March 2011 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: fubar: still having a problem with getting clustalw2 to print sequence indices - test does not cover so passes
by Bitbucket 23 Mar '11

23 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/620b060c31c7/ changeset: r5264:620b060c31c7 user: fubar date: 2011-03-24 00:32:32 summary: still having a problem with getting clustalw2 to print sequence indices - test does not cover so passes affected #: 1 file (35 bytes) --- a/tools/rgenetics/rgClustalw.xml Wed Mar 23 19:14:14 2011 -0400 +++ b/tools/rgenetics/rgClustalw.xml Wed Mar 23 19:32:32 2011 -0400 @@ -7,9 +7,9 @@ #end if #if ($outcontrol.outform=="clustal") -f "CLUSTAL" + #if ($outcontrol.out_seqnos=="ON") +-q "ON" #end if - #if ($outcontrol.outform=="clustal" and $outcontrol.out_seqnos=="ON") --q "ON" #end if #if ($outcontrol.outform=="phylip") -f "PHYLIP" 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: python wrapper for clustalw tool
by Bitbucket 23 Mar '11

23 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/cd05024e5b2a/ changeset: r5263:cd05024e5b2a user: fubar date: 2011-03-24 00:14:14 summary: python wrapper for clustalw tool affected #: 1 file (0 bytes) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Allow users to import copies of their own workflows.
by Bitbucket 23 Mar '11

23 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/589e769ceab5/ changeset: r5262:589e769ceab5 user: dan date: 2011-03-23 23:06:04 summary: Allow users to import copies of their own workflows. affected #: 1 file (189 bytes) --- a/lib/galaxy/web/controllers/workflow.py Wed Mar 23 17:20:47 2011 -0400 +++ b/lib/galaxy/web/controllers/workflow.py Wed Mar 23 18:06:04 2011 -0400 @@ -329,8 +329,6 @@ stored = self.get_stored_workflow( trans, id, check_ownership=False ) if stored.importable == False: return trans.show_error_message( "The owner of this workflow has disabled imports via this link. You can %s" % referer_message, use_panels=True ) - elif stored.user == trans.user: - return trans.show_error_message( "You can't import this workflow because you own it. You can %s" % referer_message, use_panels=True ) elif stored.deleted: return trans.show_error_message( "You can't import this workflow because it has been deleted. You can %s" % referer_message, use_panels=True ) else: 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: 2 new changesets
by Bitbucket 23 Mar '11

23 Mar '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6f1d1bcb0b9c/ changeset: r5260:6f1d1bcb0b9c user: fubar date: 2011-03-23 22:18:29 summary: Fixes to clustalw tool - need a python wrapper to take care of Clustalw's bad habit of writing to an output path determined from the input path - naughty..Also added the dendrogram to the log output so test output sample updated; version bumped affected #: 1 file (34 bytes) --- a/tools/rgenetics/rgClustalw.xml Wed Mar 23 16:42:14 2011 -0400 +++ b/tools/rgenetics/rgClustalw.xml Wed Mar 23 17:18:29 2011 -0400 @@ -1,21 +1,22 @@ <tool id="clustalw" name="ClustalW" version="0.1"><description>multiple sequence alignment program for DNA or proteins</description> - <command> + <command interpreter="python"> + rgClustalw.py -i "$input" -o "$output" -s "$out_order" -l "$outlog" -t "$outname" -d "$dnarna" #if ($range.mode=="part") - clustalw2 -infile=$input -outfile=$output -OUTORDER=$out_order -RANGE=$range.seq_range_start,$range.seq_range_end - #elif ($range.mode=="complete") - clustalw2 -infile=$input -outfile=$output -OUTORDER=$out_order +-b "$range.seq_range_start" -e "$range.seq_range_end" #end if #if ($outcontrol.outform=="clustal") - -SEQNOS=$outcontrol.out_seqnos +-f "CLUSTAL" + #end if + #if ($outcontrol.outform=="clustal" and $outcontrol.out_seqnos=="ON") +-q "ON" #end if #if ($outcontrol.outform=="phylip") - -OUTPUT=PHYLIP +-f "PHYLIP" #end if #if ($outcontrol.outform=="fasta") - -OUTPUT=FASTA +-f "FASTA" #end if - -TYPE=$dnarna 1>$outlog 2>&1 </command><inputs><page> http://bitbucket.org/galaxy/galaxy-central/changeset/72f60642853b/ changeset: r5261:72f60642853b user: fubar date: 2011-03-23 22:20:47 summary: test data updated for clustalw test affected #: 1 file (664 bytes) --- a/test-data/rgClustal_testout.log Wed Mar 23 17:18:29 2011 -0400 +++ b/test-data/rgClustal_testout.log Wed Mar 23 17:20:47 2011 -0400 @@ -87,7 +87,7 @@ Sequences (10:11) Aligned. Score: 64 Sequences (10:12) Aligned. Score: 76 Sequences (11:12) Aligned. Score: 46 -Guide tree file created: [/share/shared/galaxy/database/files/002/dataset_2705.dnd] +Guide tree file created: [infile_copy.dnd] There are 11 groups Start of Multiple Alignment @@ -105,8 +105,40 @@ Group 10: Sequences: 4 Score:945 Group 11: Sequences: 12 Score:380 Alignment Score 6283 -firstres = 1 lastres = 63 -FASTA file created! -Fasta-Alignment file created [/share/shared/galaxy/database/files/002/dataset_2726.dat] +CLUSTAL-Alignment file created [/share/shared/galaxy/database/files/002/dataset_2801.dat] + +Clustal created the following dnd file for your information: +( +( +c_briggsae-chrII_+_/43862-46313:0.07349, +c_brenneri-Cbre_Contig60_+_/627772-630087:0.04317) +:0.02387, +( +c_remanei-Crem_Contig172_-_/123228-124941:0.06114, +c_elegans-II_+_/9706834-9708803:0.07219) +:0.01779, +( +( +( +c_briggsae-chrIfooI_+_/43862-46313:0.10368, +c_brenneri-Cbre_Contig60gak_+_/627772-630087:0.06298) +:0.01654, +( +c_remanei-Crem_Contig172foo_-_/123228-124941:0.05765, +c_elegans-II_+_more/9706834-9708803:0.05902) +:0.06262) +:0.31533, +( +( +c_briggsae-chrII_+_bar/43862-46313:0.02327, +c_brenneri-Cbre_Contig60fee_+_/627772-630087:0.13463) +:0.05016, +( +c_remanei-Crem_Contig172zot_-_/123228-124941:0.11667, +c_elegans-II_+_meh/9706834-9708803:0.11737) +:0.12013) +:0.20951) +:0.30133); + 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: Slight output difference on the buildbot for weblogo, hopefully the difference is static.
by Bitbucket 23 Mar '11

23 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a9d745a274e3/ changeset: r5259:a9d745a274e3 user: natefoo date: 2011-03-23 21:42:14 summary: Slight output difference on the buildbot for weblogo, hopefully the difference is static. affected #: 1 file (34 bytes) Binary file test-data/rgWebLogo3_test.jpg 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.

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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.

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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.

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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( 'bam' ) # 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 Copy data into Galaxy? 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. 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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.

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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.

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