@ -137,6 +143,15 @@
opts += ' -r %s' % options.mate_inner_dist
if options.report_discordant_pairs:
opts += ' --report-discordant-pair-alignments'
+ # Read group options.
+ if options.rgid:
+ if not options.rglb or not options.rgpl or not options.rgsm:
+ stop_err( 'If you want to specify read groups, you must include the ID, LB, PL, and SM tags.' )
+ opts += ' --rg-id %s' % options.rgid
+ opts += ' --rg-library %s' % options.rglb
+ opts += ' --rg-platform %s' % options.rgpl
+ opts += ' --rg-sample %s' % options.rgsm
+
if options.settings == 'preSet':
cmd = cmd % ( opts, index_path, reads )
else:
diff -r 29957b479e5d1e376a2b47dfdf7bd76dcd980fc6 -r 715063d652abc9dc3197617012763284143e7ab2 tools/ngs_rna/tophat2_wrapper.xml
--- a/tools/ngs_rna/tophat2_wrapper.xml
+++ b/tools/ngs_rna/tophat2_wrapper.xml
@@ -113,6 +113,14 @@
#end if
#end if
+
+ ## Read group information.
+ #if $readGroup.specReadGroup == "yes"
+ --rgid="$readGroup.rgid"
+ --rglb="$readGroup.rglb"
+ --rgpl="$readGroup.rgpl"
+ --rgsm="$readGroup.rgsm"
+ #end if
</command><inputs><conditional name="singlePaired">
@@ -291,6 +299,19 @@
</conditional></when><!-- full --></conditional><!-- params -->
+ <conditional name="readGroup">
+ <param name="specReadGroup" type="select" label="Specify read group?">
+ <option value="yes">Yes</option>
+ <option value="no" selected="True">No</option>
+ </param>
+ <when value="yes">
+ <param name="rgid" type="text" size="25" label="Read group identifier (ID). Each @RG line must have a unique ID. The value of ID is used in the RG tags of alignment records. Must be unique among all read groups in header section." help="Required if RG specified. Read group IDs may be modified when merging SAM files in order to handle collisions." />
+ <param name="rglb" type="text" size="25" label="Library name (LB)" help="Required if RG specified" />
+ <param name="rgpl" type="text" size="25" label="Platform/technology used to produce the reads (PL)" help="Required if RG specified. Valid values : CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT and PACBIO" />
+ <param name="rgsm" type="text" size="25" label="Sample (SM)" help="Required if RG specified. Use pool name where a pool is being sequenced" />
+ </when>
+ <when value="no" />
+ </conditional><!-- readGroup --></inputs><outputs>
@@ -387,6 +408,7 @@
<param name="genomeSource" value="indexed" /><param name="index" value="tophat_test" /><param name="settingsType" value="preSet" />
+ <param name="specReadGroup" value="No" /><output name="junctions" file="tophat_out1j.bed" /><output name="accepted_hits" file="tophat_out1h.bam" compare="sim_size" /></test>
@@ -404,6 +426,7 @@
<param name="ownFile" ftype="fasta" value="tophat_in1.fasta" /><param name="mate_inner_distance" value="20" /><param name="settingsType" value="preSet" />
+ <param name="specReadGroup" value="No" /><output name="junctions" file="tophat2_out2j.bed" /><output name="accepted_hits" file="tophat_out2h.bam" compare="sim_size" /></test>
@@ -452,6 +475,7 @@
<param name="multireads" value="4" /><param name="multipairs" value="5" /><param name="ignore_chromosomes" value="chrM"/>
+ <param name="specReadGroup" value="No" /><output name="insertions" file="tophat_out3i.bed" /><output name="deletions" file="tophat_out3d.bed" /><output name="junctions" file="tophat2_out3j.bed" />
@@ -500,6 +524,7 @@
<param name="multireads" value="4" /><param name="multipairs" value="5" /><param name="ignore_chromosomes" value="chrM"/>
+ <param name="specReadGroup" value="No" /><output name="junctions" file="tophat2_out4j.bed" /><output name="accepted_hits" file="tophat_out4h.bam" compare="sim_size" /></test>
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/c961f5647673/
changeset: c961f5647673
user: inithello
date: 2012-12-18 16:50:47
summary: Removed reference to suc. in suc.
affected #: 1 file
diff -r 166303bbdd86eefc263d9947b35c65ec3847ddc9 -r c961f5647673a8cbe5f0f7275b82513e2067afc9 lib/galaxy/util/shed_util_common.py
--- a/lib/galaxy/util/shed_util_common.py
+++ b/lib/galaxy/util/shed_util_common.py
@@ -1488,7 +1488,7 @@
if shed_tool_conf == shed_tool_conf_dict[ 'config_filename' ]:
return index, shed_tool_conf_dict
else:
- file_name = suc.strip_path( shed_tool_conf_dict[ 'config_filename' ] )
+ file_name = strip_path( shed_tool_conf_dict[ 'config_filename' ] )
if shed_tool_conf == file_name:
return index, shed_tool_conf_dict
def get_tool_panel_config_tool_path_install_dir( app, repository ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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