galaxy-commits August 2011

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commit/galaxy-central: dan: Add samtools rmdup tool.
by Bitbucket 31 Aug '11

31 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/55f8f2d8ac18/ changeset: 55f8f2d8ac18 user: dan date: 2011-08-31 22:50:58 summary: Add samtools rmdup tool. affected #: 4 files (105 bytes) --- a/tool_conf.xml.main Wed Aug 31 11:44:52 2011 -0400 +++ b/tool_conf.xml.main Wed Aug 31 16:50:58 2011 -0400 @@ -382,6 +382,7 @@ <tool file="samtools/pileup_parser.xml" /><tool file="samtools/pileup_interval.xml" /><tool file="samtools/samtools_flagstat.xml" /> + <tool file="samtools/samtools_rmdup.xml" /></section><section name="NGS: Indel Analysis" id="indel_analysis"><tool file="indels/sam_indel_filter.xml" /> --- a/tool_conf.xml.sample Wed Aug 31 11:44:52 2011 -0400 +++ b/tool_conf.xml.sample Wed Aug 31 16:50:58 2011 -0400 @@ -352,8 +352,9 @@ <tool file="samtools/pileup_parser.xml" /><tool file="samtools/pileup_interval.xml" /><tool file="samtools/samtools_flagstat.xml" /> + <tool file="samtools/samtools_rmdup.xml" /></section> - <section name="NGS: GATK Tools" id="gatk"> + <section name="NGS: GATK Tools (beta)" id="gatk"><label text="Realignment" id="gatk_realignment" /><tool file="gatk/realigner_target_creator.xml" /><tool file="gatk/indel_realigner.xml" /> --- a/tools/samtools/samtools_flagstat.xml Wed Aug 31 11:44:52 2011 -0400 +++ b/tools/samtools/samtools_flagstat.xml Wed Aug 31 16:50:58 2011 -0400 @@ -3,7 +3,7 @@ <requirement type="package">samtools</requirement></requirements><description>provides simple stats on BAM files</description> - <command>samtools flagstat $input1 > $output1 + <command>samtools flagstat "$input1" > "$output1" </command><inputs><param name="input1" type="data" format="bam" label="BAM File to Convert" /> 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: Trackster: add mode parameter to draw_tile and use to support better overview drawing.
by Bitbucket 31 Aug '11

31 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/52e6f9a13e34/ changeset: 52e6f9a13e34 user: jgoecks date: 2011-08-31 17:44:52 summary: Trackster: add mode parameter to draw_tile and use to support better overview drawing. affected #: 1 file (38 bytes) --- a/static/scripts/trackster.js Tue Aug 30 16:56:52 2011 -0400 +++ b/static/scripts/trackster.js Wed Aug 31 11:44:52 2011 -0400 @@ -2240,7 +2240,7 @@ // Draw tile if necessary. if (!tile) { - tile = track.draw_tile(overview_data, resolution, 0, w_scale); + tile = track.draw_tile(overview_data, "Auto", resolution, 0, w_scale); track.tile_cache.set(key, tile); } @@ -2395,7 +2395,7 @@ // If we can draw now, do so if ( can_draw_now ) { extend( tile_data, more_tile_data ); - var tile = track.draw_tile(tile_data, resolution, tile_index, w_scale, seq_data); + var tile = track.draw_tile(tile_data, track.mode, resolution, tile_index, w_scale, seq_data); track.tile_cache.set(key, tile); // Don't show if no tile if (tile !== undefined) { @@ -2558,7 +2558,7 @@ /** * Draw ReferenceTrack tile. */ - draw_tile: function(seq, resolution, tile_index, w_scale) { + draw_tile: function(seq, mode, resolution, tile_index, w_scale) { var track = this, tile_length = DENSITY * resolution; @@ -2696,7 +2696,7 @@ /** * Draw LineTrack tile. */ - draw_tile: function(result, resolution, tile_index, w_scale) { + draw_tile: function(result, mode, resolution, tile_index, w_scale) { if (this.vertical_range === undefined) { return; } @@ -2713,7 +2713,7 @@ // Paint line onto full canvas var ctx = canvas.getContext("2d"); - var painter = new painters.LinePainter(result.data, tile_low, tile_low + tile_length, this.prefs, this.mode); + var painter = new painters.LinePainter(result.data, tile_low, tile_low + tile_length, this.prefs, mode); painter.draw(ctx, width, height); return new Tile(tile_index, resolution, canvas, result.data); @@ -2968,18 +2968,18 @@ /** * Draw FeatureTrack tile. * @param result result from server + * @param mode mode to draw in * @param resolution view resolution * @param tile_index index of tile to be drawn * @param w_scale base pairs per pixel * @param ref_seq reference sequence data */ - draw_tile: function(result, resolution, tile_index, w_scale, ref_seq) { + draw_tile: function(result, mode, resolution, tile_index, w_scale, ref_seq) { var track = this, tile_low = tile_index * DENSITY * resolution, tile_high = (tile_index + 1) * DENSITY * resolution, tile_span = tile_high - tile_low, width = Math.ceil(tile_span * w_scale), - mode = this.mode, min_height = 25, left_offset = this.left_offset, slots, 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: Add basic VCF4.1 support.
by Bitbucket 30 Aug '11

30 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/de06e2e6cc7f/ changeset: de06e2e6cc7f user: dan date: 2011-08-30 22:56:52 summary: Add basic VCF4.1 support. affected #: 1 file (78 bytes) --- a/lib/galaxy_utils/sequence/vcf.py Tue Aug 30 15:52:10 2011 -0400 +++ b/lib/galaxy_utils/sequence/vcf.py Tue Aug 30 16:56:52 2011 -0400 @@ -55,9 +55,12 @@ def __init__( self, vcf_line, metadata, sample_names ): VariantCall33.__init__( self, vcf_line, metadata, sample_names) +class VariantCall41( VariantCall40 ): + version = 'VCFv4.1' + #VCF Format version lookup dict VCF_FORMATS = {} -for format in [ VariantCall33, VariantCall40 ]: +for format in [ VariantCall33, VariantCall40, VariantCall41 ]: VCF_FORMATS[format.version] = format class Reader( object ): 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: Update FIMO test datasets.
by Bitbucket 30 Aug '11

30 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/95c6e622b350/ changeset: 95c6e622b350 user: dan date: 2011-08-30 21:52:10 summary: Update FIMO test datasets. affected #: 5 files (174.7 KB) Diff too large to display. 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: Add SICER to tool_conf.xml.main.
by Bitbucket 30 Aug '11

30 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5d2a2ac4710f/ changeset: 5d2a2ac4710f user: dan date: 2011-08-30 16:02:17 summary: Add SICER to tool_conf.xml.main. affected #: 1 file (50 bytes) --- a/tool_conf.xml.main Tue Aug 30 09:33:10 2011 -0400 +++ b/tool_conf.xml.main Tue Aug 30 10:02:17 2011 -0400 @@ -390,6 +390,7 @@ </section><section name="NGS: Peak Calling" id="peak_calling"><tool file="peak_calling/macs_wrapper.xml" /> + <tool file="peak_calling/sicer_wrapper.xml" /><tool file="genetrack/genetrack_indexer.xml" /><tool file="genetrack/genetrack_peak_prediction.xml" /></section> 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: Update for wavelet variance tool contributed by Erika Kvikstad.
by Bitbucket 30 Aug '11

30 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/cddcdadea10d/ changeset: cddcdadea10d user: dan date: 2011-08-30 15:33:10 summary: Update for wavelet variance tool contributed by Erika Kvikstad. affected #: 1 file (72 bytes) --- a/tools/discreteWavelet/execute_dwt_var_perFeature.pl Mon Aug 29 14:42:04 2011 -0400 +++ b/tools/discreteWavelet/execute_dwt_var_perFeature.pl Tue Aug 30 09:33:10 2011 -0400 @@ -41,10 +41,10 @@ #library(\"wavethresh\"); #library(\"waveslim\"); # turn off diagnostics for de-bugging only, turn back on for functional tests on test - require(\"Rwave\",quietly=TRUE,warn.conflicts = FALSE); - require(\"wavethresh\",quietly=TRUE,warn.conflicts = FALSE); - require(\"waveslim\",quietly=TRUE,warn.conflicts = FALSE); - require(\"bitops\",quietly=TRUE,warn.conflicts = FALSE); + suppressMessages(require(\"Rwave\",quietly=TRUE,warn.conflicts = FALSE)); + suppressMessages(require(\"wavethresh\",quietly=TRUE,warn.conflicts = FALSE)); + suppressMessages(require(\"waveslim\",quietly=TRUE,warn.conflicts = FALSE)); + suppressMessages(require(\"bitops\",quietly=TRUE,warn.conflicts = FALSE)); # to determine if data is properly formatted 2^N observations is.power2<- function(x){x && !(bitAnd(x,x - 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: natefoo: Missing import in library_contents.py
by Bitbucket 29 Aug '11

29 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/949e4f5fa03a/ changeset: 949e4f5fa03a user: natefoo date: 2011-08-29 20:42:04 summary: Missing import in library_contents.py affected #: 2 files (77 bytes) --- a/lib/galaxy/web/api/library_contents.py Mon Aug 29 11:29:31 2011 -0400 +++ b/lib/galaxy/web/api/library_contents.py Mon Aug 29 14:42:04 2011 -0400 @@ -7,6 +7,7 @@ from galaxy.web.base.controller import * from galaxy.util.sanitize_html import sanitize_html from galaxy.model.orm import * +from galaxy.web.api.util import * log = logging.getLogger( __name__ ) --- a/scripts/api/common.py Mon Aug 29 11:29:31 2011 -0400 +++ b/scripts/api/common.py Mon Aug 29 14:42:04 2011 -0400 @@ -88,6 +88,8 @@ print '------------------' for k, v in r.items(): print '%s: %s' % ( k, v ) + elif type( r ) == str: + print r else: print 'response is unknown type: %s' % type( r ) 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: greg: Add a guid to tool shed repository tool metadata and add some fixes for previewing tool shed repository tools.
by Bitbucket 29 Aug '11

29 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e08716dfa2d5/ changeset: e08716dfa2d5 user: greg date: 2011-08-29 17:29:31 summary: Add a guid to tool shed repository tool metadata and add some fixes for previewing tool shed repository tools. affected #: 5 files (1.6 KB) --- a/lib/galaxy/webapps/community/app.py Mon Aug 29 11:22:54 2011 -0400 +++ b/lib/galaxy/webapps/community/app.py Mon Aug 29 11:29:31 2011 -0400 @@ -13,6 +13,8 @@ self.config = config.Configuration( **kwargs ) self.config.check() config.configure_logging( self.config ) + # Set up datatypes registry + self.datatypes_registry = galaxy.datatypes.registry.Registry( self.config.root, self.config.datatypes_config ) # Determine the database url if self.config.database_connection: db_url = self.config.database_connection --- a/lib/galaxy/webapps/community/config.py Mon Aug 29 11:22:54 2011 -0400 +++ b/lib/galaxy/webapps/community/config.py Mon Aug 29 11:29:31 2011 -0400 @@ -39,11 +39,21 @@ self.file_path = resolve_path( kwargs.get( "file_path", "database/files" ), self.root ) self.new_file_path = resolve_path( kwargs.get( "new_file_path", "database/tmp" ), self.root ) self.cookie_path = kwargs.get( "cookie_path", "/" ) + self.datatypes_config = kwargs.get( 'datatypes_config_file', 'datatypes_conf.xml' ) self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root ) self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" ) + # Tool stuff self.tool_secret = kwargs.get( "tool_secret", "" ) self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "tool-data" ), os.getcwd() ) self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root ) + self.ftp_upload_dir = kwargs.get( 'ftp_upload_dir', None ) + # Location for dependencies + if 'tool_dependency_dir' in kwargs: + self.tool_dependency_dir = resolve_path( kwargs.get( "tool_dependency_dir" ), self.root ) + self.use_tool_dependencies = True + else: + self.tool_dependency_dir = None + self.use_tool_dependencies = False self.use_remote_user = string_as_bool( kwargs.get( "use_remote_user", "False" ) ) self.remote_user_maildomain = kwargs.get( "remote_user_maildomain", None ) self.remote_user_logout_href = kwargs.get( "remote_user_logout_href", None ) --- a/lib/galaxy/webapps/community/controllers/common.py Mon Aug 29 11:22:54 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Mon Aug 29 11:29:31 2011 -0400 @@ -145,11 +145,22 @@ # The received metadata_dict includes no metadata for workflows, so a new repository_metadata table # record is not needed. return False +def generate_tool_guid( trans, repository, tool ): + """ + Generate a guid for the received tool. The form of the guid is + <tool shed host>/repos/<tool shed username>/<tool shed repo name>/<tool id>/<tool version> + """ + return '%s/repos/%s/%s/%s/%s' % ( trans.request.host, + repository.user.username, + repository.name, + tool.id, + tool.version ) def generate_tool_metadata( trans, id, changeset_revision, root, name, tool, metadata_dict ): """ Update the received metadata_dict with changes that have been applied to the received tool. """ + repository = get_repository( trans, id ) tool_requirements = [] for tr in tool.requirements: requirement_dict = dict( name=tr.name, @@ -165,6 +176,7 @@ outputs=ttb.outputs ) tool_tests.append( test_dict ) tool_dict = dict( id=tool.id, + guid = generate_tool_guid( trans, repository, tool ), name=tool.name, version=tool.version, description=tool.description, --- a/templates/webapps/community/repository/tool_form.mako Mon Aug 29 11:22:54 2011 -0400 +++ b/templates/webapps/community/repository/tool_form.mako Mon Aug 29 11:29:31 2011 -0400 @@ -4,7 +4,7 @@ <% from galaxy.util.expressions import ExpressionContext from galaxy import util - from galaxy.tools.parameters.basic import DataToolParameter, ColumnListParameter, SelectToolParameter + from galaxy.tools.parameters.basic import DataToolParameter, ColumnListParameter, GenomeBuildParameter, SelectToolParameter from galaxy.web.form_builder import SelectField is_admin = trans.user_is_admin() @@ -60,8 +60,8 @@ %endif %elif input.type == "upload_dataset": %if input.get_datatype( trans, other_values ).composite_type is None: - # Have non-composite upload appear as before - ${do_inputs( input.inputs, tool_state[input.name][0], prefix + input.name + "_" + str( 0 ) + "|", other_values )} + ## Have non-composite upload appear as before + ${do_inputs( input.inputs, 'files', prefix + input.name + "_" + str( 0 ) + "|", other_values )} %else: <div class="repeat-group"><div class="form-title-row"> @@ -82,7 +82,7 @@ <%def name="row_for_param( prefix, param, parent_state, other_values )"><% label = param.get_label() - if isinstance( param, DataToolParameter ) or isinstance( param, ColumnListParameter ): + if isinstance( param, DataToolParameter ) or isinstance( param, ColumnListParameter ) or isinstance( param, GenomeBuildParameter ): field = SelectField( param.name ) field.add_option( param.name, param.name ) field_html = field.get_html() --- a/templates/webapps/community/repository/view_tool_metadata.mako Mon Aug 29 11:22:54 2011 -0400 +++ b/templates/webapps/community/repository/view_tool_metadata.mako Mon Aug 29 11:29:31 2011 -0400 @@ -137,6 +137,13 @@ <div style="clear: both"></div></div> %endif + %if 'guid' in metadata: + <div class="form-row"> + <label>Guid:</label> + ${metadata[ 'guid' ]} + <div style="clear: both"></div> + </div> + %endif %if 'version' in metadata: <div class="form-row"><label>Version:</label> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Add wavelet variance tool contributed by Erika Kvikstad.
by Bitbucket 29 Aug '11

29 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c8d224f51d7e/ changeset: c8d224f51d7e user: dan date: 2011-08-29 17:22:54 summary: Add wavelet variance tool contributed by Erika Kvikstad. affected #: 6 files (80 bytes) --- a/tool_conf.xml.sample Mon Aug 29 10:57:08 2011 -0400 +++ b/tool_conf.xml.sample Mon Aug 29 11:22:54 2011 -0400 @@ -146,15 +146,16 @@ <label text="GFF" id="gff" /><tool file="stats/count_gff_features.xml" /></section> - </section> - --><section name="Graph/Display Data" id="plots"><tool file="plotting/histogram2.xml" /><tool file="plotting/scatterplot.xml" /> 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: Properly handle error conditions in library_common.upload_dataset when uploading via the API.
by Bitbucket 29 Aug '11

29 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/832538ba7258/ changeset: 832538ba7258 user: natefoo date: 2011-08-29 16:57:08 summary: Properly handle error conditions in library_common.upload_dataset when uploading via the API. affected #: 1 file (152 bytes) --- a/lib/galaxy/web/controllers/library_common.py Mon Aug 29 09:32:26 2011 -0400 +++ b/lib/galaxy/web/controllers/library_common.py Mon Aug 29 10:57:08 2011 -0400 @@ -852,6 +852,8 @@ # created_outputs_dict can be a string only if cntrller == 'api' if type( created_outputs_dict ) == str: return 400, created_outputs_dict + elif type( created_outputs_dict ) == tuple: + return created_outputs_dict[0], created_outputs_dict[1] return 200, created_outputs_dict total_added = len( created_outputs_dict.keys() ) ldda_id_list = [ str( v.id ) for k, v in created_outputs_dict.items() ] 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 August 2011