- galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: greg: Fix unit tests by renaming ~/datatypes/test/3.bam to be 3unsorted.bam.
by Bitbucket 23 Mar '11

23 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/914c0bd963e9/ changeset: r5258:914c0bd963e9 user: greg date: 2011-03-23 19:55:27 summary: Fix unit tests by renaming ~/datatypes/test/3.bam to be 3unsorted.bam. affected #: 2 files (0 bytes) Binary file lib/galaxy/datatypes/test/3.bam has changed 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.

1 0

commit/galaxy-central: dan: Remove 'data.file_name = data.file_name' from Rgenetics code files.
by Bitbucket 23 Mar '11

23 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/1b17af87c21b/ changeset: r5257:1b17af87c21b user: dan date: 2011-03-23 17:41:39 summary: Remove 'data.file_name = data.file_name' from Rgenetics code files. affected #: 5 files (5 bytes) --- a/tools/rgenetics/rgClean_code.py Wed Mar 23 12:18:57 2011 -0400 +++ b/tools/rgenetics/rgClean_code.py Wed Mar 23 12:41:39 2011 -0400 @@ -17,7 +17,7 @@ title = basename.translate(trantab) info = '%s filtered by rgClean.py at %s' % (title,timenow()) data.change_datatype('pbed') - data.file_name = data.file_name + #data.file_name = data.file_name data.metadata.base_name = title data.name = '%s.pbed' % title data.info = info --- a/tools/rgenetics/rgLDIndep_code.py Wed Mar 23 12:18:57 2011 -0400 +++ b/tools/rgenetics/rgLDIndep_code.py Wed Mar 23 12:41:39 2011 -0400 @@ -15,7 +15,7 @@ trantab = string.maketrans(killme,'_'*len(killme)) title = basename.encode().translate(trantab) info = '%s filtered by rgLDIndep.py at %s' % (title,timenow()) - data.file_name = data.file_name + #data.file_name = data.file_name data.metadata.base_name = title data.name = '%s.pbed' % title data.info = info --- a/tools/rgenetics/rgPedSub_code.py Wed Mar 23 12:18:57 2011 -0400 +++ b/tools/rgenetics/rgPedSub_code.py Wed Mar 23 12:41:39 2011 -0400 @@ -70,7 +70,7 @@ trantab = string.maketrans(killme,'_'*len(killme)) title = title.translate(trantab) info = '%s filtered by rgPedSub.py at %s' % (title,timenow()) - data.file_name = data.file_name + #data.file_name = data.file_name data.metadata.base_name = basename data.name = '%s.lped' % title data.info = info --- a/tools/rgenetics/rgfakePed_code.py Wed Mar 23 12:18:57 2011 -0400 +++ b/tools/rgenetics/rgfakePed_code.py Wed Mar 23 12:41:39 2011 -0400 @@ -40,7 +40,7 @@ ftype,pext = lookup[outFormat] data.name = '%s.%s' % (base_name,pext) # that's how they've been named in rgfakePhe.py data.change_datatype(pext) - data.file_name = data.file_name + #data.file_name = data.file_name data.metadata.base_name = base_name data.readonly = True out_data[pname] = data --- a/tools/rgenetics/rgfakePhe_code.py Wed Mar 23 12:18:57 2011 -0400 +++ b/tools/rgenetics/rgfakePhe_code.py Wed Mar 23 12:41:39 2011 -0400 @@ -35,7 +35,7 @@ base_name = base_name.translate(ptran) data = out_data['ppheout'] data.name = '%s.phe' % (base_name) # that's how they've been named in rgfakePhe.py - data.file_name = data.file_name + #data.file_name = data.file_name data.metadata.base_name = base_name out_data['pheout'] = data app.model.context.flush() 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.

1 0

commit/galaxy-central: greg: Improved checking to determine if a bam file is sorted. If the version of samtools being used is 0.1.13 or newer, determination of bam sorting is now much more robust. Add a new functional test to the test_library_features script that tests uploading a library_dataset (where the file is an unsorted bam file) using a combination of 'upload_paths' and 'link_to_files'. Rename the test-data file previously named 3.bam to now be named 3unsorted.bam to clarify that it
by Bitbucket 23 Mar '11

23 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4acde9321b63/ changeset: r5256:4acde9321b63 user: greg date: 2011-03-23 17:18:57 summary: Improved checking to determine if a bam file is sorted. If the version of samtools being used is 0.1.13 or newer, determination of bam sorting is now much more robust. Add a new functional test to the test_library_features script that tests uploading a library_dataset (where the file is an unsorted bam file) using a combination of 'upload_paths' and 'link_to_files'. Rename the test-data file previously named 3.bam to now be named 3unsorted.bam to clarify that it is an unsorted bam file. affected #: 10 files (5.6 KB) --- a/lib/galaxy/datatypes/binary.py Wed Mar 23 11:46:10 2011 -0400 +++ b/lib/galaxy/datatypes/binary.py Wed Mar 23 12:18:57 2011 -0400 @@ -51,16 +51,72 @@ """Class describing a BAM binary file""" file_ext = "bam" MetadataElement( name="bam_index", desc="BAM Index File", param=metadata.FileParameter, readonly=True, no_value=None, visible=False, optional=True ) - - def _is_coordinate_sorted(self, filename): - """Check if the input BAM file is sorted from the header information. - """ - params = ["samtools", "view", "-H", filename] - output = subprocess.Popen(params, stderr=subprocess.PIPE, stdout=subprocess.PIPE).communicate()[0] + + def _get_samtools_version( self ): + # Determine the version of samtools being used. Wouldn't it be nice if + # samtools provided a version flag to make this much simpler? + version = '0.0.0' + output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] + lines = output.split( '\n' ) + for line in lines: + if line.lower().startswith( 'version' ): + # Assuming line looks something like: version: 0.1.12a (r862) + version = line.split()[1] + break + return version + def _is_coordinate_sorted( self, file_name ): + """See if the input BAM file is sorted from the header information.""" + params = [ "samtools", "view", "-H", file_name ] + output = subprocess.Popen( params, stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[0] # find returns -1 if string is not found - return output.find("SO:coordinate") != -1 or output.find("SO:sorted") != -1 + return output.find( "SO:coordinate" ) != -1 or output.find( "SO:sorted" ) != -1 def dataset_content_needs_grooming( self, file_name ): - return not self._is_coordinate_sorted( file_name ) + """See if file_name is a sorted BAM file""" + version = self._get_samtools_version() + if version < '0.1.13': + return not self._is_coordinate_sorted( file_name ) + else: + # Samtools version 0.1.13 or newer produces an error condition when attempting to index an + # unsorted bam file - see http://biostar.stackexchange.com/questions/5273/is-my-bam-file-sorted. + # So when using a newer version of samtools, we'll first check if the input BAM file is sorted + # from the header information. If the header is present and sorted, we do nothing by returning False. + # If it's present and unsorted or if it's missing, we'll index the bam file to see if it produces the + # error. If it does, sorting is needed so we return True (otherwise False). + # + # TODO: we're creating an index file here and throwing it away. We then create it again when + # the set_meta() method below is called later in the job process. We need to enhance this overall + # process so we don't create an index twice. In order to make it worth the time to implement the + # upload tool / framework to allow setting metadata from directly within the tool itself, it should be + # done generically so that all tools will have the ability. In testing, a 6.6 gb BAM file took 128 + # seconds to index with samtools, and 45 minutes to sort, so indexing is relatively inexpensive. + if self._is_coordinate_sorted( file_name ): + return False + index_name = tempfile.NamedTemporaryFile( prefix = "bam_index" ).name + stderr_name = tempfile.NamedTemporaryFile( prefix = "bam_index_stderr" ).name + command = 'samtools index %s %s' % ( file_name, index_name ) + proc = subprocess.Popen( args=command, shell=True, stderr=open( stderr_name, 'wb' ) ) + exit_code = proc.wait() + stderr = open( stderr_name ).read().strip() + if stderr: + try: + os.unlink( index_name ) + except OSError: + pass + try: + os.unlink( stderr_name ) + except OSError: + pass + # Return True if unsorted error condition is found (find returns -1 if string is not found). + return stderr.find( "[bam_index_core] the alignment is not sorted" ) != -1 + try: + os.unlink( index_name ) + except OSError: + pass + try: + os.unlink( stderr_name ) + except OSError: + pass + return False def groom_dataset_content( self, file_name ): """ Ensures that the Bam file contents are sorted. This function is called @@ -104,7 +160,6 @@ index_file = dataset.metadata.bam_index if not index_file: index_file = dataset.metadata.spec['bam_index'].param.new_file( dataset = dataset ) - # Create the Bam index ##$ samtools index ##Usage: samtools index <in.bam> [<out.index>] --- a/lib/galaxy/datatypes/sniff.py Wed Mar 23 11:46:10 2011 -0400 +++ b/lib/galaxy/datatypes/sniff.py Wed Mar 23 12:18:57 2011 -0400 @@ -267,7 +267,7 @@ >>> fname = get_test_fname('1.bam') >>> guess_ext(fname) 'bam' - >>> fname = get_test_fname('3.bam') + >>> fname = get_test_fname('3unsorted.bam') >>> guess_ext(fname) 'bam' """ --- a/scripts/functional_tests.py Wed Mar 23 11:46:10 2011 -0400 +++ b/scripts/functional_tests.py Wed Mar 23 12:18:57 2011 -0400 @@ -93,6 +93,7 @@ nginx_x_accel_redirect_base = '/_x_accel_redirect', nginx_upload_store = nginx_upload_store, nginx_upload_path = '/_upload', + allow_library_path_paste = 'True', cluster_files_directory = cluster_files_directory, job_working_directory = job_working_directory, outputs_to_working_directory = 'True', @@ -102,7 +103,7 @@ track_jobs_in_database = 'True', job_scheduler_policy = 'FIFO', start_job_runners = 'pbs', - default_cluster_job_runner = default_cluster_job_runner, ) + default_cluster_job_runner = default_cluster_job_runner ) psu_production = True else: if 'GALAXY_TEST_DBPATH' in os.environ: @@ -161,6 +162,7 @@ allow_user_creation = True, allow_user_deletion = True, admin_users = 'test(a)bx.psu.edu', + allow_library_path_paste = True, library_import_dir = galaxy_test_file_dir, user_library_import_dir = os.path.join( galaxy_test_file_dir, 'users' ), global_conf = global_conf, Binary file test-data/3.bam has changed --- a/test/base/twilltestcase.py Wed Mar 23 11:46:10 2011 -0400 +++ b/test/base/twilltestcase.py Wed Mar 23 12:18:57 2011 -0400 @@ -2007,9 +2007,9 @@ # Library dataset stuff def upload_library_dataset( self, cntrller, library_id, folder_id, filename='', server_dir='', replace_id='', upload_option='upload_file', file_type='auto', dbkey='hg18', space_to_tab='', - link_data_only='copy_files', preserve_dirs='Yes', roles=[], ldda_message='', hda_ids='', - template_refresh_field_name='1_field_name', template_refresh_field_contents='', template_fields=[], - show_deleted='False', strings_displayed=[] ): + link_data_only='copy_files', preserve_dirs='Yes', filesystem_paths='', roles=[], + ldda_message='', hda_ids='', template_refresh_field_name='1_field_name', + template_refresh_field_contents='', template_fields=[], show_deleted='False', strings_displayed=[] ): """Add datasets to library using any upload_option""" # NOTE: due to the library_wait() method call at the end of this method, no tests should be done # for strings_displayed_after_submit. @@ -2050,10 +2050,10 @@ tc.fv( "add_history_datasets_to_library", "hda_ids", '1' ) tc.submit( 'add_history_datasets_to_library_button' ) else: - if upload_option == 'filesystem_paths' or upload_option == 'upload_directory': + if upload_option in [ 'upload_paths', 'upload_directory' ]: tc.fv( "1", "link_data_only", link_data_only ) - if upload_option == 'filesystem_paths' and preserve_dirs == 'Yes': - tc.fv( "1", "preserve_dirs", preserve_dirs ) + if upload_option == 'upload_paths': + tc.fv( "1", "filesystem_paths", filesystem_paths ) if upload_option == 'upload_directory' and server_dir: tc.fv( "1", "server_dir", server_dir ) if upload_option == 'upload_file': @@ -2085,6 +2085,19 @@ for check_str in strings_displayed: self.check_page_for_string( check_str ) self.home() + def ldda_info( self, cntrller, library_id, folder_id, ldda_id, strings_displayed=[], strings_not_displayed=[] ): + """View library_dataset_dataset_association information""" + self.visit_url( "%s/library_common/ldda_info?cntrller=%s&library_id=%s&folder_id=%s&id=%s" % \ + ( self.url, cntrller, library_id, folder_id, ldda_id ) ) + for check_str in strings_displayed: + self.check_page_for_string( check_str ) + for check_str in strings_not_displayed: + try: + self.check_page_for_string( check_str ) + raise AssertionError, "String (%s) should not have been displayed on ldda info page." % check_str + except: + pass + self.home() def ldda_edit_info( self, cntrller, library_id, folder_id, ldda_id, ldda_name, new_ldda_name='', template_refresh_field_name='1_field_name', template_refresh_field_contents='', template_fields=[], strings_displayed=[], strings_not_displayed=[] ): """Edit library_dataset_dataset_association information, optionally template element information""" --- a/test/functional/test_get_data.py Wed Mar 23 11:46:10 2011 -0400 +++ b/test/functional/test_get_data.py Wed Mar 23 12:18:57 2011 -0400 @@ -395,18 +395,18 @@ assert hda.metadata.bam_index is not None, "Bam index was not correctly created for 1.bam" self.delete_history( id=self.security.encode_id( history.id ) ) def test_0155_upload_file( self ): - """Test uploading 3.bam, which is an unsorted Bam file, NOT setting the file format""" + """Test uploading 3unsorted.bam, which is an unsorted Bam file, NOT setting the file format""" self.check_history_for_string( 'Your history is empty' ) history = get_latest_history_for_user( admin_user ) - self.upload_file( '3.bam' ) + self.upload_file( '3unsorted.bam' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" - # Since 3.bam is not sorted, we cannot verify dataset correctness since the uploaded + # Since 3unsorted.bam is not sorted, we cannot verify dataset correctness since the uploaded # dataset will be sorted. However, the check below to see if the index was created is # sufficient. self.check_history_for_string( '<span class="bam">bam</span>' ) # Make sure the Bam index was created - assert hda.metadata.bam_index is not None, "Bam index was not correctly created for 3.bam" + assert hda.metadata.bam_index is not None, "Bam index was not correctly created for 3unsorted.bam" self.delete_history( id=self.security.encode_id( history.id ) ) def test_0160_url_paste( self ): """Test url paste behavior""" --- a/test/functional/test_library_features.py Wed Mar 23 11:46:10 2011 -0400 +++ b/test/functional/test_library_features.py Wed Mar 23 12:18:57 2011 -0400 @@ -534,6 +534,25 @@ self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library3.id ), strings_displayed=[ folder5.name, folder5.description, ldda7.name ] ) + def test_135_upload_unsorted_bam_to_library_using_file_path_with_link_to_file( self ): + """Test uploading 3unsorted.bam, using filesystem_paths option in combination with link_to_files""" + filename = '3unsorted.bam' + self.upload_library_dataset( cntrller='library_admin', + library_id=self.security.encode_id( library2.id ), + folder_id=self.security.encode_id( library2.root_folder.id ), + upload_option='upload_paths', + link_data_only='link_to_files', + filesystem_paths='test-data/3unsorted.bam' ) + global ldda8 + ldda8 = get_latest_ldda_by_name( filename ) + assert ldda8 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda8 from the database' + # The upload above should produce an error condition in the uploaded library dataset since + # the uploaded bam file is not sorted, and we are linking to the file. + self.ldda_info( cntrller='library_admin', + library_id=self.security.encode_id( library2.id ), + folder_id=self.security.encode_id( library2.root_folder.id ), + ldda_id=self.security.encode_id( ldda8.id ), + strings_displayed=[ 'The uploaded files need grooming, so change your <b>Copy data into Galaxy?</b> selection to be' ] ) def test_999_reset_data_for_later_test_runs( self ): """Reseting data to enable later test runs to pass""" # Logged in as admin_user --- a/tools/samtools/bam_to_sam.xml Wed Mar 23 11:46:10 2011 -0400 +++ b/tools/samtools/bam_to_sam.xml Wed Mar 23 12:18:57 2011 -0400 @@ -18,7 +18,7 @@ <test><param name="input1" value="1.bam" ftype="bam" /><output name="output1" file="bam_to_sam_out1.sam" sorted="True" /> @@ -28,7 +28,7 @@ Bam-to-Sam command: samtools view -o bam_to_sam_out2.sam test-data/1.bam --> - <param name="input1" value="3.bam" ftype="bam" /> + <param name="input1" value="3unsorted.bam" ftype="bam" /><output name="output1" file="bam_to_sam_out2.sam" sorted="True" /></test></tests> --- a/tools/samtools/samtools_flagstat.xml Wed Mar 23 11:46:10 2011 -0400 +++ b/tools/samtools/samtools_flagstat.xml Wed Mar 23 12:18:57 2011 -0400 @@ -13,7 +13,7 @@ </outputs><tests><test> - <param name="input1" value="3.bam" ftype="bam" /> + <param name="input1" value="3unsorted.bam" ftype="bam" /><output name="output1" file="samtools_flagstat_out1.txt" /></test></tests> 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.

1 0

commit/galaxy-central: fubar: fixed typo that broke weblogo test
by Bitbucket 23 Mar '11

23 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/49053ae670da/ changeset: r5255:49053ae670da user: fubar date: 2011-03-23 16:46:10 summary: fixed typo that broke weblogo test affected #: 1 file (1 byte) --- a/tools/rgenetics/rgWebLogo3.xml Wed Mar 23 11:20:23 2011 -0400 +++ b/tools/rgenetics/rgWebLogo3.xml Wed Mar 23 11:46:10 2011 -0400 @@ -68,7 +68,7 @@ <param name="input" value="rgClustal_testout.fasta" /><param name = "logoname" value="Galaxy/Rgenetics weblogo" /><param name = "outformat" value="jpeg" /> - <param name = "range" value="complete" /> + <param name = "mode" value="complete" /><param name = "size" value="medium" /><param name = "colours" value="auto" /><output name="output" file="rgWebLogo3_test.jpg" ftype="jpg" /> 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.

1 0

commit/galaxy-central: fubar: Added subsequence and colour options to weblogo3 sequence logo generator; tweaks to clustalw tool help
by Bitbucket 23 Mar '11

23 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/f2d655fb02d7/ changeset: r5254:f2d655fb02d7 user: fubar date: 2011-03-23 16:20:23 summary: Added subsequence and colour options to weblogo3 sequence logo generator; tweaks to clustalw tool help affected #: 2 files (1.3 KB) --- a/tools/rgenetics/rgClustalw.xml Wed Mar 23 10:59:26 2011 -0400 +++ b/tools/rgenetics/rgClustalw.xml Wed Mar 23 11:20:23 2011 -0400 @@ -79,7 +79,7 @@ <param name = "mode" value="complete" /><param name = "out_order" value="ALIGNED" /><output name="output" file="rgClustal_testout.fasta" ftype="fasta" /> - <output name="output" file="rgClustal_testout.log" ftype="txt" lines_diff="5" /> + <output name="outlog" file="rgClustal_testout.log" ftype="txt" lines_diff="5" /></test></tests><help> @@ -109,9 +109,9 @@ The first iteration of this Galaxy wrapper was written by Hans-Rudolf Hotz - see Clustfirst_ -It was modified by Ross Lazarus for the rgenetics project +It was modified by Ross Lazarus for the rgenetics project - tests and some additional parameters were added -This wrapper is now LGPL +This wrapper is released licensed under the LGPL_ .. _ClustalW2: http://www.ebi.ac.uk/2can/tutorials/protein/clustalw.html @@ -119,6 +119,8 @@ .. _Clustfirst: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003732.html +.. _LGPL: http://www.gnu.org/copyleft/lesser.html + </help></tool> --- a/tools/rgenetics/rgWebLogo3.xml Wed Mar 23 10:59:26 2011 -0400 +++ b/tools/rgenetics/rgWebLogo3.xml Wed Mar 23 11:20:23 2011 -0400 @@ -1,13 +1,16 @@ <tool id="weblogo3" name="Sequence Logo" version="0.1"><description>generator for fasta (eg Clustal alignments)</description><command> - weblogo -F $outformat -s $size -f $input -o $output -t "$logoname" + weblogo -F $outformat -s $size -f $input -o $output -t "$logoname" -c "$colours" +#if $range.mode == 'part' +-l "$range.seqstart" -u "$range.seqend" +#end if </command><inputs><page><param format="fasta" name="input" type="data" label="Fasta File" /> - <param name="logoname" label="Name for output logo - will appear on graphics" type="text" size="50" value="Galaxy/Rgenetics weblogo" /> - <param name="outformat" type="select" label="Output weblogo format" > + <param name="logoname" label="Title for output Sequence Logo" type="text" size="50" value="Galaxy-Rgenetics Sequence Logo" /> + <param name="outformat" type="select" label="Output format for image (or text report)" ><option value="png" selected="True">PNG screen quality</option><option value="png_print">High quality printable PNG</option><option value="pdf">PDF</option> @@ -15,6 +18,32 @@ <option value="eps">EPS</option><option value="txt">Text (shows the detailed calculations for each position - no image)</option></param> + <param name="colours" type="select" label="Colour scheme for output Sequence Logo" + help="Note that some of these only make sense for protein sequences!"> + <option value="auto" selected="True">Default automatic colour selection</option> + <option value="base pairing">Base pairing</option> + <option value="charge">Charge colours</option> + <option value="chemistry">Chemistry colours</option> + <option value="classic">Classical colours</option> + <option value="hydrophobicity">Hydrophobicity</option> + <option value="monochrome">monochrome</option> + </param> + + <conditional name="range"> + <param name="mode" type="select" label="Include entire sequence (default) or specify a subsequence range to use"> + <option value="complete" selected="true">complete sequence</option> + <option value="part">Only use a part of the sequence</option> + </param> + <when value="complete"> + </when> + <when value="part"> + <param name="seqstart" size="5" type="integer" value="1" help="WARNING: Specifying indexes outside the sequence lengths will cause unpredictable but bad consequences!" + label="Index (eg 1=first letter) of the start of the sequence range to include in the logo"> + </param> + <param name="seqend" size="5" type="integer" value="99999" label="Index (eg 75=75th letter) of the end of the sequence range to include in the logo" > + </param> + </when> + </conditional><param name="size" type="select" label="Output weblogo size" ><option value="large" selected="True">Large</option><option value="medium">Medium</option> @@ -39,8 +68,9 @@ <param name="input" value="rgClustal_testout.fasta" /><param name = "logoname" value="Galaxy/Rgenetics weblogo" /><param name = "outformat" value="jpeg" /> - <param name = "size" value="medium" /> - + <param name = "range" value="complete" /> + <param name = "size" value="medium" /> + <param name = "colours" value="auto" /><output name="output" file="rgWebLogo3_test.jpg" ftype="jpg" /></test> @@ -51,33 +81,21 @@ This tool uses Weblogo3_ in Galaxy to generate a sequence logo. The input file must be a fasta file in your current history. +It is recommended for (eg) viewing multiple sequence alignments output from the clustalw tool - set the output to fasta and feed +it in to this tool. + A typical output looks like this .. image:: ./static/images/rgWebLogo3_test.jpg ---- -**Why use WebLogo in Galaxy?** - -Weblogo3_ is a good example of an easy to use tool and there are plenty of other web accessible weblogo generator sites available. - -However, none of those offer the combination of: - -1) persistence of analyses and data in multiple shareable histories, pages and libraries - -2) convenient access to shared data libraries, workflows and user controlled pages, and to 3rd party data sources like UCSC tables. - -3) analyses integrated with many other applicable generic and specialized tools already available for downstream processing. - -that you get for free when you use Galaxy. No muss; no fuss. - ----- **Attribution** Weblogo attribution and associated documentation are available at Weblogo3_ -This wrapper was written by Ross Lazarus for the rgenetics project and the source code is licensed under the LGPL_ like other rgenetics artefacts +This Galaxy wrapper was written by Ross Lazarus for the rgenetics project and the source code is licensed under the LGPL_ like other rgenetics artefacts .. _Weblogo3: http://weblogo.berkeley.edu/ 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.

1 0

commit/galaxy-central: natefoo: Set the ftype of SRMA test outputs so the BAMs are compared as SAMs
by Bitbucket 23 Mar '11

23 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5774231adb8d/ changeset: r5253:5774231adb8d user: natefoo date: 2011-03-23 15:59:26 summary: Set the ftype of SRMA test outputs so the BAMs are compared as SAMs affected #: 1 file (24 bytes) --- a/tools/sr_mapping/srma_wrapper.xml Wed Mar 23 09:57:06 2011 -0400 +++ b/tools/sr_mapping/srma_wrapper.xml Wed Mar 23 10:59:26 2011 -0400 @@ -91,7 +91,7 @@ <param name="ref" value="hg18chr21" /><param name="input" value="srma_in1.bam" type="bam" /><param name="source_select" value="pre_set" /> - <output name="output" file="srma_out1.bam"/> + <output name="output" file="srma_out1.bam" ftype="bam"/></test><test><!-- Commands to run to prepare test files (uses custom genome): @@ -118,7 +118,7 @@ <param name="correctBases" value="true" /><param name="useSequenceQualities" value="true" /><param name="maxHeapSize" value="8192" /> - <output name="output" file="srma_out2.bam"/> + <output name="output" file="srma_out2.bam" ftype="bam"/></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.

1 0

commit/galaxy-central: dan: Add IGV as an external display application. Contributed by Tobias Wohlfrom.
by Bitbucket 23 Mar '11

23 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a62cec23a157/ changeset: r5252:a62cec23a157 user: dan date: 2011-03-23 14:57:06 summary: Add IGV as an external display application. Contributed by Tobias Wohlfrom. Provides two links for IGV: 1) web - to view with Java web start IGV if the user has no IGV installed 2) local - to view in the user's running IGV instance (requires remote port enabled in IGV) affected #: 2 files (52 bytes) --- a/datatypes_conf.xml.sample Wed Mar 23 09:03:13 2011 -0400 +++ b/datatypes_conf.xml.sample Wed Mar 23 09:57:06 2011 -0400 @@ -9,6 +9,7 @@ <converter file="bam_to_summary_tree_converter.xml" target_datatype="summary_tree" depends_on="bai"/><display file="ucsc/bam.xml" /><display file="ensembl/ensembl_bam.xml" /> + </datatype><datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true"><converter file="bed_to_gff_converter.xml" target_datatype="gff"/> 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.

1 0

commit/galaxy-central: dan: Add SGD Yeast genome Gbrowse display site.
by Bitbucket 23 Mar '11

23 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/7fb3d490b0ec/ changeset: r5251:7fb3d490b0ec user: dan date: 2011-03-23 14:03:13 summary: Add SGD Yeast genome Gbrowse display site. affected #: 3 files (127 bytes) --- a/lib/galaxy/config.py Wed Mar 23 08:42:01 2011 -0400 +++ b/lib/galaxy/config.py Wed Mar 23 09:03:13 2011 -0400 @@ -94,7 +94,7 @@ self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) ) self.log_events = string_as_bool( kwargs.get( 'log_events', 'False' ) ) self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",") - self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "wormbase,tair,modencode_worm,modencode_fly" ).lower().split(",") + self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "wormbase,tair,modencode_worm,modencode_fly,sgd_yeast" ).lower().split(",") self.genetrack_display_sites = kwargs.get( 'genetrack_display_sites', "main,test" ).lower().split(",") self.brand = kwargs.get( 'brand', None ) self.wiki_url = kwargs.get( 'wiki_url', 'http://g2.trac.bx.psu.edu/' ) --- a/tool-data/shared/gbrowse/gbrowse_build_sites.txt Wed Mar 23 08:42:01 2011 -0400 +++ b/tool-data/shared/gbrowse/gbrowse_build_sites.txt Wed Mar 23 09:03:13 2011 -0400 @@ -9,3 +9,6 @@ modencode_worm http://modencode.oicr.on.ca/fgb2/gbrowse/worm ce6 modencode_fly http://modencode.oicr.on.ca/fgb2/gbrowse/fly dm2 +#SGD +sgd_yeast http://browse.yeastgenome.org/fgb2/gbrowse/scgenome Saccharomcyes_cerevisiae_S288C_SGD2010 + --- a/universe_wsgi.ini.sample Wed Mar 23 08:42:01 2011 -0400 +++ b/universe_wsgi.ini.sample Wed Mar 23 09:03:13 2011 -0400 @@ -182,7 +182,7 @@ #ucsc_display_sites = main,test,archaea,ucla # GBrowse servers: tool-data/shared/gbrowse/gbrowse_build_sites.txt -#gbrowse_display_sites = wormbase,tair,modencode_worm,modencode_fly +#gbrowse_display_sites = wormbase,tair,modencode_worm,modencode_fly,yeast_sgd # GeneTrack servers: tool-data/shared/genetrack/genetrack_sites.txt #genetrack_display_sites = main,test 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.

1 0

commit/galaxy-central: dan: Disable functional test for not being able to import your own history which was enabled in 5248:dc9efb540f61.
by Bitbucket 23 Mar '11

23 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/ce872e9673aa/ changeset: r5250:ce872e9673aa user: dan date: 2011-03-23 13:42:01 summary: Disable functional test for not being able to import your own history which was enabled in 5248:dc9efb540f61. affected #: 1 file (73 bytes) --- a/test/functional/test_history_functions.py Tue Mar 22 20:29:32 2011 -0400 +++ b/test/functional/test_history_functions.py Wed Mar 23 08:42:01 2011 -0400 @@ -189,9 +189,10 @@ if not history3.importable: raise AssertionError, "History 3 is not marked as importable after make_accessible_via_link" # Try importing history3 - self.import_history_via_url( self.security.encode_id( history3.id ), - admin_user.email, - strings_displayed_after_submit=[ 'You cannot import your own history.' ] ) + #Importing your own history was enabled in 5248:dc9efb540f61. + #self.import_history_via_url( self.security.encode_id( history3.id ), + # admin_user.email, + # strings_displayed_after_submit=[ 'You cannot import your own history.' ] ) # Disable access via link for history3. self.disable_access_via_link( self.security.encode_id( history3.id ), strings_displayed=[ 'Anyone can view and import this history' ], 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.

1 0

commit/galaxy-central: dan: Remove link target from intermine datasource tools.
by Bitbucket 23 Mar '11

23 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/49732a00b9bd/ changeset: r5249:49732a00b9bd user: dan date: 2011-03-23 01:29:32 summary: Remove link target from intermine datasource tools. affected #: 6 files (84 bytes) --- a/tools/data_source/flymine.xml Tue Mar 22 19:43:32 2011 -0400 +++ b/tools/data_source/flymine.xml Tue Mar 22 20:29:32 2011 -0400 @@ -7,7 +7,7 @@ <tool name="Flymine" id="flymine" tool_type="data_source"><description>server</description><command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> - <inputs action="http://www.flymine.org" check_values="false" method="get" target="_top"> + <inputs action="http://www.flymine.org" check_values="false" method="get"><display>go to Flymine server $GALAXY_URL</display><param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=flymine" /></inputs> --- a/tools/data_source/flymine_test.xml Tue Mar 22 19:43:32 2011 -0400 +++ b/tools/data_source/flymine_test.xml Tue Mar 22 20:29:32 2011 -0400 @@ -7,7 +7,7 @@ <tool name="Flymine test" id="flymine_test" tool_type="data_source"><description>server</description><command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> - <inputs action="http://preview.flymine.org/preview/begin.do" check_values="false" method="get" target="_top"> + <inputs action="http://preview.flymine.org/preview/begin.do" check_values="false" method="get"><display>go to Flymine server $GALAXY_URL</display><param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=flymine" /></inputs> --- a/tools/data_source/metabolicmine.xml Tue Mar 22 19:43:32 2011 -0400 +++ b/tools/data_source/metabolicmine.xml Tue Mar 22 20:29:32 2011 -0400 @@ -2,7 +2,7 @@ <tool name="metabolicMine" id="metabolicmine" tool_type="data_source"><description>server</description><command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> - <inputs action="http://www.metabolicmine.org/beta/begin.do" check_values="false" method="get" target="_top"> + <inputs action="http://www.metabolicmine.org/beta/begin.do" check_values="false" method="get"><display>go to metabolicMine server $GALAXY_URL</display></inputs><uihints minwidth="800"/> --- a/tools/data_source/modmine.xml Tue Mar 22 19:43:32 2011 -0400 +++ b/tools/data_source/modmine.xml Tue Mar 22 20:29:32 2011 -0400 @@ -7,7 +7,7 @@ <tool name="modENCODE modMine" id="modmine" tool_type="data_source"><description>server</description><command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> - <inputs action="http://intermine.modencode.org/" check_values="false" method="get" target="_top"> + <inputs action="http://intermine.modencode.org/" check_values="false" method="get"><display>go to modENCODE modMine server $GALAXY_URL</display></inputs><uihints minwidth="800"/> --- a/tools/data_source/ratmine.xml Tue Mar 22 19:43:32 2011 -0400 +++ b/tools/data_source/ratmine.xml Tue Mar 22 20:29:32 2011 -0400 @@ -7,7 +7,7 @@ <tool name="Ratmine" id="ratmine" tool_type="data_source"><description>server</description><command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> - <inputs action="http://ratmine.mcw.edu/ratmine/begin.do" check_values="false" method="get" target="_top"> + <inputs action="http://ratmine.mcw.edu/ratmine/begin.do" check_values="false" method="get"><display>go to Ratmine server $GALAXY_URL</display><param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=ratmine" /></inputs> --- a/tools/data_source/yeastmine.xml Tue Mar 22 19:43:32 2011 -0400 +++ b/tools/data_source/yeastmine.xml Tue Mar 22 20:29:32 2011 -0400 @@ -2,7 +2,7 @@ <tool name="YeastMine" id="yeastmine" tool_type="data_source"><description>server</description><command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> - <inputs action="http://yeastmine.yeastgenome.org/yeastmine/begin.do" check_values="false" method="get" target="_top"> + <inputs action="http://yeastmine.yeastgenome.org/yeastmine/begin.do" check_values="false" method="get"><display>go to yeastMine server $GALAXY_URL</display></inputs><uihints minwidth="800"/> 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.

1 0