June 2013 - galaxy-dev - lists.galaxyproject.org

tool shed tools are not recognised in jobs_conf.xml
by Björn Grüning 25 Jun '13

25 Jun '13

Hi, I tried to increase the h_vmem setting for a tool shed tool in jobs_conf.xml, but nothing from the documented options [1] worked for me. However, it works for non tool shed tools. Did anyone see such a behaviour? We are using SGE/drmaa. Thanks, Björn [1] id="toolshed.example.org/repos/nate/filter_tool_repo/filter_tool/1.0.0" or id="toolshed.example.org/repos/nate/filter_tool_repo/filter_tool" or id="filter_tool"

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Bowtie2 on a new local instance
by Mathew Moore 25 Jun '13

25 Jun '13

I installed a local instance of Galaxy, and (i believe) downloaded all of the dependencies, indexes, and modified the appropriate .loc files. Pretty much all of the tools work, except for Bowtie2. (I installed the bowtie tool, and it works perfectly) The bowtie2 sequence assembler completes with appropriate output from the command-line, but not from the WEB-GUI interface. When you run Bowtie2 from the web-GUI, it completes almost immediately, not with an error, but with a 62byte bam file. The output box in the gui indicates the file contents are 'binary bam alignments file'. For the record, I installed the bowtie2 example lamda indexes in Galaxy and modified the loc file. After running the example FQ files through the WEB-GUI I received the same 62Byte output, indicating it's not a file or index problem. Running this example on the command-line completes as expected. Has anyone seen this. I'm sure I did something stupid somewhere, I just can't seem to find it. Any assistance would be appreciated. Kind regards, Mat

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galaxy cuffdiff running too long
by Robert Chase 25 Jun '13

25 Jun '13

Hello, When we run cuffdiff from the command line we get this; [galaxy@q ~]$ /bin/cuffdiff /bin/cuffdiff: /usr/lib64/libz.so.1: no version information available (required by /bin/cuffdiff) cuffdiff v2.0.2 (3522) It looks like we are using a more recent version of cuffdiff than is supported by the galaxy tool wrappers (0.0.5 and 0.0.6). Using the 0.0.5 tool gives empty outputs. Using the 0.0.6 tool results in runs that last for five days without terminating. Has this behavior been seen before? How can we get good outputs to feed into cummeRbund? -Rob

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BAM pileups bugging out
by Andrew Guo 25 Jun '13

25 Jun '13

After using tools to convert a SAM to a BAM file, I am trying to filter the BAM pileup. However, the filter BAM tool is not picking up on the dataset that I just created. It should show up under 10 column pileup, but an error message is saying "History does not include a dataset of the required format/build". Could you provide any insight into this? Thanks, Andrew

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Error in using Trackster: datatypes_conf.xml
by Perez, Ricardo 25 Jun '13

25 Jun '13

Dear all, I am trying to set up trackster for my local instance in galaxy. I did the following: Uncommented from the universe_wsgi.ini; len_file_path = path/to/file/galaxy-dist/tool-data/shared/ucsc/chrom Also I ran the following commands: mkdir ./tool-data/shared/ucsc/chrom/ python ./cron/build_chrom_db.py ./tool-data/shared/ucsc/chrom/ However when I try to use trackster, I get the following message: "A converted for this file is not installed. Please heck your datatypes_conf.xml file." How exactly do I find out which converted files I am missing? I did the above steps in another instance of galaxy and Trackster works fine in there. Thank you for your time, --Ricardo Perez

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validation for tools
by מירב . 25 Jun '13

25 Jun '13

Hi, I want to do some checks on tools I'm using(in this case I'm checking svdetect). I have a program that creats .fasta file of genome with some structural variants. Now I need a tool wich will simulate the illumina's sequencing read and output .fastq files(or .sam files). Does galaxy have such tool? If not, do you have suggestion for something out of galaxy? Thanks for your help merav

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Proxy error while testing FASTX tools?
by Sebastian Schaaf 25 Jun '13

25 Jun '13

Hi all, I've got a relatively fresh installed Galaxy instance running within a locked network, where internet access is allowed only via a proxy. So far, so simple; indeed I get internet access via a terminal (e.g. calling Google with lynx), also wget and mercurial have the chance to access target URL's. The variables $http_proxy, $https_proxy and $ftp_proxy are set. My problem occurs when I try to execute the automatic tests (using 'run_functional_tests.sh') for the FASTX toolbox, described here right at the end: http://hannonlab.cshl.edu/fastx_toolkit/download.html The calls of the scripts generally end up in an error block of the following scheme: ##### functional_tests.py DEBUG 2013-06-25 14:15:40,406 Attempting to serve app on randomly chosen port: 8720 functional_tests.py INFO 2013-06-25 14:15:40,468 Embedded web server started base.asserts DEBUG 2013-06-25 14:15:40,506 base.asserts.text base.asserts DEBUG 2013-06-25 14:15:40,506 base.asserts.tabular base.asserts DEBUG 2013-06-25 14:15:40,506 base.asserts.xml functional_tests.py INFO 2013-06-25 14:15:40,506 Functional tests will be run against localhost:8720 nose.plugins.manager DEBUG 2013-06-25 14:15:40,518 DefaultPluginManager load plugin nosetestdiff = nosetestdiff.plugin:NoseTes tDiff nose.plugins.manager DEBUG 2013-06-25 14:15:40,520 DefaultPluginManager load plugin nosehtml = nosehtml.plugin:NoseHTML Uncollapse ( cshl_fastx_uncollapser ) > Test-1 ... ERROR ====================================================================== ERROR: Uncollapse ( cshl_fastx_uncollapser ) > Test-1 ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/galaxy/galaxy-dist/test/base/twilltestcase.py", line 53, in setUp self.home() File "/home/galaxy/galaxy-dist/test/base/twilltestcase.py", line 1141, in home self.visit_url( self.url ) File "/home/galaxy/galaxy-dist/test/base/twilltestcase.py", line 1324, in visit_url tc.code( 200 ) File "/home/galaxy/galaxy-dist/eggs/twill-0.9-py2.6.egg/twill/commands.py", line 133, in code should_be)) TwillAssertionError: code is 403 != 200 ---------------------------------------------------------------------- Ran 1 test in 0.011s FAILED (errors=1) ##### For me it reads like there is problem while testing to call the URL in self.url, which resolves to 'localhost:9441'. URL and port are drawn from the environment in the script ".../galaxy-dist/test/base/twilltestcase.py": ##### class TwillTestCase( unittest.TestCase ): def setUp( self ): [...] self.host = os.environ.get( 'GALAXY_TEST_HOST' ) self.port = os.environ.get( 'GALAXY_TEST_PORT ) self.url = "http://%s:%s" % ( self.host, self.port ) [...] ##### I could neither observe any process listening to port 9441 during the test script execution, nor any of the text files within the galaxy root dir contained '9441' as part of a configuration option. Finally I'm a bit confused what that means to me, beyond just not to be able to use the test suite. Anyone an idea what could and/or should be fixed or checked? Thanks in advance, Sebastian -- Sebastian Schaaf, M.Sc. Bioinformatics Department of Medical Informatics, Biometry and Epidemiology (IBE) University of Munich

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How to enable auto option for newly added file formats
by shashi shekhar 24 Jun '13

24 Jun '13

Hi, I want to enable option auto option for some format ..how will i proceed . I have alreadu added the format in galaxy ., which works without auto option. Regards shashi

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account avatar
by Philipe Moncuquet 24 Jun '13

24 Jun '13

Hi, We are running a local instance of Galaxy behind firewall. How can one modify the picture associated with is galaxy account in the configuration ? Regards, Philippe

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GATK tools not showing up in cloudman Galaxy installation
by Marco Ocana 24 Jun '13

24 Jun '13

Hi, When starting up Galaxy from Cloudman and updating the latest version from repository, most of the GATK tools do not show up in the tool bar. I have attached the log file. There are other errors in the log file, but I have pasted what I believe the relavant section of the log. Any pointers on how to fix the problem would be appreciated. Thanks Marco Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 396, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 515, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 855, in __init__ self.parse( root, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1028, in parse self.parse_inputs( root ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1112, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1516, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1583, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1621, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 1361, in __init__ ToolParameter.__init__( self, tool, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 43, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 23, in from_element return validator_types[type].from_element( param, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 279, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py", line 25, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'gatk_picard_indexes' galaxy.tools ERROR 2013-06-20 17:54:00,272 Error reading tool from path: gatk/indel_realigner.xml Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 396, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 515, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 855, in __init__ self.parse( root, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1028, in parse self.parse_inputs( root ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1112, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1516, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1583, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1621, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 1361, in __init__ ToolParameter.__init__( self, tool, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 43, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 23, in from_element return validator_types[type].from_element( param, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 279, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py", line 25, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'gatk_picard_indexes' galaxy.tools ERROR 2013-06-20 17:54:00,281 Error reading tool from path: gatk/count_covariates.xml Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 396, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 515, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 855, in __init__ self.parse( root, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1028, in parse self.parse_inputs( root ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1112, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1516, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1583, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1621, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 1361, in __init__ ToolParameter.__init__( self, tool, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 43, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 23, in from_element return validator_types[type].from_element( param, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 279, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py", line 25, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'gatk_picard_indexes' galaxy.tools ERROR 2013-06-20 17:54:00,290 Error reading tool from path: gatk/table_recalibration.xml Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 396, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 515, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 855, in __init__ self.parse( root, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1028, in parse self.parse_inputs( root ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1112, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1516, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1583, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1621, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 1361, in __init__ ToolParameter.__init__( self, tool, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 43, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 23, in from_element return validator_types[type].from_element( param, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 279, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py", line 25, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'gatk_picard_indexes' galaxy.tools ERROR 2013-06-20 17:54:00,323 Error reading tool from path: gatk/unified_genotyper.xml Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 396, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 515, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 855, in __init__ self.parse( root, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1028, in parse self.parse_inputs( root ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1112, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1516, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1583, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1539, in parse_input_elem group.inputs = self.parse_input_elem( elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1621, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 1361, in __init__ ToolParameter.__init__( self, tool, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 43, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 23, in from_element return validator_types[type].from_element( param, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 279, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py", line 25, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'gatk_picard_indexes'

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