June 2012 - galaxy-dev - lists.galaxyproject.org

(no subject)
by Carlos Reyes 28 Jun '12

28 Jun '12

Hello, I have never used this support route before however I have a question about a Galaxy wrapper that I made for a python tool. I have a text input box connected to a $command_line_spot in an attempt to run a string such as "IN[4]=='gene'" on the command line (quotations included) through text box input. When I put "IN[4]=='gene'" directly in the command line it runs fine, however when I put it through my text box it puts the string on the command line as __dq__IN__ob__4__cb__==__sq__gene__sq____dq__ "IN[4]=='gene'" instead of just "IN[4]=='gene'". Sorry if this email makes no sense whatsoever, it is very out of context but I thought I'd ask. Note: I am running the latest release of galaxy which I pulled from mercurial. Thanks, Carlos The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

2 1

DrmCommunicationException: code 2: unable to contact qmaster using port 6444 on host "login"
by Sarah Maman 28 Jun '12

28 Jun '12

Hello Galaxy group, I did not achieve to run again my Galaxy local instance. The error is: galaxy.jobs DEBUG 2012-06-28 11:57:36,785 Loaded job runner: galaxy.jobs.runners.local:LocalJobRunner Traceback (most recent call last): File "/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/app.py", line 124, in __init__ self.job_manager = jobs.JobManager( self ) File "/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 44, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File "/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1190, in __init__ self._load_plugin( name ) File "/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1207, in _load_plugin self.job_runners[name] = runner( self.app ) File "/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 100, in __init__ self.ds.initialize() File "/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/drmaa-0.4b3-py2.6.egg/drmaa/__init__.py", line 274, in init ialize _w.init(contactString) File "/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/drmaa-0.4b3-py2.6.egg/drmaa/wrappers.py", line 59, in init return _lib.drmaa_init(contact, error_buffer, sizeof(error_buffer)) File "/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/drmaa-0.4b3-py2.6.egg/drmaa/errors.py", line 90, in error_c heck raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value)) DrmCommunicationException: code 2: unable to contact qmaster using port 6444 on host "login" I didn't find an answer here: http://gmod.827538.n3.nabble.com/Galaxy-Hang-after-DrmCommunicationExceptio… Could you please help me ? Thanks in advance, Sarah Maman

1 0

questions about uploading and working with directories
by Jemma Wu 28 Jun '12

28 Jun '12

Dear all, I have installed a Galaxy instance on my local server and it runs well. However I have some problems with directories. I want to create a workflow that takes a directory of files (e.g. 10) and repeatedly working on all files and then output another set of files (10) which are piped into the next tool. I searched over this forum, but couldn't find the solution (maybe I missed something). Does Galaxy directly support tools which work on a whole directory? Any suggestions/comments on this would be much appreciated! Regards, Jemma

1 0

xsendfile error
by Kenichi Dedachi 27 Jun '12

27 Jun '12

Dear community members, Now I try install Galaxy into our local servers, and I largely-successful run Galaxy at local server with Apache-proxy. However, I encounter problem in relation to xsendfile, the details of my configuration are shown below, 1. I Installed mod_xsendfile 2. set up universe_wsgi.ini [app:main] apache_xsendfile = True 3. set up httpd.conf <Location "/galaxy"> XsendFile on XsendFilePath /galaxy </Location> After above configuration, I restart Galaxy and run jobs (e.g. FastQC). However, when I click floppy icon to download the result file, the right history window go white background and shows following error message, "OK The requested URL /galaxy/datasets/1877a09319a433f5/ display was not found on this server." If I change the apache_xsendfile setting to False, I can download files as usual. Why I can not use xsenfile module? I would like to know some ideas for solution of this problem. Thank you very much in advance. kenichi

1 0

Bug: "Galaxy" logo link doesn't account for proxy-prefix
by Steven Peckins 27 Jun '12

27 Jun '12

The "Galaxy" logo link in the top left corner of every page has href="/" regardless of proxy-prefix. <div class="title"> <a href="/"> <img border="0" src="/galaxy/static/images/galaxyIcon_noText.png"> Galaxy </a> </div>

2 1

scripts in welcome.html?
by Smithies, Russell 27 Jun '12

27 Jun '12

To stop users forgetting whether they're on our development or production servers I'd like to put a simple script in welcome.html to echo the hostname (or some other stuff) I've tried both javascript and php but no luck. Is this supported or should I dig further into our Apache config? Or is there a better way to do it? Thanx, Russell Smithies ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. =======================================================================

3 3

Server Error after fresh installation of Galaxy
by Iry Witham 27 Jun '12

27 Jun '12

I have recently performed a fresh installation of Galaxy utilizing the latest distribution and am getting a sizable number of errors when attempting to start the server. The issue started when I performed a merge so I decided to do the clean install as a test. The server appears to start just fine, but with errors reported in the logs. The web0.log gives the following errors and warnings (I am truncating the file for space): galaxy.model.migrate.check DEBUG 2012-06-20 18:29:20,497 psycopg2 egg successfully loaded for postgres dialect galaxy.model.migrate.check INFO 2012-06-20 18:29:20,599 At database version 97 galaxy.tool_shed.migrate.check DEBUG 2012-06-20 18:29:20,630 psycopg2 egg successfully loaded for postgres dialect galaxy.tool_shed.migrate.check INFO 2012-06-20 18:29:20,649 At migrate_tools version 2 galaxy.model.custom_types DEBUG 2012-06-20 18:29:20,654 psycopg2 egg successfully loaded for postgres dialect galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658 Loading references to tool sheds from tool_sheds_conf.xml galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658 Loaded reference to tool shed: Galaxy main tool shed galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658 Loaded reference to tool shed: Galaxy test tool shed galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,014 Loading datatypes from datatypes_conf.xml galaxy.datatypes.registry WARNING 2012-06-20 18:29:21,015 Overriding conflicting datatype with extension 'coverage', using datatype from datatypes_conf.xml. galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,025 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,025 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,025 Loaded sniffer for datatype 'galaxy.datatypes.xml:BlastXml' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer for datatype 'galaxy.datatypes.images:Html' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' galaxy.tools.data DEBUG 2012-06-20 18:29:21,059 Loaded tool data table 'all_fasta' galaxy.tools.data DEBUG 2012-06-20 18:29:21,060 Loaded tool data table 'bfast_indexes' galaxy.tools.data DEBUG 2012-06-20 18:29:21,061 Loaded tool data table 'blastdb' galaxy.tools.data DEBUG 2012-06-20 18:29:21,062 Loaded tool data table 'blastdb_p' galaxy.tools.data DEBUG 2012-06-20 18:29:21,065 Loaded tool data table 'bowtie_indexes' galaxy.tools.data DEBUG 2012-06-20 18:29:21,066 Loaded tool data table 'bowtie_indexes_color' galaxy.tools.data DEBUG 2012-06-20 18:29:21,068 Loaded tool data table 'rsem_indexes' galaxy.tools.data DEBUG 2012-06-20 18:29:21,075 Loaded tool data table 'bwa_indexes' galaxy.tools.data DEBUG 2012-06-20 18:29:21,079 Loaded tool data table 'bwa_indexes_color' galaxy.tools.data DEBUG 2012-06-20 18:29:21,081 Loaded tool data table 'indexed_maf_files' galaxy.tools.data DEBUG 2012-06-20 18:29:21,084 Loaded tool data table 'ngs_sim_fasta' galaxy.tools.data DEBUG 2012-06-20 18:29:21,087 Loaded tool data table 'lastz_seqs' galaxy.tools.data DEBUG 2012-06-20 18:29:21,089 Loaded tool data table 'perm_base_indexes' galaxy.tools.data DEBUG 2012-06-20 18:29:21,091 Loaded tool data table 'perm_color_indexes' galaxy.tools.data DEBUG 2012-06-20 18:29:21,094 Loaded tool data table 'picard_indexes' galaxy.tools.data DEBUG 2012-06-20 18:29:21,095 Loaded tool data table 'gatk_picard_indexes' galaxy.tools.data DEBUG 2012-06-20 18:29:21,096 Loaded tool data table 'srma_indexes' galaxy.tools.data DEBUG 2012-06-20 18:29:21,097 Loaded tool data table 'tophat_indexes' galaxy.tools.data DEBUG 2012-06-20 18:29:21,098 Loaded tool data table 'tophat_indexes_color' galaxy.tools.data DEBUG 2012-06-20 18:29:21,100 Loaded tool data table 'ccat_configurations' galaxy.tools.data DEBUG 2012-06-20 18:29:21,101 Loaded tool data table 'mosaik_indexes' galaxy.tools.data DEBUG 2012-06-20 18:29:21,104 Loaded tool data table 'mousedivgeno_anno' galaxy.tools.data DEBUG 2012-06-20 18:29:21,106 Loaded tool data table 'mousedivgeno_background_cel_dirs' galaxy.tools.data DEBUG 2012-06-20 18:29:21,108 Loaded tool data table 'cnv_seq_refs' galaxy.tools INFO 2012-06-20 18:29:21,125 Parsing the tool configuration ./tool_conf.xml galaxy.tools.test DEBUG 2012-06-20 18:29:21,579 Error in add_param for input: Unable to determine parameter type of test input 'input'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2012-06-20 18:29:21,579 Error in add_param for input: Unable to determine parameter type of test input 'input'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2012-06-20 18:29:21,706 Error in add_param for input: Unable to determine parameter type of test input 'input'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2012-06-20 18:29:21,706 Error in add_param for input: Unable to determine parameter type of test input 'input'. Ensure that the parameter exists and that any container groups are defined first. docutils WARNING 2012-06-20 18:29:25,232 <string>:8: (WARNING/2) Title underline too short. This tool uses raw orthologous microsatellite clusters (identified by the tool "Extract orthologous microsatellites") to identify microsatellite births and deaths along individual lineages of a phylogenetic tree. ----- galaxy.tools WARNING 2012-06-20 18:29:26,871 A when tag has been defined for 'manipulation (manipulation_selector) --> modify_each_score', but does not appear to be selectable. galaxy.tools WARNING 2012-06-20 18:29:28,304 A when tag has been defined for 'input (format) --> None', but does not appear to be selectable. galaxy.tools WARNING 2012-06-20 18:29:28,304 A when tag has not been defined for 'useci (ci) --> no', assuming empty inputs. docutils WARNING 2012-06-20 18:29:28,360 <string>:285: (ERROR/3) Unexpected indentation. docutils WARNING 2012-06-20 18:29:28,362 <string>:301: (ERROR/3) Unexpected indentation. docutils WARNING 2012-06-20 18:29:28,484 <string>:50: (WARNING/2) Literal block expected; none found. galaxy.tools.test DEBUG 2012-06-20 18:29:28,495 Error in add_param for min_coverage_intron: Unable to determine parameter type of test input 'min_coverage_intron'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2012-06-20 18:29:28,495 Error in add_param for max_coverage_intron: Unable to determine parameter type of test input 'max_coverage_intron'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools WARNING 2012-06-20 18:29:28,760 A when tag has not been defined for 'indel (call_indels) --> false', assuming empty inputs. galaxy.tools ERROR 2012-06-20 18:29:29,082 Error reading tool from path: None Traceback (most recent call last): File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", line 315, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/usr/lib64/python2.6/posixpath.py", line 65, in join if b.startswith('/'): AttributeError: 'NoneType' object has no attribute 'startswith' galaxy.tools.parameters.dynamic_options WARNING 2012-06-20 18:29:29,382 Data table named 'gatk_annotations' is required by tool but not configured galaxy.tools ERROR 2012-06-20 18:29:29,382 Error reading tool from path: gatk/unified_genotyper.xml Traceback (most recent call last): File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", line 315, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", line 433, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", line 769, in __init__ self.parse( root, guid=guid ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", line 933, in parse self.parse_inputs( root ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", line 1015, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", line 1214, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", line 1281, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", line 1307, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", line 1319, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 626, in __init__ self.options = dynamic_options.DynamicOptions( options, self ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py", line 449, in __init__ self.filters.append( Filter.from_element( self, filter_elem ) ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py", line 22, in from_element return filter_types[type.strip()]( d_option, elem ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py", line 213, in __init__ self.columns = [ d_option.column_spec_to_index( column ) for column in columns.split( "," ) ] File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py", line 571, in column_spec_to_index return int( column_spec ) ValueError: invalid literal for int() with base 10: 'tools_valid_for' galaxy.tools.parameters.dynamic_options WARNING 2012-06-20 18:29:29,398 Data table named 'gatk_annotations' is required by tool but not configured galaxy.tools ERROR 2012-06-20 18:29:29,398 Error reading tool from path: gatk/variant_annotator.xml Traceback (most recent call last): File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", line 315, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", line 433, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", line 769, in __init__ self.parse( root, guid=guid ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", line 933, in parse self.parse_inputs( root ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", line 1015, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", line 1214, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", line 1281, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", line 1307, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", line 1319, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 626, in __init__ self.options = dynamic_options.DynamicOptions( options, self ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py", line 449, in __init__ self.filters.append( Filter.from_element( self, filter_elem ) ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py", line 22, in from_element return filter_types[type.strip()]( d_option, elem ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py", line 213, in __init__ self.columns = [ d_option.column_spec_to_index( column ) for column in columns.split( "," ) ] File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py", line 571, in column_spec_to_index return int( column_spec ) ValueError: invalid literal for int() with base 10: 'tools_valid_for' galaxy.tools.parameters.dynamic_options WARNING 2012-06-20 18:29:29,445 Data table named 'gatk_annotations' is required by tool but not configured galaxy.tools ERROR 2012-06-20 18:29:29,445 Error reading tool from path: gatk/variant_recalibrator.xml Traceback (most recent call last): File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", line 315, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", line 433, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", line 769, in __init__ self.parse( root, guid=guid ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", line 933, in parse self.parse_inputs( root ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", line 1015, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", line 1214, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", line 1307, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", line 1319, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 626, in __init__ self.options = dynamic_options.DynamicOptions( options, self ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py", line 449, in __init__ self.filters.append( Filter.from_element( self, filter_elem ) ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py", line 22, in from_element return filter_types[type.strip()]( d_option, elem ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py", line 213, in __init__ self.columns = [ d_option.column_spec_to_index( column ) for column in columns.split( "," ) ] File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py", line 571, in column_spec_to_index return int( column_spec ) ValueError: invalid literal for int() with base 10: 'tools_valid_for' galaxy.tools.test DEBUG 2012-06-20 18:29:29,993 Error in add_param for force: Unable to determine parameter type of test input 'force'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools INFO 2012-06-20 18:29:30,785 Parsing the tool configuration ./migrated_tools_conf.xml galaxy.tools DEBUG 2012-06-20 18:29:30,787 Loading section: JAX Custom Tools galaxy.tools DEBUG 2012-06-20 18:29:30,787 Loaded tool id: export_to_igv, version: 1.0.0. -- -- galaxy.tools.imp_exp DEBUG 2012-06-20 18:29:33,190 Loaded history export tool: __EXPORT_HISTORY__ galaxy.tools.imp_exp DEBUG 2012-06-20 18:29:33,191 Loaded history import tool: __IMPORT_HISTORY__ galaxy.jobs.runners.local INFO 2012-06-20 18:29:33,204 starting workers galaxy.jobs.runners.local DEBUG 2012-06-20 18:29:33,205 5 workers ready galaxy.jobs.handler DEBUG 2012-06-20 18:29:33,205 Loaded job runner: galaxy.jobs.runners.local:LocalJobRunner galaxy.jobs.handler INFO 2012-06-20 18:29:33,206 job handler stop queue started galaxy.jobs.manager INFO 2012-06-20 18:29:33,211 job manager queue started galaxy.jobs.manager INFO 2012-06-20 18:29:33,211 job manager stop queue started galaxy.jobs.handler INFO 2012-06-20 18:29:33,214 job handler queue started galaxy.sample_tracking.external_service_types ERROR 2012-06-20 18:29:33,214 ExternalServiceTypesCollection error reading ./external_service_types_conf.xml Traceback (most recent call last): File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/sample_tracking/external_service_types.py", line 21, in __init__ self.load_all( config_filename ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/sample_tracking/external_service_types.py", line 26, in load_all tree = util.parse_xml( config_filename ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/util/__init__.py", line 105, in parse_xml tree = ElementTree.parse(fname) File "build/bdist.linux-x86_64-ucs4/egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "build/bdist.linux-x86_64-ucs4/egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './external_service_types_conf.xml' galaxy.web.framework.base DEBUG 2012-06-20 18:29:33,224 Enabling 'async' controller, class: ASync galaxy.web.framework.base DEBUG 2012-06-20 18:29:33,251 Enabling 'workflow' controller, class: WorkflowController galaxy.web.framework.base DEBUG 2012-06-20 18:29:33,267 Enabling 'admin_toolshed' controller, class: AdminGalaxy -- -- galaxy.web.buildapp DEBUG 2012-06-20 18:29:33,654 Enabling 'config' middleware galaxy.web.buildapp DEBUG 2012-06-20 18:29:33,655 Enabling 'x-forwarded-host' middleware Starting server in PID 956. serving on 0.0.0.0:8080 view at http://127.0.0.1:8080 10.20.22.8 - - [20/Jun/2012:18:29:57 -0400] "GET / HTTP/1.0" 500 - "-" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.2.19) Gecko/20110707 Firefox/3.6.19" Error - <type 'exceptions.AttributeError'>: 'Configuration' object has no attribute 'cloud_controller_instance' -------------------------------------------- The runner0.log contains most the same errors as the web0.log with the following addition: galaxy.jobs.runners.local INFO 2012-06-20 16:18:25,622 starting workers galaxy.jobs.runners.local DEBUG 2012-06-20 16:18:25,622 3 workers ready galaxy.jobs.handler DEBUG 2012-06-20 16:18:25,623 Loaded job runner: galaxy.jobs.runners.local:LocalJobRunner galaxy.jobs.handler ERROR 2012-06-20 16:18:25,758 Job runner is not loadable: galaxy.jobs.runners.pbs Traceback (most recent call last): File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/jobs/handler.py", line 375, in _load_plugin module = __import__( module_name ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", line 30, in <module> raise Exception( egg_message % str( e ) ) Exception: The 'pbs' runner depends on 'pbs_python' which is not installed or not configured properly. Galaxy's "scramble" system should make this installation simple, please follow the instructions found at: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster Additional errors may follow: ['pbs_python'] galaxy.jobs.handler INFO 2012-06-20 16:18:25,761 job handler stop queue started galaxy.jobs.manager INFO 2012-06-20 16:18:25,766 job manager queue started galaxy.jobs.manager INFO 2012-06-20 16:18:25,767 job manager stop queue started galaxy.jobs.handler INFO 2012-06-20 16:18:25,770 job handler queue started galaxy.sample_tracking.external_service_types ERROR 2012-06-20 16:18:25,771 ExternalServiceTypesCollection error reading ./external_service_types_conf.xml Traceback (most recent call last): File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/sample_tracking/external_service_types.py", line 21, in __init__ self.load_all( config_filename ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/sample_tracking/external_service_types.py", line 26, in load_all tree = util.parse_xml( config_filename ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/util/__init__.py", line 105, in parse_xml tree = ElementTree.parse(fname) File "build/bdist.linux-x86_64-ucs4/egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "build/bdist.linux-x86_64-ucs4/egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './external_service_types_conf.xml' galaxy.web.framework.base DEBUG 2012-06-20 16:18:25,782 Enabling 'async' controller, class: ASync galaxy.web.framework.base DEBUG 2012-06-20 16:18:25,816 Enabling 'workflow' controller, class: WorkflowController galaxy.web.framework.base DEBUG 2012-06-20 16:18:25,835 Enabling 'admin_toolshed' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2012-06-20 16:18:25,836 Enabling 'admin_toolshed' controller, class: AdminToolshed This is the server error from the browser: URL: http://galaxy2/ Module paste.exceptions.errormiddleware:143 in __call__ << <http://galaxy2/#> try: __traceback_supplement__ = Supplement, self, environ app_iter = self.application(environ, start_response) return self.make_catching_iter(app_iter, environ) except:>> <http://galaxy2/#> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ << <http://galaxy2/#> try: status, headers, body = wsgilib.intercept_output( environ, self.app) if status is None: # Some error occurred>> <http://galaxy2/#> environ, self.app) Module paste.wsgilib:539 in intercept_output << <http://galaxy2/#> data.append(headers) return output.write app_iter = application(environ, replacement_start_response) if data[0] is None: return (None, None, app_iter)>> <http://galaxy2/#> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ << <http://galaxy2/#> environ['paste.recursive.script_name'] = my_script_name try: return self.application(environ, start_response) except ForwardRequestException, e: middleware = CheckForRecursionMiddleware(>> <http://galaxy2/#> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ << <http://galaxy2/#> []).append(HTTPException) try: return self.application(environ, start_response) except HTTPException, exc: return exc(environ, start_response)>> <http://galaxy2/#> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ << <http://galaxy2/#> kwargs.pop( '_', None ) try: body = method( trans, **kwargs ) except Exception, e: body = self.handle_controller_exception( e, trans, **kwargs )>> <http://galaxy2/#> body = method( trans, **kwargs ) Module galaxy.web.controllers.root:25 in index << <http://galaxy2/#> tool_id=tool_id, workflow_id=workflow_id, m_c=m_c, m_a=m_a ) ## ---- Tool related ----------------------------------------------------->> <http://galaxy2/#> m_c=m_c, m_a=m_a ) Module galaxy.web.framework:733 in fill_template << <http://galaxy2/#> self.get_user() if filename.endswith( ".mako" ): return self.fill_template_mako( filename, **kwargs ) else: template = Template( file=os.path.join(self.app.config.template_path, filename),>> <http://galaxy2/#> return self.fill_template_mako( filename, **kwargs ) Module galaxy.web.framework:744 in fill_template_mako << <http://galaxy2/#> data.update( self.template_context ) data.update( kwargs ) return template.render( **data ) def stream_template_mako( self, filename, **kwargs ): template = self.webapp.mako_template_lookup.get_template( filename )>> <http://galaxy2/#> return template.render( **data ) Module mako.template:296 in render << <http://galaxy2/#> """ return runtime._render(self, self.callable_, args, data) def render_unicode(self, *args, **data):>> <http://galaxy2/#> return runtime._render(self, self.callable_, args, data) Module mako.runtime:660 in _render << <http://galaxy2/#> _render_context(template, callable_, context, *args, **_kwargs_for_callable(callable_, data)) return context._pop_buffer().getvalue()>> <http://galaxy2/#> **_kwargs_for_callable(callable_, data)) Module mako.runtime:692 in _render_context << <http://galaxy2/#> # if main render method, call from the base of the inheritance stack (inherit, lclcontext) = _populate_self_namespace(context, tmpl) _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) else: # otherwise, call the actual rendering method specified>> <http://galaxy2/#> _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) Module mako.runtime:718 in _exec_template << <http://galaxy2/#> _render_error(template, context, e) else: callable_(context, *args, **kwargs) def _render_error(template, context, error):>> <http://galaxy2/#> callable_(context, *args, **kwargs) Module _base_panels_mako:53 in render_body << <http://galaxy2/#> __M_writer(u'<html>\n ') # SOURCE LINE 206 __M_writer(unicode(self.init())) __M_writer(u' \n <head>\n <title>') # SOURCE LINE 208>> <http://galaxy2/#> __M_writer(unicode(self.init())) Module root_index_mako:58 in render_init << <http://galaxy2/#> # SOURCE LINE 186 if trans.app.config.cloud_controller_instance: self.has_left_panel=False self.has_right_panel=False>> <http://galaxy2/#> if trans.app.config.cloud_controller_instance: AttributeError: 'Configuration' object has no attribute 'cloud_controller_instance' I am not quite sure where the issue lies, but your help will be appreciated. Thanks, Iry Witham Scientific Applications Administrator Scientific Computing Group Computational Sciences Dept. The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 Phone: 207-288-6744 email: iry.witham(a)jax.org The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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mapping software doesn't start - Main
by Artem Pankin 27 Jun '12

27 Jun '12

Dear All, I am trying to start mapping of my Illumina dataset using Bowtie and BWA on the Main server. The process goes to the queue but never starts. I have been waiting for more than 24 hours (26-27 June) and it is still queued. I tried exactly the same workflow on the Test server and it worked. Is it a temporary problem with the mapping software on the Main or a user-specific issue? Thank you in advance, Artem

1 0

Are there any database test scripts?
by Anthonius deBoer 26 Jun '12

26 Jun '12

Hi, I am still having serious issues with running galaxy workflows from the API on my installation... I am getting random files on which the workflows are run, rather than the files I select in my script. I am suspecting that my database may be corrupt...Is there any test script that can test my theory? I am running postgres and the database may have become corrupted, although running the same WF from the UI has no problems, so I still suspect the API... Thanks Thon

1 0

Tophat Troubles
by Kristen Roop 26 Jun '12

26 Jun '12

Hello, I am having an issue on the Galaxy Main server. I had reached my maximum disk space this morning. So I cleaned out some items until my space was down to 61%. I then tried to run Tophat for RNA seq and the tool is doing nothing. I know the datasets aren't too large because I would have received an error message. The job simply goes into my queue as gray and says waiting to run. Any ideas on what is going on? Thanks, Kristen Roop

3 2