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

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.

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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.

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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.

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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.

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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.

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commit/galaxy-central: dan: Allow importing one's own history.
by Bitbucket 23 Mar '11

23 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/dc9efb540f61/ changeset: r5248:dc9efb540f61 user: dan date: 2011-03-23 00:43:32 summary: Allow importing one's own history. affected #: 1 file (49 bytes) --- a/lib/galaxy/web/controllers/history.py Tue Mar 22 17:49:09 2011 -0400 +++ b/lib/galaxy/web/controllers/history.py Tue Mar 22 19:43:32 2011 -0400 @@ -669,8 +669,9 @@ if not trans.user_is_admin() and not self.security_check( user, import_history, check_ownership=False, check_accessible=True ): return trans.show_error_message( "You cannot access this history.<br>You can %s." % referer_message, use_panels=True ) if user: - if import_history.user_id == user.id: - return trans.show_error_message( "You cannot import your own history.<br>You can %s." % referer_message, use_panels=True ) + #dan: I can import my own history. + #if import_history.user_id == user.id: + # return trans.show_error_message( "You cannot import your own history.<br>You can %s." % referer_message, use_panels=True ) new_history = import_history.copy( target_user=user ) new_history.name = "imported: " + new_history.name new_history.user_id = user.id 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: Refactor Grouping tool and fix bug where data after a blank value in the group_by column returns the wrong data.
by Bitbucket 22 Mar '11

22 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4d521da04318/ changeset: r5247:4d521da04318 user: kanwei date: 2011-03-22 22:49:09 summary: Refactor Grouping tool and fix bug where data after a blank value in the group_by column returns the wrong data. affected #: 2 files (5.1 KB) --- a/tools/stats/grouping.py Tue Mar 22 14:08:32 2011 -0400 +++ b/tools/stats/grouping.py Tue Mar 22 17:49:09 2011 -0400 @@ -1,10 +1,12 @@ #!/usr/bin/env python -#Guruprasad Ananda +# Guruprasad Ananda +# Refactored 2011, Kanwei Li """ This tool provides the SQL "group by" functionality. """ import sys, string, re, commands, tempfile, random from rpy import * +from itertools import groupby def stop_err(msg): sys.stderr.write(msg) @@ -53,10 +55,10 @@ stop_err( "Group column not specified." ) str_ops = ['c', 'length', 'unique', 'random', 'cuniq', 'Mode'] #ops that can handle string/non-numeric inputs - for k,col in enumerate(cols): + for k, col in enumerate(cols): col = int(col)-1 if ops[k] not in str_ops: - # We'll get here only if the user didn't choose 'Concatenate' or 'Count' or 'Count Distinct' or 'pick randmly', which are the + # We'll get here only if the user didn't choose 'Concatenate' or 'Count' or 'Count Distinct' or 'pick randomly', which are the # only aggregation functions that can be used on columns containing strings. try: float( elems[col] ) @@ -90,191 +92,94 @@ if error_code != 0: stop_err( "Sorting input dataset resulted in error: %s: %s" %( error_code, stdout )) - prev_item = "" - prev_vals = [] + prev_item = None skipped_lines = 0 - first_invalid_line = 0 - invalid_line = '' + first_invalid_line = None invalid_value = '' invalid_column = 0 fout = open(sys.argv[1], "w") - for ii, line in enumerate( file( tmpfile.name )): - if line and not line.startswith( '#' ): - line = line.rstrip( '\r\n' ) - try: - fields = line.split("\t") - item = fields[group_col] - if ignorecase == 1: - item = item.lower() - if prev_item != "": - # At this level, we're grouping on values (item and prev_item) in group_col - if item == prev_item: - # Keep iterating and storing values until a new value is encountered. - for i, col in enumerate(cols): - col = int(col)-1 - valid = True - # Before appending the current value, make sure it is numeric if the - # operation for the column requires it. - if ops[i] not in str_ops: - try: - float( fields[col].strip()) - except: - valid = False - skipped_lines += 1 - if not first_invalid_line: - first_invalid_line = ii+1 - invalid_value = fields[col] - invalid_column = col+1 - if valid: - prev_vals[i].append(fields[col].strip()) - else: - """ - When a new value is encountered, write the previous value and the - corresponding aggregate values into the output file. This works - due to the sort on group_col we've applied to the data above. - """ - out_str = prev_item - multiple_modes = False - mode_index = None - for i, op in enumerate( ops ): - if op == 'cuniq': - rfunc = "r.c" - else: - rfunc = "r." + op - if op not in str_ops: - for j, elem in enumerate( prev_vals[i] ): - prev_vals[i][j] = float( elem ) - rout = eval( rfunc )( prev_vals[i] ) - if rounds[i] == 'yes': - rout = int(round(float(rout))) - else: - rout = '%g' %(float(rout)) - else: - if op != 'random': - rout = eval( rfunc )( prev_vals[i] ) - else: - try: - rand_index = random.randint(0,len(prev_vals[i])-1) #if the two inputs to randint are equal, it seems to throw a ValueError. This can't be reproduced with the python interpreter in its interactive mode. - except Exception, ValueError: - rand_index = 0 - rout = prev_vals[i][rand_index] - - if op == 'Mode' and rout == '>1 mode': - multiple_modes = True - mode_index = i - if op == 'unique': - rfunc = "r.length" - rout = eval( rfunc )( rout ) - if op in ['c', 'cuniq']: - if op == 'c': - if type(rout) == type([]): - out_str += "\t" + ','.join(rout) - else: - out_str += "\t" + str(rout) - else: - if type(rout) == type([]): - out_str += "\t" + ','.join(list(set(rout))) - else: - out_str += "\t" + str(rout) - else: - out_str += "\t" + str(rout) - if multiple_modes and mode_index != None: - out_str_list = out_str.split('\t') - for val in prev_vals[mode_index]: - out_str = '\t'.join(out_str_list[:mode_index+1]) + '\t' + str(val) + '\t' + '\t'.join(out_str_list[mode_index+2:]) - print >>fout, out_str.rstrip('\t') - else: - print >>fout, out_str - - prev_item = item - prev_vals = [] - for col in cols: - col = int(col)-1 - val_list = [] - val_list.append(fields[col].strip()) - prev_vals.append(val_list) - else: - # This only occurs once, right at the start of the iteration. - prev_item = item - for col in cols: - col = int(col)-1 - val_list = [] - val_list.append(fields[col].strip()) - prev_vals.append(val_list) - - except Exception, exc: - skipped_lines += 1 - if not first_invalid_line: - first_invalid_line = ii+1 - else: - skipped_lines += 1 - if not first_invalid_line: - first_invalid_line = ii+1 - - # Handle the last grouped value - out_str = prev_item - multiple_modes = False - mode_index = None - for i, op in enumerate(ops): - if op == 'cuniq': - rfunc = "r.c" - else: - rfunc = "r." + op - try: + def is_new_item(line): + item = line.strip().split("\t")[group_col] + if ignorecase == 1: + item = item.lower() + return item + + for key, line_list in groupby(tmpfile, key=is_new_item): + op_vals = [ [] for op in cols ] + out_str = key + multiple_modes = False + mode_index = None + + for line in line_list: + fields = line.strip().split("\t") + for i, col in enumerate(cols): + col = int(col)-1 # cXX from galaxy is 1-based + val = fields[col].strip() + # Before appending the current value, make sure it is numeric if the + # operation for the column requires it. + if ops[i] not in str_ops: + try: + float(val) + except ValueError: + skipped_lines += 1 + if first_invalid_line is None: + first_invalid_line = i+1 + invalid_value = fields[col] + invalid_column = col+1 + break + + op_vals[i].append(val) + + for i, op in enumerate( ops ): + if op == 'cuniq': + rfunc = "r.c" + else: + rfunc = "r." + op if op not in str_ops: - for j, elem in enumerate( prev_vals[i] ): - prev_vals[i][j] = float( elem ) - rout = eval( rfunc )( prev_vals[i] ) + for j, elem in enumerate( op_vals[i] ): + op_vals[i][j] = float( elem ) + rout = eval( rfunc )( op_vals[i] ) if rounds[i] == 'yes': - rout = int(round(float(rout))) + rout = round(float(rout)) else: rout = '%g' %(float(rout)) else: if op != 'random': - rout = eval( rfunc )( prev_vals[i] ) + rout = eval( rfunc )( op_vals[i] ) else: try: - rand_index = random.randint(0,len(prev_vals[i])-1) #if the two inputs to randint are equal, it seems to throw a ValueError. This can't be reproduced with the python interpreter in its interactive mode. - except Exception, ValueError: + rand_index = random.randint(0,len(op_vals[i])-1) #if the two inputs to randint are equal, it seems to throw a ValueError. This can't be reproduced with the python interpreter in its interactive mode. + except: rand_index = 0 - rout = prev_vals[i][rand_index] + rout = op_vals[i][rand_index] if op == 'Mode' and rout == '>1 mode': multiple_modes = True - mode_index = i + mode_index = i if op == 'unique': rfunc = "r.length" - rout = eval( rfunc )( rout ) - if op in ['c','cuniq']: - if op == 'c': - if type(rout) == type([]): - out_str += "\t" + ','.join(rout) - else: - out_str += "\t" + str(rout) + rout = eval( rfunc )( rout ) + if op in ['c', 'cuniq']: + if isinstance(rout, list): + if op == 'cuniq': + rout = set(rout) + out_str += "\t" + ','.join(rout) else: - if type(rout) == type([]): - out_str += "\t" + ','.join(list(set(rout))) - else: - out_str += "\t" + str(rout) + out_str += "\t" + str(rout) else: - out_str += "\t" + str( rout ) - except: - skipped_lines += 1 - if not first_invalid_line: - first_invalid_line = ii+1 - - if multiple_modes and mode_index != None: - out_str_list = out_str.split('\t') - for val in prev_vals[mode_index]: - out_str = '\t'.join(out_str_list[:mode_index+1]) + '\t' + str(val) + '\t' + '\t'.join(out_str_list[mode_index+2:]) - print >>fout, out_str.rstrip('\t') - else: - print >>fout, out_str + out_str += "\t" + str(rout) + if multiple_modes and mode_index != None: + out_str_list = out_str.split('\t') + for val in op_vals[mode_index]: + out_str = '\t'.join(out_str_list[:mode_index+1]) + '\t' + str(val) + '\t' + '\t'.join(out_str_list[mode_index+2:]) + fout.write(out_str.rstrip('\t') + "\n") + else: + fout.write(out_str + "\n") # Generate a useful info message. msg = "--Group by c%d: " %(group_col+1) - for i,op in enumerate(ops): + for i, op in enumerate(ops): if op == 'c': op = 'concat' elif op == 'length': --- a/tools/stats/grouping.xml Tue Mar 22 14:08:32 2011 -0400 +++ b/tools/stats/grouping.xml Tue Mar 22 17:49:09 2011 -0400 @@ -1,4 +1,4 @@ -<tool id="Grouping1" name="Group" version="1.9.3"> +<tool id="Grouping1" name="Group" version="1.9.4"><description>data by a column and perform aggregate operation on other columns.</description><command interpreter="python"> grouping.py Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: fubar: Adding two new tool wrappers and tests - clustalw (http://www.clustal.org) for multiple alignments and a sequence motif generator based on weblogo3 (http://weblogo.berkeley.edu) which works on fasta files such as alignments from clustalw
by Bitbucket 22 Mar '11

22 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0319becf5e76/ changeset: r5246:0319becf5e76 user: fubar date: 2011-03-22 19:08:32 summary: Adding two new tool wrappers and tests - clustalw (http://www.clustal.org) for multiple alignments and a sequence motif generator based on weblogo3 (http://weblogo.berkeley.edu) which works on fasta files such as alignments from clustalw affected #: 8 files (155 bytes) --- a/tool_conf.xml.sample Tue Mar 22 13:45:31 2011 -0400 +++ b/tool_conf.xml.sample Tue Mar 22 14:08:32 2011 -0400 @@ -204,6 +204,10 @@ </section><section name="Motif Tools" id="motifs"><tool file="meme/meme.xml"/> + <tool file="rgenetics/rgWebLogo3.xml" /> + </section> + <section name="Multiple Alignments" id="clustal"> + <tool file="rgenetics/rgClustalw.xml" /></section><section name="Metagenomic analyses" id="tax_manipulation"><tool file="taxonomy/gi2taxonomy.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: richard_burhans: fixed comment bug and added additional error messages for SIFT tool
by Bitbucket 22 Mar '11

22 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/1113dcc5aaa7/ changeset: r5245:1113dcc5aaa7 user: richard_burhans date: 2011-03-22 18:45:31 summary: fixed comment bug and added additional error messages for SIFT tool affected #: 1 file (2.0 KB) --- a/tools/human_genome_variation/sift_variants_wrapper.sh Tue Mar 22 10:50:27 2011 -0400 +++ b/tools/human_genome_variation/sift_variants_wrapper.sh Tue Mar 22 13:45:31 2011 -0400 @@ -16,10 +16,48 @@ sift_input="$working_dir/sift_input.txt" sift_output="$working_dir/sift_output.txt" +################################################################################ +## make sure input file column selections are mutually exclusive ## +################################################################################ +ERROR=0 +declare -a col_use -## -## get/check the db directory from the argument org,db_loc -## +function check_col () { + local col=$1 + local use=$2 + local int=$3 + + if [ -n "${col//[0-9]}" ]; then + if [ $int -eq 1 ]; then + echo "ERROR: invalid value for $use column: $col" 1>&2 + ERROR=1 + fi + return + fi + + local cur=${col_use[$col]} + if [ -n "$cur" ]; then + echo "ERROR: $use column is the same as $cur column" 1>&2 + col_use[$col]="${cur},$use" + ERROR=1 + else + col_use[$col]=$use + fi +} + +check_col $chrom_col 'chromosome' 1 +check_col $pos_col 'position' 1 +check_col $allele_col 'allele' 1 +check_col $strand_col 'strand' 0 +check_col $comment_col 'comment' 0 + +if [ $ERROR -ne 0 ]; then + exit 1 +fi + +################################################################################ +## get/check the db directory from the argument org,db_loc ## +################################################################################ db_dir=$( awk '$1 == org { print $2 }' org=$org $db_loc ) if [ -z "$db_dir" ]; then @@ -32,9 +70,9 @@ exit 1 fi -## -## create input file for SIFT_exome_nssnvs.pl -## +################################################################################ +## create input file for SIFT_exome_nssnvs.pl ## +################################################################################ if [ ! -r "$input_file" ]; then echo "Can't read input file \"$input_file\"" 1>&2 exit 1 @@ -57,32 +95,26 @@ strand='"-1"' else strand="\$$strand_col" - strand_cvt='if ( '"${strand}"' == "+") { '"${strand}"' = "1" } else if ( '"${strand}"' == "-") { '"${strand}"' = "-1"}' + strand_cvt='if ('"${strand}"' == "+") {'"${strand}"' = "1"} else if ('"${strand}"' == "-") {'"${strand}"' = "-1"}' fi -if [ "$comment_col" = "-" ]; then - is_comment=0 -else - is_comment=1 +print_row='print $'"${chrom_col}"', $'"${beg_col}"', $'"${end_col}"', '"${strand}"', $'"${allele_col}"'' +if [ "$comment_col" != "-" ]; then + print_row=''"${print_row}"', $'"${comment_col}"'' fi awk ' BEGIN {FS="\t";OFS=","} +$'"${chrom_col}"' ~ /^[cC][hH][rR]/ {$'"${chrom_col}"' = substr($'"${chrom_col}"',4)} { - $'"${chrom_col}"' = tolower($'"${chrom_col}"') - sub(/^chr/, "", $'"${chrom_col}"') '"${strand_cvt}"' - if ('"${is_comment}"') { - print $'"${chrom_col}"', $'"${beg_col}"', $'"${end_col}"', '"${strand}"', $'"${allele_col}"', $'"${comment_col}"' - } else { - print $'"${chrom_col}"', $'"${beg_col}"', $'"${end_col}"', '"${strand}"', $'"${allele_col}"' - } + '"${print_row}"' } ' "$input_file" > "$sift_input" -## -## run SIFT variants command line program -## +################################################################################ +## run SIFT_exome_nssnvs.pl command line program ## +################################################################################ if [ "$output_opts" = "None" ]; then output_opts="" else @@ -92,18 +124,18 @@ SIFT_exome_nssnvs.pl -i "$sift_input" -d "$db_dir" -o "$working_dir" $output_opts &> "$sift_output" if [ $? -ne 0 ]; then - echo "failed: SIFT_exome_nssnvs.pl -i \"$sift_input\" -d \"$db_dir\" -o \"$working_dir\" $output_opts" - exit 1 + echo "failed: SIFT_exome_nssnvs.pl -i \"$sift_input\" -d \"$db_dir\" -o \"$working_dir\" $output_opts" + exit 1 fi -## -## locate the output file -## +################################################################################ +## locate the SIFT_exome_nssnvs.pl output file ## +################################################################################ sift_pid=$( sed -n -e 's/^.*Your job id is $[0-9][0-9]*$ and is currently running.*$/\1/p' "$sift_output" ) if [ -z "$sift_pid" ]; then - echo "Can't find SIFT pid in \"$sift_output\"" 1>&2 - exit 1 + echo "Can't find SIFT pid in \"$sift_output\"" 1>&2 + exit 1 fi sift_outdir="$working_dir/$sift_pid" @@ -118,9 +150,9 @@ exit 1 fi -## -## create output file -## +################################################################################ +## create galaxy output file ## +################################################################################ awk ' BEGIN {FS="\t";OFS="\t"} NR == 1 { @@ -139,14 +171,14 @@ print "#" $0 } NR != 1 { - if ($3 == "1") { $3 = "+" } else if ($3 == "-1") { $3 = "-" } + if ($3 == "1") {$3 = "+"} else if ($3 == "-1") {$3 = "-"} '"${pos_adj}"' print } ' > "$output_file" -## -## cleanup -## +################################################################################ +## cleanup ## +################################################################################ rm -rf "$sift_outdir" "$sift_input" "$sift_output" Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fix for bug introduced in change set 5243:45b772580403.
by Bitbucket 22 Mar '11

22 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/47f813d8cd6a/ changeset: r5244:47f813d8cd6a user: greg date: 2011-03-22 15:50:27 summary: Fix for bug introduced in change set 5243:45b772580403. affected #: 1 file (0 bytes) --- a/lib/galaxy/web/controllers/user.py Tue Mar 22 10:33:42 2011 -0400 +++ b/lib/galaxy/web/controllers/user.py Tue Mar 22 10:50:27 2011 -0400 @@ -494,7 +494,7 @@ else: status = 'error' if webapp == 'galaxy': - user_type_form_definition = self.__get_user_type_form_definition( trans, user=user, **kwd ) + user_type_form_definition = self.__get_user_type_form_definition( trans, user=None, **kwd ) user_type_fd_id = params.get( 'user_type_fd_id', 'none' ) if user_type_fd_id == 'none' and user_type_form_definition is not None: user_type_fd_id = trans.security.encode_id( user_type_form_definition.id ) 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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