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commit/galaxy-central: kanwei: New pysam for solaris fixes
by Bitbucket 19 Apr '11

19 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/2de8ac3adb53/ changeset: r5414:2de8ac3adb53 user: kanwei date: 2011-04-19 06:07:36 summary: New pysam for solaris fixes affected #: 1 file (0 bytes) --- a/eggs.ini Mon Apr 18 18:07:52 2011 -0400 +++ b/eggs.ini Tue Apr 19 00:07:36 2011 -0400 @@ -21,7 +21,7 @@ pbs_python = 4.1.0 psycopg2 = 2.0.13 pycrypto = 2.0.1 -pysam = 0.4.1 +pysam = 0.4.2 pysqlite = 2.5.6 python_lzo = 1.08_2.03_static simplejson = 2.1.1 @@ -69,7 +69,7 @@ bx_python = _494c2d1d68b3 GeneTrack = _dev_48da9e998f0caf01c5be731e926f4b0481f658f0 SQLAlchemy = _dev_r6498 -pysam = _kanwei_595e4f94f935 +pysam = _kanwei_6255075f4401 ; dependency source urls, necessary for scrambling. for an explanation, see ; the wiki page above 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:
by Bitbucket 19 Apr '11

19 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/fd714d78e05e/ changeset: r5413:fd714d78e05e user: kanwei date: 2011-04-19 00:07:52 summary: trackster: - Use tabix (through pysam) as the indexer for feature formats. Bed support included in this commit - Add bigBed format support (same interface as bigWig) - Improve implicit converter error handling affected #: 11 files (3.2 KB) --- a/datatypes_conf.xml.sample Mon Apr 18 17:02:32 2011 -0400 +++ b/datatypes_conf.xml.sample Mon Apr 18 18:07:52 2011 -0400 @@ -14,7 +14,8 @@ <datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true"><converter file="bed_to_gff_converter.xml" target_datatype="gff"/><converter file="interval_to_coverage.xml" target_datatype="coverage"/> - <converter file="bed_to_interval_index_converter.xml" target_datatype="interval_index"/> + <converter file="bed_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="bed_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/><converter file="bed_to_summary_tree_converter.xml" target_datatype="summary_tree"/><display file="genetrack.xml" /> @@ -131,6 +132,7 @@ <datatype extension="summary_tree" type="galaxy.datatypes.data:Data" /><datatype extension="interval_index" type="galaxy.datatypes.data:Data" /><datatype extension="tabix" type="galaxy.datatypes.data:Data" /> + <datatype extension="bgzip" type="galaxy.datatypes.data:Data" /><datatype extension="acedb" type="galaxy.datatypes.data:Text"/><datatype extension="asn1" type="galaxy.datatypes.data:Text"/> --- a/eggs.ini Mon Apr 18 17:02:32 2011 -0400 +++ b/eggs.ini Mon Apr 18 18:07:52 2011 -0400 @@ -69,7 +69,7 @@ bx_python = _494c2d1d68b3 GeneTrack = _dev_48da9e998f0caf01c5be731e926f4b0481f658f0 SQLAlchemy = _dev_r6498 -pysam = _kanwei_ae2bd50d9945 +pysam = _kanwei_595e4f94f935 ; dependency source urls, necessary for scrambling. for an explanation, see ; the wiki page above --- a/lib/galaxy/datatypes/binary.py Mon Apr 18 17:02:32 2011 -0400 +++ b/lib/galaxy/datatypes/binary.py Mon Apr 18 18:07:52 2011 -0400 @@ -288,3 +288,7 @@ Binary.__init__( self, **kwd ) self._magic = 0x8789F2EB self._name = "BigBed" + + def get_track_type( self ): + return "LineTrack", {"data_standalone": "bigbed"} + --- a/lib/galaxy/datatypes/interval.py Mon Apr 18 17:02:32 2011 -0400 +++ b/lib/galaxy/datatypes/interval.py Mon Apr 18 18:07:52 2011 -0400 @@ -533,7 +533,7 @@ except: return False def get_track_type( self ): - return "FeatureTrack", {"data": "interval_index", "index": "summary_tree"} + return "FeatureTrack", {"data": "tabix", "index": "summary_tree"} class BedStrict( Bed ): """Tab delimited data in strict BED format - no non-standard columns allowed""" --- a/lib/galaxy/model/__init__.py Mon Apr 18 17:02:32 2011 -0400 +++ b/lib/galaxy/model/__init__.py Mon Apr 18 18:07:52 2011 -0400 @@ -21,6 +21,18 @@ datatypes_registry = galaxy.datatypes.registry.Registry() #Default Value Required for unit tests +class NoConverterException(Exception): + def __init__(self, value): + self.value = value + def __str__(self): + return repr(self.value) + +class ConverterDependencyException(Exception): + def __init__(self, value): + self.value = value + def __str__(self): + return repr(self.value) + def set_datatypes_registry( d_registry ): """ Set up datatypes_registry @@ -709,15 +721,33 @@ if not assoc.deleted and assoc.type == file_type: return assoc.dataset return None + def get_converted_dataset_deps(self, trans, target_ext): + """ + Returns dict of { "dependency" => HDA } + """ + converted_dataset = self.get_converted_files_by_type( target_ext ) + # List of string of dependencies + try: + depends_list = trans.app.datatypes_registry.converter_deps[self.extension][target_ext] + except KeyError: + depends_list = [] + return dict([ (dep, self.get_converted_dataset(trans, dep)) for dep in depends_list ]) def get_converted_dataset(self, trans, target_ext): """ - Return converted dataset(s) if they exist. If not converted yet, do so and return None (the first time). - If unconvertible, raise exception. + Return converted dataset(s) if they exist, along with a dict of dependencies. + If not converted yet, do so and return None (the first time). If unconvertible, raise exception. """ # See if we can convert the dataset if target_ext not in self.get_converter_types(): raise ValueError("Conversion from '%s' to '%s' not possible", self.extension, target_ext) + deps = {} + # List of string of dependencies + try: + depends_list = trans.app.datatypes_registry.converter_deps[self.extension][target_ext] + except KeyError: + depends_list = [] + # See if converted dataset already exists converted_dataset = self.get_converted_files_by_type( target_ext ) if converted_dataset: @@ -725,20 +755,22 @@ # Conversion is possible but hasn't been done yet, run converter. # Check if we have dependencies - deps = {} + try: - fail_dependencies = False - depends_on = trans.app.datatypes_registry.converter_deps[self.extension][target_ext] - for dependency in depends_on: + for dependency in depends_list: dep_dataset = self.get_converted_dataset(trans, dependency) - if dep_dataset is None or dep_dataset.state != trans.app.model.Job.states.OK: - fail_dependencies = True - else: - deps[dependency] = dep_dataset - if fail_dependencies: - return None + if dep_dataset is None: + # None means converter is running first time + return None + elif dep_dataset.state == trans.app.model.Job.states.ERROR: + raise ConverterDependencyException("A dependency (%s) was in an error state." % dependency) + elif dep_dataset.state != trans.app.model.Job.states.OK: + # Pending + return None + + deps[dependency] = dep_dataset except ValueError: - raise ValueError("A dependency could not be converted.") + raise NoConverterException("A dependency (%s) is missing a converter." % dependency) except KeyError: pass # No deps --- a/lib/galaxy/visualization/tracks/data_providers.py Mon Apr 18 17:02:32 2011 -0400 +++ b/lib/galaxy/visualization/tracks/data_providers.py Mon Apr 18 18:07:52 2011 -0400 @@ -21,7 +21,7 @@ from galaxy.datatypes.interval import Bed, Gff, Gtf from galaxy.datatypes.util.gff_util import parse_gff_attributes -from pysam import csamtools +from pysam import csamtools, ctabix MAX_VALS = 5000 # only display first MAX_VALS features ERROR_MAX_VALS = "Only the first " + str(MAX_VALS) + " %s in this tile are displayed." @@ -45,10 +45,11 @@ """ col_name_data_attr_mapping = {} - def __init__( self, converted_dataset=None, original_dataset=None ): + def __init__( self, converted_dataset=None, original_dataset=None, dependencies=None ): """ Create basic data provider. """ self.converted_dataset = converted_dataset self.original_dataset = original_dataset + self.dependencies = dependencies def write_data_to_file( self, chrom, start, end, filename ): """ @@ -419,36 +420,27 @@ f.close() return results -class BigWigDataProvider( TracksDataProvider ): +class BBIDataProvider( TracksDataProvider ): """ - BigWig data provider for the Galaxy track browser. + BBI data provider for the Galaxy track browser. """ - def _get_dataset( self ): - if self.converted_dataset is not None: - f = open( self.converted_dataset.file_name ) - else: - f = open( self.original_dataset.file_name ) - return f - def valid_chroms( self ): # No way to return this info as of now return None def has_data( self, chrom ): - f = self._get_dataset() - bw = BigWigFile(file=f) - all_dat = bw.query(chrom, 0, 2147483647, 1) + f, bbi = self._get_dataset() + all_dat = bbi.query(chrom, 0, 2147483647, 1) f.close() return all_dat is not None def get_data( self, chrom, start, end, **kwargs ): # Bigwig has the possibility of it being a standalone bigwig file, in which case we use # original_dataset, or coming from wig->bigwig conversion in which we use converted_dataset - f = self._get_dataset() - bw = BigWigFile(file=f) + f, bbi = self._get_dataset() if 'stats' in kwargs: - all_dat = bw.query(chrom, 0, 2147483647, 1) + all_dat = bbi.query(chrom, 0, 2147483647, 1) f.close() if all_dat is None: return None @@ -464,7 +456,7 @@ if (end - start) < num_points: num_points = end - start - data = bw.query(chrom, start, end, num_points) + data = bbi.query(chrom, start, end, num_points) f.close() pos = start @@ -477,6 +469,20 @@ return result +class BigBedDataProvider( BBIDataProvider ): + def _get_dataset( self ): + # Nothing converts to bigBed so we don't consider converted dataset + f = open( self.original_dataset.file_name ) + return f, BigBedFile(file=f) + +class BigWigDataProvider (BBIDataProvider ): + def _get_dataset( self ): + if self.converted_dataset is not None: + f = open( self.converted_dataset.file_name ) + else: + f = open( self.original_dataset.file_name ) + return f, BigWigFile(file=f) + class IntervalIndexDataProvider( TracksDataProvider ): """ Interval index data provider for the Galaxy track browser. @@ -557,10 +563,25 @@ return filters +class TabixDataProvider( IntervalIndexDataProvider ): + """ + Tabix index data provider for the Galaxy track browser. + + Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ] + """ + def get_data( self, chrom, start, end, **kwargs ): + if end >= 2<<29: + end = (2<<29 - 1) # Tabix-enforced maximum start, end = int(start), int(end) - source = open( self.original_dataset.file_name ) - index = Indexes( self.converted_dataset.file_name ) + + # {'bgzip': (<galaxy.model.HistoryDatasetAssociation object at 0x85fbe90>, {})} + bgzip_fname = self.dependencies['bgzip'].file_name + + # if os.path.getsize(self.converted_dataset.file_name) == 0: + # return { 'kind': messages.ERROR, 'message': "Tabix converted size was 0, meaning the input file had invalid values." } + tabix = ctabix.Tabixfile(bgzip_fname, index_filename=self.converted_dataset.file_name) + results = [] count = 0 message = None @@ -569,7 +590,7 @@ # characters (e.g. 'chr') and see if that works. This enables the # provider to handle chrome names defined as chrXXX and as XXX. chrom = str(chrom) - if chrom not in index.indexes and chrom[3:] in index.indexes: + if chrom not in tabix.contigs and ("chr" + chrom[3:]) in tabix.contigs: chrom = chrom[3:] # @@ -581,12 +602,12 @@ # filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) ) no_detail = ( "no_detail" in kwargs ) - for start, end, offset in index.find(chrom, start, end): + + for line in tabix.fetch(reference=chrom, start=start, end=end): if count >= MAX_VALS: message = ERROR_MAX_VALS % "features" break count += 1 - source.seek( offset ) # TODO: can we use column metadata to fill out payload? # TODO: use function to set payload data if isinstance( self.original_dataset.datatype, Gff ): @@ -597,35 +618,38 @@ payload.insert( 0, offset ) elif isinstance( self.original_dataset.datatype, Bed ): # BED dataset. - payload = [ offset, start, end ] - if not no_detail: - feature = source.readline().split() - length = len(feature) - - # Simpler way to add stuff, but type casting is not done. - # Name, score, strand, thick start, thick end. - #end = min( len( feature ), 8 ) - #payload.extend( feature[ 3:end ] ) - - # Name, strand, thick start, thick end. - if length >= 4: - payload.append(feature[3]) - if length >= 6: - payload.append(feature[5]) - if length >= 8: - payload.append(int(feature[6])) - payload.append(int(feature[7])) + feature = line.split() + length = len(feature) + payload = [ feature[1]+"-"+feature[2]+":"+str(count), int(feature[1]), int(feature[2]) ] + + if no_detail: + results.append( payload ) + continue + + # Simpler way to add stuff, but type casting is not done. + # Name, score, strand, thick start, thick end. + #end = min( len( feature ), 8 ) + #payload.extend( feature[ 3:end ] ) + + # Name, strand, thick start, thick end. + if length >= 4: + payload.append(feature[3]) + if length >= 6: + payload.append(feature[5]) + if length >= 8: + payload.append(int(feature[6])) + payload.append(int(feature[7])) - # Blocks. - if length >= 12: - block_sizes = [ int(n) for n in feature[10].split(',') if n != ''] - block_starts = [ int(n) for n in feature[11].split(',') if n != '' ] - blocks = zip( block_sizes, block_starts ) - payload.append( [ ( start + block[1], start + block[1] + block[0] ) for block in blocks ] ) - - # Score (filter data) - if length >= 5 and filter_cols and filter_cols[0] == "Score": - payload.append( float(feature[4]) ) + # Blocks. + if length >= 12: + block_sizes = [ int(n) for n in feature[10].split(',') if n != ''] + block_starts = [ int(n) for n in feature[11].split(',') if n != '' ] + blocks = zip( block_sizes, block_starts ) + payload.append( [ ( int(feature[1]) + block[1], int(feature[1]) + block[1] + block[0] ) for block in blocks ] ) + + # Score (filter data) + if length >= 5 and filter_cols and filter_cols[0] == "Score": + payload.append( float(feature[4]) ) results.append( payload ) @@ -671,10 +695,12 @@ # is original dataset type. TODO: This needs to be more flexible. dataset_type_name_to_data_provider = { "array_tree": ArrayTreeDataProvider, + "tabix": TabixDataProvider, "interval_index": { "vcf": VcfDataProvider, "default" : IntervalIndexDataProvider }, "bai": BamDataProvider, "summary_tree": SummaryTreeDataProvider, - "bigwig": BigWigDataProvider + "bigwig": BigWigDataProvider, + "bigbed": BigBedDataProvider } dataset_type_to_data_provider = { --- a/lib/galaxy/web/controllers/tracks.py Mon Apr 18 17:02:32 2011 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Mon Apr 18 18:07:52 2011 -0400 @@ -14,7 +14,7 @@ from galaxy.web.framework.helpers import time_ago, grids from galaxy.util.bunch import Bunch from galaxy.datatypes.interval import Gff - +from galaxy.model import NoConverterException, ConverterDependencyException from galaxy.visualization.tracks.data_providers import * from galaxy.visualization.tracks.visual_analytics import get_tool_def, get_dataset_job @@ -458,7 +458,8 @@ # Check for data in the genome window. if data_sources.get( 'index' ): tracks_dataset_type = data_sources['index']['name'] - indexer = get_data_provider( tracks_dataset_type )( dataset.get_converted_dataset( trans, tracks_dataset_type ), dataset ) + converted_dataset = dataset.get_converted_dataset( trans, tracks_dataset_type ) + indexer = get_data_provider( tracks_dataset_type )( converted_dataset, dataset ) if not indexer.has_data( chrom ): return messages.NO_DATA valid_chroms = indexer.valid_chroms() @@ -505,7 +506,8 @@ # # Have to choose between indexer and data provider tracks_dataset_type = data_sources['index']['name'] - indexer = get_data_provider( tracks_dataset_type )( dataset.get_converted_dataset( trans, tracks_dataset_type ), dataset ) + converted_dataset = dataset.get_converted_dataset( trans, tracks_dataset_type ) + indexer = get_data_provider( tracks_dataset_type )( converted_dataset, dataset ) summary = indexer.get_summary( chrom, low, high, **kwargs ) if summary is None: return { 'dataset_type': tracks_dataset_type, 'data': None } @@ -525,7 +527,9 @@ else: tracks_dataset_type = data_sources['data']['name'] data_provider_class = get_data_provider( name=tracks_dataset_type, original_dataset=dataset ) - data_provider = data_provider_class( dataset.get_converted_dataset(trans, tracks_dataset_type), dataset ) + converted_dataset = dataset.get_converted_dataset( trans, tracks_dataset_type ) + deps = dataset.get_converted_dataset_deps( trans, tracks_dataset_type ) + data_provider = data_provider_class( converted_dataset=converted_dataset, original_dataset=dataset, dependencies=deps ) # Get and return data from data_provider. data = data_provider.get_data( chrom, low, high, **kwargs ) @@ -724,6 +728,7 @@ track_type, data_sources = input_dataset.datatype.get_track_type() data_source = data_sources[ 'data' ] converted_dataset = input_dataset.get_converted_dataset( trans, data_source ) + deps = input_dataset.get_converted_dataset_deps( trans, data_source ) # # Create new HDA for input dataset's subset. @@ -742,7 +747,8 @@ # Write subset of data to new dataset data_provider_class = get_data_provider( original_dataset=input_dataset ) data_provider = data_provider_class( original_dataset=input_dataset, - converted_dataset=converted_dataset ) + converted_dataset=converted_dataset, + deps=deps ) data_provider.write_data_to_file( chrom, low, high, new_dataset.file_name ) # TODO: size not working. @@ -828,9 +834,11 @@ # necessary. try: converted_dataset = dataset.get_converted_dataset( trans, target_type ) - except ValueError: + except NoConverterException: return messages.NO_CONVERTER - + except ConverterDependencyException, dep_error: + return { 'kind': messages.ERROR, 'message': dep_error.value } + # Check dataset state and return any messages. msg = None if converted_dataset and converted_dataset.state == model.Dataset.states.ERROR: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: kanwei: trackster: Small UI tweaks
by Bitbucket 18 Apr '11

18 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/3b4b5a2d9f10/ changeset: r5412:3b4b5a2d9f10 user: kanwei date: 2011-04-18 23:02:32 summary: trackster: Small UI tweaks affected #: 3 files (240 bytes) --- a/lib/galaxy/web/controllers/tracks.py Mon Apr 18 16:43:35 2011 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Mon Apr 18 17:02:32 2011 -0400 @@ -60,7 +60,7 @@ datasets_param = "f-history" columns = [ NameColumn( "History Name", key="name", filterable="standard" ), - grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), + grids.GridColumn( "Last Updated", key="update_time", format=time_ago, visible=False ), DbKeyPlaceholderColumn( "Dbkey", key="dbkey", model_class=model.HistoryDatasetAssociation, visible=False ) ] num_rows_per_page = 10 --- a/templates/grid_base.mako Mon Apr 18 16:43:35 2011 -0400 +++ b/templates/grid_base.mako Mon Apr 18 17:02:32 2011 -0400 @@ -631,9 +631,11 @@ } .page-link a, .inactive-link { padding: 0px 7px 0px 7px; + color: #555; } .inactive-link, .current-filter { - font-style: italic; + font-weight: bold; + color: #000; } .submit-image { background: url(${h.url_for('/static/images/fugue/magnifier-left.png')}) no-repeat right transparent; @@ -976,6 +978,9 @@ min_page = 1 %> Page: + % if min_page > 1: + <span class='page-link'><a href="${url( page=1 )}" page_num="1">1</a></span> ... + % endif %for page_index in range(min_page, max_page + 1): %if page_index == cur_page_num: <span class='page-link inactive-link' id="page-link-${page_index}">${page_index}</span> @@ -984,16 +989,14 @@ <span class='page-link' id="page-link-${page_index}"><a href="${url( args )}" page_num='${page_index}'>${page_index}</a></span> %endif %endfor - %if max_page != num_pages: + %if max_page < num_pages: ... + <span class='page-link'><a href="${url( page=num_pages )}" page_num="${num_pages}">${num_pages}</a></span> %endif </span> - ## First, last, all links. - | - <span class='page-link'><a href="${url( page=1 )}" page_num="1">First</a></span> - <span class='page-link'><a href="${url( page=num_pages )}" page_num="${num_pages}">Last</a></span> - <span class='page-link' id='show-all-link-span'><a href="${url( page='all' )}" page_num="all">All</a></span> + ## Show all link + <span class='page-link' id='show-all-link-span'> | <a href="${url( page='all' )}" page_num="all">Show All</a></span></td></tr> %endif --- a/templates/tracks/history_select_grid.mako Mon Apr 18 16:43:35 2011 -0400 +++ b/templates/tracks/history_select_grid.mako Mon Apr 18 17:02:32 2011 -0400 @@ -28,6 +28,9 @@ }); </script><style> + .dialog-box .body { + overflow-x: hidden; + } .addtracktab { margin: 0px 5px; padding: 5px; @@ -36,6 +39,7 @@ text-align: center; float: left; background-color: #ccc; + border: 1px solid #ccc; border-bottom: 0px; -webkit-border-top-left-radius: 10px; -webkit-border-top-right-radius: 10px; 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: 4 new changesets
by Bitbucket 18 Apr '11

18 Apr '11

4 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/326c1dd14ae3/ changeset: r5408:326c1dd14ae3 user: natefoo date: 2011-04-18 22:40:43 summary: Scramble script for bx-python on Solaris (needs some C99 defines). affected #: 1 file (890 bytes) --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/scramble/scripts/bx_python-solaris.py Mon Apr 18 16:40:43 2011 -0400 @@ -0,0 +1,33 @@ +import os, sys + +# change back to the build dir +if os.path.dirname( sys.argv[0] ) != "": + os.chdir( os.path.dirname( sys.argv[0] ) ) + +# find setuptools +sys.path.append( os.path.join( '..', '..', '..', 'lib' ) ) +from scramble_lib import * + +tag = get_tag() # get the tag +get_deps() # require any dependent eggs +clean() # clean up any existing stuff (could happen if you run scramble.py by hand) + +# reset args for distutils +me = sys.argv[0] +sys.argv = [ me ] +sys.argv.append( "egg_info" ) +if tag is not None: + sys.argv.append( "--tag-build=%s" %tag ) +# svn revision (if any) is handled directly in tag-build +sys.argv.append( "--no-svn-revision" ) +sys.argv.append( "bdist_egg" ) + +# apply patches (if any) +apply_patches() + +cc = get_solaris_compiler() +if cc == 'cc': + os.environ['CFLAGS'] = '-xc99=all -D_X_OPEN_SOURCE=600 -D_XPG6=1' + +# do it +execfile( "setup.py", globals(), locals() ) http://bitbucket.org/galaxy/galaxy-central/changeset/77889e2ca8c1/ changeset: r5409:77889e2ca8c1 user: natefoo date: 2011-04-18 22:41:38 summary: Just build on Solaris 10 for sparc. Apologies to anyone running a 9+ year old OS. ;) affected #: 1 file (1010 bytes) --- a/dist-eggs.ini Mon Apr 18 16:40:43 2011 -0400 +++ b/dist-eggs.ini Mon Apr 18 16:41:38 2011 -0400 @@ -29,14 +29,6 @@ py2.4-solaris-2.10-i86pc_64-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_64-ucs2/bin/python2.4 py2.5-solaris-2.10-i86pc_64-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_64-ucs2/bin/python2.5 py2.6-solaris-2.10-i86pc_64-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_64-ucs2/bin/python2.6 -py2.4-solaris-2.8-sun4u_32-ucs2 = troegs.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.4 -py2.5-solaris-2.8-sun4u_32-ucs2 = troegs.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.5 -py2.6-solaris-2.8-sun4u_32-ucs2 = troegs.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.6 -py2.4-solaris-2.8-sun4u_64-ucs2 = troegs.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_64-ucs2/bin/python2.4 -py2.5-solaris-2.8-sun4u_64-ucs2 = troegs.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_64-ucs2/bin/python2.5 -py2.6-solaris-2.8-sun4u_64-ucs2 = troegs.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_64-ucs2/bin/python2.6 - -; pysam doesn't build on solaris < 10, so for it alone we need these hosts py2.4-solaris-2.10-sun4u_32-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.4 py2.5-solaris-2.10-sun4u_32-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.5 py2.6-solaris-2.10-sun4u_32-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.6 @@ -69,9 +61,9 @@ py2.4-solaris-i86pc = py2.4-solaris-2.10-i86pc_32-ucs2 py2.4-solaris-2.10-i86pc_64-ucs2 py2.5-solaris-i86pc = py2.5-solaris-2.10-i86pc_32-ucs2 py2.5-solaris-2.10-i86pc_64-ucs2 py2.6-solaris-i86pc = py2.6-solaris-2.10-i86pc_32-ucs2 py2.6-solaris-2.10-i86pc_64-ucs2 -py2.4-solaris-sun4u = py2.4-solaris-2.8-sun4u_32-ucs2 py2.4-solaris-2.8-sun4u_64-ucs2 -py2.5-solaris-sun4u = py2.5-solaris-2.8-sun4u_32-ucs2 py2.5-solaris-2.8-sun4u_64-ucs2 -py2.6-solaris-sun4u = py2.6-solaris-2.8-sun4u_32-ucs2 py2.6-solaris-2.8-sun4u_64-ucs2 +py2.4-solaris-sun4u = py2.4-solaris-2.10-sun4u_32-ucs2 py2.4-solaris-2.10-sun4u_64-ucs2 +py2.5-solaris-sun4u = py2.5-solaris-2.10-sun4u_32-ucs2 py2.5-solaris-2.10-sun4u_64-ucs2 +py2.6-solaris-sun4u = py2.6-solaris-2.10-sun4u_32-ucs2 py2.6-solaris-2.10-sun4u_64-ucs2 py2.4-solaris = py2.4-solaris-i86pc py2.4-solaris-sun4u py2.5-solaris = py2.5-solaris-i86pc py2.5-solaris-sun4u py2.6-solaris = py2.6-solaris-i86pc py2.6-solaris-sun4u @@ -97,5 +89,4 @@ [ignore] GeneTrack = py2.4 python-daemon = py2.4 -pysam = py2.4-solaris-2.8-sun4u_32-ucs2 py2.5-solaris-2.8-sun4u_32-ucs2 py2.6-solaris-2.8-sun4u_32-ucs2 py2.4-solaris-2.8-sun4u_64-ucs2 py2.5-solaris-2.8-sun4u_64-ucs2 py2.6-solaris-2.8-sun4u_64-ucs2 -ctypes = py2.5-linux-i686-ucs2 py2.5-linux-i686-ucs4 py2.6-linux-i686-ucs2 py2.6-linux-i686-ucs4 py2.5-linux-x86_64-ucs2 py2.5-linux-x86_64-ucs4 py2.6-linux-x86_64-ucs2 py2.6-linux-x86_64-ucs4 py2.5-macosx-10.3-fat-ucs2 py2.6-macosx-10.3-fat-ucs2 py2.6-macosx-10.6-universal-ucs2 py2.5-solaris-2.10-i86pc_32-ucs2 py2.6-solaris-2.10-i86pc_32-ucs2 py2.5-solaris-2.10-i86pc_64-ucs2 py2.6-solaris-2.10-i86pc_64-ucs2 py2.5-solaris-2.8-sun4u_32-ucs2 py2.6-solaris-2.8-sun4u_32-ucs2 py2.5-solaris-2.8-sun4u_64-ucs2 py2.6-solaris-2.8-sun4u_64-ucs2 +ctypes = py2.5-linux-i686-ucs2 py2.5-linux-i686-ucs4 py2.6-linux-i686-ucs2 py2.6-linux-i686-ucs4 py2.5-linux-x86_64-ucs2 py2.5-linux-x86_64-ucs4 py2.6-linux-x86_64-ucs2 py2.6-linux-x86_64-ucs4 py2.5-macosx-10.3-fat-ucs2 py2.6-macosx-10.3-fat-ucs2 py2.6-macosx-10.6-universal-ucs2 py2.5-solaris-2.10-i86pc_32-ucs2 py2.6-solaris-2.10-i86pc_32-ucs2 py2.5-solaris-2.10-i86pc_64-ucs2 py2.6-solaris-2.10-i86pc_64-ucs2 py2.5-solaris-2.10-sun4u_32-ucs2 py2.6-solaris-2.10-sun4u_32-ucs2 py2.5-solaris-2.10-sun4u_64-ucs2 py2.6-solaris-2.10-sun4u_64-ucs2 http://bitbucket.org/galaxy/galaxy-central/changeset/0194ab30a730/ changeset: r5410:0194ab30a730 user: natefoo date: 2011-04-18 22:42:12 summary: Update bx-python to the tip. affected #: 1 file (0 bytes) --- a/eggs.ini Mon Apr 18 16:41:38 2011 -0400 +++ b/eggs.ini Mon Apr 18 16:42:12 2011 -0400 @@ -66,7 +66,7 @@ psycopg2 = _8.4.2_static pysqlite = _3.6.17_static MySQL_python = _5.1.41_static -bx_python = _14b6a6c95da6 +bx_python = _494c2d1d68b3 GeneTrack = _dev_48da9e998f0caf01c5be731e926f4b0481f658f0 SQLAlchemy = _dev_r6498 pysam = _kanwei_ae2bd50d9945 http://bitbucket.org/galaxy/galaxy-central/changeset/20782642367a/ changeset: r5411:20782642367a user: natefoo date: 2011-04-18 22:43:35 summary: merge affected #: 2 files (759 bytes) --- a/tools/samtools/bam_to_sam.py Mon Apr 18 16:42:12 2011 -0400 +++ b/tools/samtools/bam_to_sam.py Mon Apr 18 16:43:35 2011 -0400 @@ -21,6 +21,7 @@ parser = optparse.OptionParser() parser.add_option( '', '--input1', dest='input1', help='The input SAM dataset' ) parser.add_option( '', '--output1', dest='output1', help='The output BAM dataset' ) + parser.add_option( '', '--header', dest='header', action='store_true', default=False, help='Write SAM Header' ) ( options, args ) = parser.parse_args() # output version # of tool @@ -87,7 +88,11 @@ try: # Extract all alignments from the input BAM file to SAM format ( since no region is specified, all the alignments will be extracted ). - command = 'samtools view -o %s %s' % ( options.output1, tmp_sorted_aligns_file_name ) + if options.header: + view_options = "-h" + else: + view_options = "" + command = 'samtools view %s -o %s %s' % ( view_options, options.output1, tmp_sorted_aligns_file_name ) tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name tmp_stderr = open( tmp, 'wb' ) proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) --- a/tools/samtools/bam_to_sam.xml Mon Apr 18 16:42:12 2011 -0400 +++ b/tools/samtools/bam_to_sam.xml Mon Apr 18 16:43:35 2011 -0400 @@ -1,4 +1,4 @@ -<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.1"> +<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.2"><requirements><requirement type="package">samtools</requirement></requirements> @@ -7,9 +7,11 @@ bam_to_sam.py --input1=$input1 --output1=$output1 + $header </command><inputs><param name="input1" type="data" format="bam" label="BAM File to Convert" /> + <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" label="Include header in output" /></inputs><outputs><data format="sam" name="output1" label="${tool.name} on ${on_string}: converted SAM" /> @@ -22,6 +24,7 @@ --><param name="input1" value="1.bam" ftype="bam" /><output name="output1" file="bam_to_sam_out1.sam" sorted="True" /> + <param name="header" value="" /></test><test><param name="input1" value="3unsorted.bam" ftype="bam" /><output name="output1" file="bam_to_sam_out2.sam" sorted="True" /> + <param name="header" value="" /> + </test> + <test> +  + <param name="input1" value="1.bam" ftype="bam" /> + <output name="output1" file="bam_to_sam_out3.sam" sorted="True" /> + <param name="header" value="True" /></test></tests><help> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Enhance BAM to SAM tool to optionally output headers.
by Bitbucket 18 Apr '11

18 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b387de5c0439/ changeset: r5407:b387de5c0439 user: dan date: 2011-04-18 22:41:51 summary: Enhance BAM to SAM tool to optionally output headers. affected #: 2 files (759 bytes) --- a/tools/samtools/bam_to_sam.py Mon Apr 18 14:35:14 2011 -0400 +++ b/tools/samtools/bam_to_sam.py Mon Apr 18 16:41:51 2011 -0400 @@ -21,6 +21,7 @@ parser = optparse.OptionParser() parser.add_option( '', '--input1', dest='input1', help='The input SAM dataset' ) parser.add_option( '', '--output1', dest='output1', help='The output BAM dataset' ) + parser.add_option( '', '--header', dest='header', action='store_true', default=False, help='Write SAM Header' ) ( options, args ) = parser.parse_args() # output version # of tool @@ -87,7 +88,11 @@ try: # Extract all alignments from the input BAM file to SAM format ( since no region is specified, all the alignments will be extracted ). - command = 'samtools view -o %s %s' % ( options.output1, tmp_sorted_aligns_file_name ) + if options.header: + view_options = "-h" + else: + view_options = "" + command = 'samtools view %s -o %s %s' % ( view_options, options.output1, tmp_sorted_aligns_file_name ) tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name tmp_stderr = open( tmp, 'wb' ) proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) --- a/tools/samtools/bam_to_sam.xml Mon Apr 18 14:35:14 2011 -0400 +++ b/tools/samtools/bam_to_sam.xml Mon Apr 18 16:41:51 2011 -0400 @@ -1,4 +1,4 @@ -<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.1"> +<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.2"><requirements><requirement type="package">samtools</requirement></requirements> @@ -7,9 +7,11 @@ bam_to_sam.py --input1=$input1 --output1=$output1 + $header </command><inputs><param name="input1" type="data" format="bam" label="BAM File to Convert" /> + <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" label="Include header in output" /></inputs><outputs><data format="sam" name="output1" label="${tool.name} on ${on_string}: converted SAM" /> @@ -22,6 +24,7 @@ --><param name="input1" value="1.bam" ftype="bam" /><output name="output1" file="bam_to_sam_out1.sam" sorted="True" /> + <param name="header" value="" /></test><test><param name="input1" value="3unsorted.bam" ftype="bam" /><output name="output1" file="bam_to_sam_out2.sam" sorted="True" /> + <param name="header" value="" /> + </test> + <test> +  + <param name="input1" value="1.bam" ftype="bam" /> + <output name="output1" file="bam_to_sam_out3.sam" sorted="True" /> + <param name="header" value="True" /></test></tests><help> 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: Fix page switch links breaking in Add Tracks menu, restore Last Updated column
by Bitbucket 18 Apr '11

18 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6ad638bf39fa/ changeset: r5406:6ad638bf39fa user: kanwei date: 2011-04-18 20:35:14 summary: trackster: Fix page switch links breaking in Add Tracks menu, restore Last Updated column affected #: 2 files (85 bytes) --- a/lib/galaxy/web/controllers/tracks.py Mon Apr 18 14:04:06 2011 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Mon Apr 18 14:35:14 2011 -0400 @@ -60,6 +60,7 @@ datasets_param = "f-history" columns = [ NameColumn( "History Name", key="name", filterable="standard" ), + grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), DbKeyPlaceholderColumn( "Dbkey", key="dbkey", model_class=model.HistoryDatasetAssociation, visible=False ) ] num_rows_per_page = 10 --- a/templates/tracks/history_select_grid.mako Mon Apr 18 14:04:06 2011 -0400 +++ b/templates/tracks/history_select_grid.mako Mon Apr 18 14:35:14 2011 -0400 @@ -12,7 +12,7 @@ <script type="text/javascript"> // Handle all label clicks. var f = function() { - $(".addtracktab, #grid-table-body a").click(function() { + $(".addtracktab, #grid-table a").click(function() { var parent_body = $(".divider").parent(); if (parent_body.length !== 0) { parent_body.load($(this).attr("href")); 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: Use Egg.fetch() instead of Egg.resolve() to get dependencies when dist-scrambling.
by Bitbucket 18 Apr '11

18 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/ca3fe3a5f94c/ changeset: r5405:ca3fe3a5f94c user: natefoo date: 2011-04-18 20:04:06 summary: Use Egg.fetch() instead of Egg.resolve() to get dependencies when dist-scrambling. affected #: 1 file (121 bytes) --- a/scripts/dist-scramble.py Fri Apr 15 16:37:56 2011 -0400 +++ b/scripts/dist-scramble.py Mon Apr 18 14:04:06 2011 -0400 @@ -34,10 +34,11 @@ for egg in eggs: try: for dependency in egg.dependencies: - print "Checking %s dependency: %s" % ( egg.name, dependency ) + print "Checking %s on %s dependency: %s" % ( egg.name, egg.platform, dependency ) # this could be in a better data structure... dep = filter( lambda x: x.platform == egg.platform, c[dependency] )[0] - dep.resolve() + if not os.path.exists( dep.distribution.location ): + dep.fetch( dep.distribution.as_requirement() ) except EggNotFetchable, e: degg = e.eggs[0] print "%s build dependency %s %s %s couldn't be" % ( egg.name, degg.name, degg.version, degg.platform ) 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: Fixes for external service file browser.
by Bitbucket 15 Apr '11

15 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/efe423619733/ changeset: r5404:efe423619733 user: greg date: 2011-04-15 22:37:56 summary: Fixes for external service file browser. affected #: 1 file (16 bytes) --- a/lib/galaxy/web/controllers/requests_admin.py Fri Apr 15 13:55:45 2011 -0400 +++ b/lib/galaxy/web/controllers/requests_admin.py Fri Apr 15 16:37:56 2011 -0400 @@ -425,17 +425,18 @@ cmd = 'ssh %s@%s "ls -oghp \'%s\'"' % ( scp_configs[ 'user_name' ], scp_configs[ 'host' ], folder_path ) - # TODO: this currently requires rsh / ssh keys to be set. If they are not, the process - # hangs. Add an event that handles the authentication message if keys are not set - the - # message is something like: "Are you sure you want to continue connecting (yes/no)." + # Handle the authentication message if ssh keys are not set - the message is + # something like: "Are you sure you want to continue connecting (yes/no)." output = pexpect.run( cmd, - events={ '.ssword:*' : scp_configs[ 'password' ] + '\r\n', + events={ '$yes\/no$\.*' : 'yes\r\n', + '.ssword:*' : scp_configs[ 'password' ] + '\r\n', pexpect.TIMEOUT : print_ticks }, timeout=10 ) - if 'Password:\r\n' in output: + for password_str in [ 'Password:\r\n', 'password:\r\n' ]: # Eliminate the output created using ssh from the tree - output = output.replace( 'Password:\r\n', '' ) - return unicode( output.replace( '\n', '<br/>' ) ) + if password_str in output: + output = output.replace( password_str, '' ) + return unicode( output.replace( '\r\n', '<br/>' ) ) @web.json def open_folder( self, trans, request_id, external_service_id, key ): # Avoid caching @@ -448,15 +449,16 @@ folder_contents = [] for filename in files_list: is_folder = False - if filename[-1] == os.sep: + if filename and filename[-1] == os.sep: is_folder = True - full_path = os.path.join( folder_path, filename ) - node = { "title": filename, - "isFolder": is_folder, - "isLazy": is_folder, - "tooltip": full_path, - "key": full_path } - folder_contents.append( node ) + if filename: + full_path = os.path.join( folder_path, filename ) + node = { "title": filename, + "isFolder": is_folder, + "isLazy": is_folder, + "tooltip": full_path, + "key": full_path } + folder_contents.append( node ) return folder_contents def __get_files( self, trans, request, external_service, folder_path ): # Retrieves the filenames to be transferred from the remote host. @@ -470,11 +472,11 @@ def print_ticks( d ): pass cmd = 'ssh %s@%s "ls -p \'%s\'"' % ( scp_configs[ 'user_name' ], scp_configs[ 'host' ], folder_path ) - # TODO: this currently requires rsh / ssh keys to be set. If they are not, the process - # hangs. Add an event that handles the authentication message if keys are not set - the - # message is something like: "Are you sure you want to continue connecting (yes/no)." + # Handle the authentication message if keys are not set - the message is + # something like: "Are you sure you want to continue connecting (yes/no)." output = pexpect.run( cmd, - events={ '.ssword:*' : scp_configs[ 'password' ] + '\r\n', + events={ '$yes\/no$\.*' : 'yes\r\n', + '.ssword:*' : scp_configs[ 'password' ] + '\r\n', pexpect.TIMEOUT : print_ticks }, timeout=10 ) if 'No such file or directory' in output: @@ -482,10 +484,9 @@ message = "No folder named (%s) exists on the external service." % folder_path ok = False if ok: - if 'Password:' in output: + if 'assword:' in output: # Eliminate the output created using ssh from the tree - output_as_list = output.splitlines() - output_as_list.remove( 'Password:' ) + output_as_list = output.splitlines()[ 1: ] else: output_as_list = output.splitlines() return output_as_list 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 visual analytics: set initial parameter values properly.
by Bitbucket 15 Apr '11

15 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/7e21bdbbdb8f/ changeset: r5402:7e21bdbbdb8f user: jgoecks date: 2011-04-15 15:42:55 summary: Trackster visual analytics: set initial parameter values properly. affected #: 2 files (260 bytes) --- a/lib/galaxy/visualization/tracks/visual_analytics.py Fri Apr 15 09:35:41 2011 -0400 +++ b/lib/galaxy/visualization/tracks/visual_analytics.py Fri Apr 15 09:42:55 2011 -0400 @@ -42,6 +42,7 @@ tool_params.append( param_dict ) elif type( input ) == SelectToolParameter and type( input.options ) != DynamicOptions: tool_params.append( { 'name' : name, 'label' : input.label, 'type' : 'select', \ + 'value' : tool_param_values.get( name, None ), \ 'html' : urllib.quote( input.get_html() ) } ) # If tool has parameters that can be interactively modified, return tool. --- a/static/scripts/trackster.js Fri Apr 15 09:35:41 2011 -0400 +++ b/static/scripts/trackster.js Fri Apr 15 09:42:55 2011 -0400 @@ -846,13 +846,14 @@ name = param_dict.name, label = param_dict.label, html = unescape(param_dict.html), + value = param_dict.value, type = param_dict.type; if (type === "number") { this.params[this.params.length] = - new NumberParameter(name, label, html, param_dict.min, param_dict.max); + new NumberParameter(name, label, html, value, param_dict.min, param_dict.max); } else if (type == "select") { - this.params[this.params.length] = new ToolParameter(name, label, html); + this.params[this.params.length] = new ToolParameter(name, label, html, value); } else { console.log("WARNING: unrecognized tool parameter type:", name, type); @@ -881,6 +882,8 @@ // Param HTML. // TODO: either generalize .slider CSS attributes or create new rule for tool input div. var html_div = $("<div/>").addClass("slider").html(param.html).appendTo(param_div); + // Set initial value. + html_div.find(":input").val(param.value); // Add to clear floating layout. $("<div style='clear: both;'/>").appendTo(param_div); @@ -990,14 +993,15 @@ /** * Tool parameters. */ -var ToolParameter = function(name, label, html) { +var ToolParameter = function(name, label, html, value) { this.name = name; this.label = label; this.html = html; + this.value = value; }; -var NumberParameter = function(name, label, html, min, max) { - ToolParameter.call(this, name, label, html) +var NumberParameter = function(name, label, html, value, min, max) { + ToolParameter.call(this, name, label, html, value) this.min = min; this.max = max; }; 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: fubar: title not alt for popups on thumbnails for Haploview outputs
by Bitbucket 15 Apr '11

15 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c663af1979e4/ changeset: r5401:c663af1979e4 user: fubar date: 2011-04-15 15:35:41 summary: title not alt for popups on thumbnails for Haploview outputs affected #: 1 file (2 bytes) --- a/tools/rgenetics/rgHaploView.py Thu Apr 14 23:40:19 2011 -0400 +++ b/tools/rgenetics/rgHaploView.py Fri Apr 15 09:35:41 2011 -0400 @@ -429,7 +429,7 @@ if not os.path.exists(os.path.join(self.outfpath,mainthumb)): outf.write('<table><tr><td colspan="3"><a href="%s">Main combined LD plot</a></td></tr></table>\n' % (mainpdf)) else: - outf.write('<table><tr><td><a href="%s"><img src="%s" alt="Main combined LD image" hspace="10" align="middle">' % (mainpdf,mainthumb)) + outf.write('<table><tr><td><a href="%s"><img src="%s" title="Main combined LD image" hspace="10" align="middle">' % (mainpdf,mainthumb)) outf.write('</td><td>Click the thumbnail at left to download the main combined LD image <a href=%s>%s</a></td></tr></table>\n' % (mainpdf,mainpdf)) else: outf.write('(No main image was generated - this usually means a Haploview error connecting to Hapmap site - please try later)<br/>\n') 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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