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GMOD Spring Training Application Deadline January 7
by Dave Clements, GMOD Help Desk 02 Jan '11

02 Jan '11

Hello all, The application deadline for the 2011 GMOD Spring Training (http://gmod.org/wiki/2011_GMOD_Spring_Training) is the end of this coming Friday, January 7. Admission is competitive, so please apply by Friday to avoid being automatically placed on the waiting list. Details are below. Thanks, and happy new year! Dave C ------- Applications are now being accepted for the 2011 GMOD Spring Training course (http://gmod.org/wiki/2011_GMOD_Spring_Training) a five-day hands-on school aimed at teaching new GMOD administrators how to install, configure and integrate popular GMOD components. The course will be held March 8-12 at the US National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, as part of GMOD Americas 2011. These components will be covered: * Apollo - genome annotation editor * Chado - biological database schema * Galaxy - analysis and data integration framework * GBrowse - genome viewer * GBrowse_syn - synteny viewer * GFF3 - genome annotation file format and tools * InterMine - biological data mining system * JBrowse - next generation genome browser * MAKER - genome annotation pipeline * Tripal - web front end to Chado databases The deadline for applying is the end of Friday, January 7, 2011. Admission is competitive and is based on the strength of the application, especially the statement of interest. The 2010 school had over 60 applicants for the 25 slots. Any application received after deadline will be automatically placed on the waiting list. The course requires some knowledge of Linux as a prerequisite. The registration fee will be $265 (only $53 per day!). There will be a limited number of scholarships available. This may be the only GMOD School offered in 2011. If you are interested, you are strongly encouraged to apply by January 7. Links: http://gmod.org/wiki/2011_GMOD_Spring_Training http://gmod.org/wiki/GMOD_Americas_2011 http://www.nescent.org/

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Re: [galaxy-dev] galaxy command line error (fasq_grromer.py)
by Dave Clements, GMOD Help Desk 02 Jan '11

02 Jan '11

I am forwarding your question to the Galaxy Dev list, which is the best place to ask this type of question. Dave C On Tue, Dec 28, 2010 at 11:27 PM, <gilgi.friedlander(a)weizmann.ac.il> wrote: > > Hi, > > I am trying to run locally the fastq_groomer.py > > My command: > > python /usr/local/src/galaxy-central/tools/fastq/fastq_groomer.py seq.txt illumina seq_out.txt sanger > > seq.txt is a fastq file with Illumina qualities. > > I get the following error: > > Traceback (most recent call last): > File "/usr/local/src/galaxy-central/tools/fastq/fastq_groomer.py", line 37, in <module> > if __name__ == "__main__": main() > File "/usr/local/src/galaxy-central/tools/fastq/fastq_groomer.py", line 10, in main > force_quality_encoding = sys.argv[5] > IndexError: list index out of range > > Does anyone know what the problem is? > -- ===> PLEASE KEEP RESPONSES ON THE LIST <=== http://gmod.org/wiki/GMOD_Americas_2011 http://gmod.org/wiki/GMOD_News http://gmod.org/wiki/Help_Desk_Feedback

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blastxml to tabular bug fix
by Peter 30 Dec '10

30 Dec '10

Hi Kanwei, Could you check and commit the following three changesets from my new branch: http://bitbucket.org/peterjc/galaxy-central/src/blastplus_nov24 i.e. these three changesets: http://bitbucket.org/peterjc/galaxy-central/changeset/8f0e5a169630 http://bitbucket.org/peterjc/galaxy-central/changeset/72fab21f9469 http://bitbucket.org/peterjc/galaxy-central/changeset/72fab21f9469 This address a problem found earlier today by Alex Bossers (CC'd) while testing the BLAST+ wrappers. The problem can occur when when the query sequence is masked (with XXXX characters), this broke my calculation of the identity and mismatch counts (failing an assert statement I'd included as a sanity check). The new unit test is a cut down version of his failing example. Note that in order to run the unit tests, you will need to first re-enable the tool in tools_conf.xml.sample - the converter tests does not depend on the BLAST+ binaries being installed. Thank you, Peter

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Strange python module error
by Assaf Gordon 29 Dec '10

29 Dec '10

Hi, After upgrading to the latest galaxy-central version, I get the following exception when listing histories: =========== Error - <type 'exceptions.AttributeError'>: 'module' object has no attribute '_magic_number' File '/data/hannon/gordon/galaxy/galaxy_prod/eggs/Paste-1.6-py2.5.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/data/hannon/gordon/galaxy/galaxy_prod/eggs/Paste-1.6-py2.5.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/data/hannon/gordon/galaxy/galaxy_prod/lib/galaxy/web/framework/middleware/remoteuser.py', line 110 in __call__ return self.app( environ, start_response ) File '/data/hannon/gordon/galaxy/galaxy_prod/eggs/Paste-1.6-py2.5.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/data/hannon/gordon/galaxy/galaxy_prod/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/data/hannon/gordon/galaxy/galaxy_prod/lib/galaxy/web/framework/__init__.py', line 84 in decorator return func( self, trans, *args, **kwargs ) File '/data/hannon/gordon/galaxy/galaxy_prod/lib/galaxy/web/controllers/history.py', line 235 in list return self.stored_list_grid( trans, status=status, message=message, **kwargs ) File '/data/hannon/gordon/galaxy/galaxy_prod/lib/galaxy/web/framework/helpers/grids.py', line 269 in __call__ kwargs=kwargs ) File '/data/hannon/gordon/galaxy/galaxy_prod/lib/galaxy/web/framework/__init__.py', line 645 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/data/hannon/gordon/galaxy/galaxy_prod/lib/galaxy/web/framework/__init__.py', line 656 in fill_template_mako return template.render( **data ) File '/data/hannon/gordon/galaxy/galaxy_prod/eggs/Mako-0.2.5-py2.5.egg/mako/template.py', line 133 in render return runtime._render(self, self.callable_, args, data) File '/data/hannon/gordon/galaxy/galaxy_prod/eggs/Mako-0.2.5-py2.5.egg/mako/runtime.py', line 364 in _render _render_context(template, callable_, context, *args, **_kwargs_for_callable(callable_, data)) File '/data/hannon/gordon/galaxy/galaxy_prod/eggs/Mako-0.2.5-py2.5.egg/mako/runtime.py', line 380 in _render_context (inherit, lclcontext) = _populate_self_namespace(context, tmpl) File '/data/hannon/gordon/galaxy/galaxy_prod/eggs/Mako-0.2.5-py2.5.egg/mako/runtime.py', line 348 in _populate_self_namespace ret = template.module._mako_inherit(template, context) File '/data/hannon/gordon/galaxy/galaxy_prod/database/compiled_templates/history/grid.mako.py', line 24 in _mako_inherit return runtime._inherit_from(context, u'../grid_base.mako', _template_uri) File '/data/hannon/gordon/galaxy/galaxy_prod/eggs/Mako-0.2.5-py2.5.egg/mako/runtime.py', line 324 in _inherit_from ret = callable_(template, lclcontext) File '/data/hannon/gordon/galaxy/galaxy_prod/database/compiled_templates/grid_base.mako.py', line 49 in _mako_inherit _mako_generate_namespaces(context) File '/data/hannon/gordon/galaxy/galaxy_prod/database/compiled_templates/grid_base.mako.py', line 45 in _mako_generate_namespaces ns = runtime.Namespace('__anon_0x19274110', context._clean_inheritance_tokens(), templateuri=u'/display_common.mako', callables=None, calling_uri=_template_uri, module=None) File '/data/hannon/gordon/galaxy/galaxy_prod/eggs/Mako-0.2.5-py2.5.egg/mako/runtime.py', line 158 in __init__ self.template = _lookup_template(context, templateuri, calling_uri) File '/data/hannon/gordon/galaxy/galaxy_prod/eggs/Mako-0.2.5-py2.5.egg/mako/runtime.py', line 339 in _lookup_template return lookup.get_template(uri) File '/data/hannon/gordon/galaxy/galaxy_prod/eggs/Mako-0.2.5-py2.5.egg/mako/lookup.py', line 85 in get_template return self.__load(srcfile, uri) File '/data/hannon/gordon/galaxy/galaxy_prod/eggs/Mako-0.2.5-py2.5.egg/mako/lookup.py', line 127 in __load self.__collection[uri] = Template(uri=uri, filename=posixpath.normpath(filename), lookup=self, module_filename=(self.modulename_callable is not None and self.modulename_callable(filename, uri) or None), **self.template_args) File '/data/hannon/gordon/galaxy/galaxy_prod/eggs/Mako-0.2.5-py2.5.egg/mako/template.py', line 85 in __init__ if module._magic_number != codegen.MAGIC_NUMBER: AttributeError: 'module' object has no attribute '_magic_number' =========== has anyone ever encountered such an error ? Any help would be appreciated. -gordon

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galaxy lims issues
by Brieanne Vaillancourt 29 Dec '10

29 Dec '10

Hi, I am going to be working with Galaxy instead of Natalie Fox (at Michigan State University). I know that she was contacting you with "bugs" or "problems" that we were having with Galaxy. I have another "bug" to report and will explain below. This problem has also happened to me several times. All while in the administrator user and before the sequencing request was submitted. 1.) Select "edit" under sequencing request actions. 2.) Change name of request, request details, or anything else in the request. 3.) Save 4.) As shown in the screenshots, it says that it did save but the name and description does not change. If you could please get back to me on this as soon as possible that would be great. Thanks, Brieanne Vaillancourt /Michigan State University Research Technician/

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empty select menu validation problems
by Leandro Hermida 27 Dec '10

27 Dec '10

Happy holidays, Apologies for a simple question, I cannot find seem to find an answer looking through the docs and Galaxy tool xml files in the distro. Is there a way to have a select menu where I don't want there to be a default selection (when the form loads it is empty) yet the user must pick something otherwise one of those nice validator red message comes up telling you to pick something? For example: <param name="organism" type="select" force_select="true" label="Organism"> <option></option> <option value="Homo_sapiens">Homo sapiens</option> <option value="Mus_musculus">Mus musculus</option> <option value="Rattus_norvegicus">Rattus norvegicus</option> </param> If I use the validator type="empty_field" or "no_options" it doesn't work, the user can hit execute with an empty select and it tries to execute. best, Leandro

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conditional with boolean parameter issue
by Leandro Hermida 27 Dec '10

27 Dec '10

Hi there, Don't know if my approach is wrong, in one of my tools I tried to create a conditional with a boolean parameter and I cannot get it to work. E.g. <conditional name="testCond"> <param name="input1" type="boolean" checked="false" truevalue="dothis" falsevalue="dothat" label="Test Checkbox"/> <when value="dothis"/> <when value="dothat"> <param name="input2" type="text" size="100" label="Test"/> </when> </conditional> The form throws and error with: Exception: ('No case matched value:', 'testCond', False) Even if I try to remove truevalue and falsevalue from the param and change the when value="True" and when value="False" I still get the same error. best, Leandro

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Connecting Galaxy to a remote cluster?
by Mattias de Hollander 27 Dec '10

27 Dec '10

Hi, Is it possible to configure Galaxy so it uses a remote cluster? In our setup it is not possible to install the Galaxy frontend on the cluster head/main node. I would like to know if you can connect to a compute cluster on a remote network from the main Galaxy application. Thanks in advance! Mattias

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Setting up microbial_data.loc given a mirror of NCBI FTP site
by Peter 23 Dec '10

23 Dec '10

Hi all, I'd like to be able to use the "Get Microbial Data" tool in our local Galaxy install, which appears as though it could allow access to a local copy of the NCBI "Bacteria" FTP site, ftp://ftp.ncbi.nih.gov/genomes/Bacteria/ >From looking at the tool's source code, I see I must populate microbial_data.loc file, however the microbial_data.loc.sample is not very helpful: #This is a sample file distributed with Galaxy that enables tools #to retrieve microbial data via a URL # #... What this doesn't tell me is the meaning of the columns. Apparently this is really three tables in one, determined by the first entry. ORG entries are used by this tool for the selection of the kingdom and species. They appear to have the following columns, one per species: 0. The "ORG" column itself, not counted in the XML offsets 1. Identifier 2. Species 3. Kingdom 4. Group 5. Comma separated list of chromosomes/plasmids 6. URL for NCBI genome project The CHR entries don't seem to be used directly by this tool. There is one entry per chromosome/plasmid. 0. The "CHR" entry, not counted in the XML offsets 1. Identifier 2. Description including species and chromosome/plasmid 4. Length of sequence (nucleotides) 5. GI number 6. None 7. URL for NCBI nucleotide database Then there are the DATA entries, which appear to reference local files. There are multiple DATA entries per CHR entry: 0. The "DATA" entry, not counted in the XML offsets 1. Identifier (composite of ORG id, CHR id, and data type) 2. Identifier of ORG line 3. Identifier of CHR line 4. Data type (CDS, tRNA, rRNA, sequence, GeneMark, Glimmer3) 5. File format (fasta or bed) 6. Filename Want I want to do is generate a microbial_data.loc file from a local mirror of ftp://ftp.ncbi.nih.gov/genomes/Bacteria/ In addition to understanding the loc file format, it also seems I need to generate some bed files from the NCBI provided data, e.g. for NC_008265 which is one of the examples in the sample loc files, I'd need the following files: NC_008265.CDS.bed NC_008265.tRNA.bed NC_008265.rRNA.bed NC_008265.fna NC_008265.GeneMark.bed NC_008265.GeneMarkHMM.bed NC_008265.Glimmer3.bed Referring to the NCBI FTP site for this organism, we have: NC_008265.GeneMark-2.5m NC_008265.GeneMarkHMM-2.6r NC_008265.Glimmer3 NC_008265.Prodigal-2.50 NC_008265.asn NC_008265.faa NC_008265.ffn NC_008265.fna NC_008265.frn NC_008265.gbk NC_008265.gff NC_008265.ptt NC_008265.rnt NC_008265.rpt NC_008265.val See ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Clostridium_perfringens_SM101_uid58… I can see for example how to map *.ptt (protein tables) into *.CDS.bed, and similarly for the Glimmer3 and GeneMark predictions. I could also probably parse *.gbk to generate bed tabular files for any annotated tRNA and rRNA entries (and the CDS entries of course.). But rather than reinventing the wheel, how do you do this at Penn State? Also, I'd like to offer access to the chromosome, CDS, tRNA, and rRNA sequences themselves (as FASTA files, not just bed tabular). Am I right that currently the "Get Microbial Data" tool doesn't offer this? Thanks, Peter

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Using input parameter's file format in tool XML
by Peter 23 Dec '10

23 Dec '10

Hi all, I've noticed from a couple of examples that when defining the command line string in an tool's XML wrapper (i.e. cheetah template), you can use $input_param_name.extension (or apparently $input_param_name.ext) to get the file format (metadata) for an input parameter called input_param_name (while of course you use $input_param_name to get the filename for this param). This doesn't seem to be documented on the tool conf wiki: http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax Most of the examples I found looking at the tool XML use the longer form (.extension), although interestingly in a recent commit Dan used just .ext in the fastx_clipper.xml file to special case Sanger FASTQ. Is that a valid alternative too? https://bitbucket.org/galaxy/galaxy-central/changeset/93d7007bd859 I'm curious about the naming here - did Galaxy once use the format name as the actual file extension? Now at least all data files seem to have .dat as the extension (which I'm sure presents a small problem for some command line tools which make file format inferences from the filename extension, requiring hacks in their Galaxy wrappers). Peter

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