galaxy-commits April 2011

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commit/galaxy-central: dan: Bug fix for 5454:2379785017d7
by Bitbucket 25 Apr '11

25 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/459cb941107e/ changeset: r5456:459cb941107e user: dan date: 2011-04-25 23:21:21 summary: Bug fix for 5454:2379785017d7 affected #: 1 file (0 bytes) --- a/lib/galaxy/tools/parameters/dynamic_options.py Mon Apr 25 15:30:21 2011 -0400 +++ b/lib/galaxy/tools/parameters/dynamic_options.py Mon Apr 25 17:21:21 2011 -0400 @@ -332,7 +332,7 @@ value = other_values.get( self.ref_name ) else: data_ref = other_values.get( self.meta_ref ) - if not isinstance( data.ref, self.dynamic_option.tool_param.tool.app.model.HistoryDatasetAssociation ) and not ( isinstance( data.ref, galaxy.tools.DatasetFilenameWrapper ) ): + if not isinstance( data_ref, self.dynamic_option.tool_param.tool.app.model.HistoryDatasetAssociation ) and not ( isinstance( data_ref, galaxy.tools.DatasetFilenameWrapper ) ): return options #cannot modify options value = data_ref.metadata.get( self.metadata_key, None ) return [ ( disp_name, optval, selected ) for disp_name, optval, selected in options if not compare_value( optval, value ) ] 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.

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commit/galaxy-central: kanwei: Add MarkupSafe egg for Mako
by Bitbucket 25 Apr '11

25 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/da651a3e9a97/ changeset: r5455:da651a3e9a97 user: kanwei date: 2011-04-25 21:30:21 summary: Add MarkupSafe egg for Mako affected #: 1 file (18 bytes) --- a/eggs.ini Mon Apr 25 14:41:54 2011 -0400 +++ b/eggs.ini Mon Apr 25 15:30:21 2011 -0400 @@ -16,6 +16,7 @@ Cheetah = 2.2.2 ctypes = 1.0.2 DRMAA_python = 0.2 +MarkupSafe = 0.12 MySQL_python = 1.2.3c1 numpy = 1.3.0 pbs_python = 4.1.0 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.

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commit/galaxy-central: dan: Fix for dynamic options when referencing a DataToolParameter that has already been wrapped.
by Bitbucket 25 Apr '11

25 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/2379785017d7/ changeset: r5454:2379785017d7 user: dan date: 2011-04-25 20:41:54 summary: Fix for dynamic options when referencing a DataToolParameter that has already been wrapped. affected #: 1 file (159 bytes) --- a/lib/galaxy/tools/parameters/dynamic_options.py Mon Apr 25 11:10:45 2011 -0400 +++ b/lib/galaxy/tools/parameters/dynamic_options.py Mon Apr 25 14:41:54 2011 -0400 @@ -6,6 +6,7 @@ import operator, sys, os, logging import basic, validation from galaxy.util import string_as_bool +import galaxy.tools log = logging.getLogger(__name__) @@ -105,7 +106,7 @@ return file_value == dataset_value assert self.ref_name in other_values or ( trans is not None and trans.workflow_building_mode), "Required dependency '%s' not found in incoming values" % self.ref_name ref = other_values.get( self.ref_name, None ) - if not isinstance( ref, self.dynamic_option.tool_param.tool.app.model.HistoryDatasetAssociation ): + if not isinstance( ref, self.dynamic_option.tool_param.tool.app.model.HistoryDatasetAssociation ) and not ( isinstance( ref, galaxy.tools.DatasetFilenameWrapper ) ): return [] #not a valid dataset meta_value = ref.metadata.get( self.key, None ) if meta_value is None: #assert meta_value is not None, "Required metadata value '%s' not found in referenced dataset" % self.key @@ -331,7 +332,7 @@ value = other_values.get( self.ref_name ) else: data_ref = other_values.get( self.meta_ref ) - if not isinstance( data_ref, self.dynamic_option.tool_param.tool.app.model.HistoryDatasetAssociation ): + if not isinstance( data.ref, self.dynamic_option.tool_param.tool.app.model.HistoryDatasetAssociation ) and not ( isinstance( data.ref, galaxy.tools.DatasetFilenameWrapper ) ): return options #cannot modify options value = data_ref.metadata.get( self.metadata_key, None ) return [ ( disp_name, optval, selected ) for disp_name, optval, selected in options if not compare_value( optval, value ) ] 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.

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commit/galaxy-central: kellyv: Fix circular references between Picard and SRMA entries in data tables sample file
by Bitbucket 25 Apr '11

25 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/74c973f5a473/ changeset: r5453:74c973f5a473 user: kellyv date: 2011-04-25 17:10:45 summary: Fix circular references between Picard and SRMA entries in data tables sample file affected #: 1 file (2 bytes) --- a/tool_data_table_conf.xml.sample Fri Apr 22 19:01:12 2011 -0400 +++ b/tool_data_table_conf.xml.sample Mon Apr 25 11:10:45 2011 -0400 @@ -68,7 +68,7 @@ <table name="picard_indexes" comment_char="#"><columns>value, dbkey, name, path</columns> - <file path="tool-data/srma_index.loc" /> + <file path="tool-data/picard_index.loc" /></table><table name="srma_indexes" comment_char="#"> 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.

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commit/galaxy-central: kanwei: trackster: new gff and vcf converters for tabix
by Bitbucket 22 Apr '11

22 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/ddaa5bfc7c3d/ changeset: r5452:ddaa5bfc7c3d user: kanwei date: 2011-04-23 01:01:12 summary: trackster: new gff and vcf converters for tabix affected #: 4 files (0 bytes) 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.

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commit/galaxy-central: kanwei: Update Mako to 0.4.1
by Bitbucket 22 Apr '11

22 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/31570d16b96c/ changeset: r5451:31570d16b96c user: kanwei date: 2011-04-22 22:43:43 summary: Update Mako to 0.4.1 affected #: 1 file (0 bytes) --- a/eggs.ini Fri Apr 22 15:10:04 2011 -0400 +++ b/eggs.ini Fri Apr 22 16:43:43 2011 -0400 @@ -37,7 +37,7 @@ elementtree = 1.2.6_20050316 GeneTrack = 2.0.0_beta_1 lrucache = 0.2 -Mako = 0.2.5 +Mako = 0.4.1 nose = 0.11.1 NoseHTML = 0.4.1 NoseTestDiff = 0.1 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.

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commit/galaxy-central: jgoecks: Remove unused var from Trackster init.
by Bitbucket 22 Apr '11

22 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5959dcd2182c/ changeset: r5445:5959dcd2182c user: jgoecks date: 2011-04-22 15:10:17 summary: Remove unused var from Trackster init. affected #: 1 file (58 bytes) --- a/templates/tracks/browser.mako Thu Apr 21 18:26:36 2011 -0400 +++ b/templates/tracks/browser.mako Fri Apr 22 09:10:17 2011 -0400 @@ -69,7 +69,6 @@ chrom_url = "${h.url_for( action='chroms' )}", dataset_state_url = "${h.url_for( action='dataset_state' )}", converted_datasets_state_url = "${h.url_for( action='converted_datasets_state' )}", - filters_url = "${h.url_for( action='filters' )}", addable_track_types = { "LineTrack": LineTrack, "FeatureTrack": FeatureTrack, "ReadTrack": ReadTrack }, view; 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.

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commit/galaxy-central: richard_burhans: initial version of Webb's genome diversity tools
by Bitbucket 21 Apr '11

21 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e736f8d97c3e/ changeset: r5442:e736f8d97c3e user: richard_burhans date: 2011-04-21 23:22:27 summary: initial version of Webb's genome diversity tools affected #: 22 files (97 bytes) --- a/datatypes_conf.xml.sample Thu Apr 21 13:12:10 2011 -0400 +++ b/datatypes_conf.xml.sample Thu Apr 21 17:22:27 2011 -0400 @@ -122,6 +122,7 @@ <converter file="vcf_to_interval_index_converter.xml" target_datatype="interval_index"/><converter file="vcf_to_summary_tree_converter.xml" target_datatype="summary_tree"/></datatype> + <datatype extension="wsf" type="galaxy.datatypes.wsf:SnpFile" display_in_upload="true"/><datatype extension="velvet" type="galaxy.datatypes.assembly:Velvet" display_in_upload="false"/><datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true"><converter file="wig_to_bigwig_converter.xml" target_datatype="bigwig"/> 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.

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commit/galaxy-central: kanwei: Small UI tweaks to Show Details
by Bitbucket 20 Apr '11

20 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/501209f17baa/ changeset: r5440:501209f17baa user: kanwei date: 2011-04-20 19:59:04 summary: Small UI tweaks to Show Details affected #: 2 files (90 bytes) --- a/templates/root/history_common.mako Wed Apr 20 12:57:03 2011 -0400 +++ b/templates/root/history_common.mako Wed Apr 20 13:59:04 2011 -0400 @@ -141,7 +141,7 @@ </div> %endif - <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title="View Details" class="icon-button information show-details"></a> + <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title="View Details" class="icon-button information tooltip"></a> %if for_editing: <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a> --- a/templates/show_params.mako Wed Apr 20 12:57:03 2011 -0400 +++ b/templates/show_params.mako Wed Apr 20 13:59:04 2011 -0400 @@ -29,7 +29,6 @@ </thead><tbody><tr><td>Created:</th><td>${history.create_time.strftime("%b %d, %Y")}</td></tr> - <tr><td>Modified:</th><td>${history.update_time.strftime("%b %d, %Y")}</td></tr> ## <tr><td>Copied from another history?</td><td>${hda.source_library_dataset}</td></tr><tr><td>Filesize:</th><td>${nice_size(hda.dataset.file_size)}</td></tr><tr><td>Dbkey:</th><td>${hda.dbkey}</td></tr> 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.

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commit/galaxy-central: natefoo: Display bug with tool tags.
by Bitbucket 20 Apr '11

20 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/8eaf07a46623/ changeset: r5439:8eaf07a46623 user: natefoo date: 2011-04-20 18:57:03 summary: Display bug with tool tags. affected #: 1 file (142 bytes) --- a/templates/root/tool_menu.mako Tue Apr 19 16:20:52 2011 +0100 +++ b/templates/root/tool_menu.mako Wed Apr 20 12:57:03 2011 -0400 @@ -321,13 +321,11 @@ else: display = "none" %> - %if trans.app.config.get_bool( 'enable_tool_tags', False ): - <div id="tool-tags" style="padding-bottom: 5px; position: relative; display: ${display}; width: 100%"> + <div id="tool-search" style="padding-bottom: 5px; position: relative; display: ${display}; width: 100%"> + %if trans.app.config.get_bool( 'enable_tool_tags', False ): <b>Tags:</b> ${render_tool_tagging_elements()} - </div> - %endif - <div id="tool-search" style="padding-bottom: 5px; position: relative; display: ${display}; width: 100%"> + %endif <input type="text" name="query" value="search tools" id="tool-search-query" autocomplete="off" style="width: 100%; font-style:italic; font-size: inherit"/><img src="${h.url_for('/static/images/loading_small_white_bg.gif')}" id="search-spinner" style="display: none; position: absolute; right: 0; top: 5px;"/></div> 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.

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galaxy-commits April 2011