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bowtie on localgalaxy
by Arun Selvam 09 Jun '11

09 Jun '11

Hi, I am new to galaxy, I just downloaded and installed galaxy on my MAC system. I also download bowtie , and it is working perfectly on the command line. But am not able to see the bowtie option under mapping in the galaxy menu. Do I have to do another modifications like move into particular folder or create some files or set path ? Could anyone please help me on this ? Thank you Arun

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select menu in conditional tag cannot be set at runtime in workflow editor
by Leandro Hermida 09 Jun '11

09 Jun '11

Hi all, In a tool XML I have a select menu param within/driving a conditional tag and in the workflow editor it doesn't let me choose to allow the user to set this select menu at runtime? Is this a bug? best, leandro

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AttributeError: 'list' object has no attribute 'missing_meta' when doing multiple="true" input datasets
by Leandro Hermida 09 Jun '11

09 Jun '11

Hi, I have a tool where the input is multi-select of datasets, e.g.: <param type="data" multiple="true" name="input1" /> I tested it to see what it would pass to my command and I get the following debug page and error in Galaxy: AttributeError: 'list' object has no attribute 'missing_meta' The last part of the stack trace looks like: >> validator.validate( value, history ) Module galaxy.tools.parameters.validation:185 in validate history <galaxy.model.History object at 0xb8ea190> self <galaxy.tools.parameters.validation.MetadataValidator object at 0xb8e6250> value [<galaxy.model.HistoryDatasetAssociation object at 0xa255550>, <galaxy.model.HistoryDataset ... Association object at 0xb8ea210>] >> if value and value.missing_meta( check = self.check, skip = self.skip ): AttributeError: 'list' object has no attribute 'missing_meta' What am I doing wrong? regards, Leandro

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format="input"
by Mariette 09 Jun '11

09 Jun '11

Hi everyone, I'm facing a little problem ... I have the following input : <param name="input" type="data" format="sff,fasta,fastq" label="454 reads" /> <param name="qual_file" type="data" format="qual" optional="true" label="Quality reads file (if input is a fasta)" /> and the following output: <data name="output" format="input" label="${tool.name} on ${on_string}: cleaned reads"/> <data name="out_qual" format="qual" label="${tool.name} on ${on_string}: cleaned reads"> <filter>qual_file != None</filter> </data> If I provide the tool a sff file, the output is sff, if I only provide a fasta file and no qual file the output will be a fasta. However if I provide a fasta+qual the output will be considered as qual file even if it's a fasta file. I don't get how it can mark my output file as a qual file knowing it's not a valid input file format. Any ideas ? thx, Jerome

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CuffDiff <output> mis-named ?
by Assaf Gordon 08 Jun '11

08 Jun '11

Hi, In "cuffdiff_wrapper.xml", there are three outputs associated with CDS: <data format="tabular" name="cds_exp_fpkm_tracking" label="${tool.name} on ${on_string}: CDS Expression FPKM Tracking"/> <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking"/> <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS diff"/> Based on the naming convention of the other outputs (and the output files from cuffdiff), I think the label of the first one should be renamed to "CDS Expression" only (assuming the relevant input file "cds_exp.diff"). -gordon

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loading tool options depending on initial parameter
by Roloff, Tim 08 Jun '11

08 Jun '11

Hello, I am working on a tool that should load a set of selected files from a group folder. The interface should only display the files in the selected group folder. I tried to use the code below to read the files as options from an external .xml file in the tool-data directory based on the group selected in the first step but I run into 2 problems: - How can I pass the information from the parameter "group" to "from_file". - Even if I hardcode the xml file to be read from tool-data, the options do not show up. In the tool annotation profiler certain meta data of the input dataset are required for the options to be displayed but in my case I do not start without input dataset. <inputs> <page> <param name="group" type="select" label="Group" help="Select your group" > <option value="group1_files.xml">group1</option> <option value="group2_files.xml">group2</option> </param> </page> <page> <param name="selectedfiles" type="drill_down" display="checkbox" hierarchy="recurse" multiple="true" label="Choose files to upload" help=" " from_file="${group}"/> </page> </inputs> Thanks for your help in advance Tim

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question/bug with cuffcompare wrapper
by Assaf Gordon 08 Jun '11

08 Jun '11

Hi, It seems the cuffcompare XML wrapper expects a file named "cc_output" to contain the "transcript accuracy" report. I guess it worked with versions 0.9.3 and 1.0.1, but at least in version 1.0.2, this file is now named "cc_output.stats", and the "transcript accuracy" file is empty. so the XML wrapper is compatible with 1.0.1 but not really with 1.0.2/3 (Unless I missed something in the XML/python/cuffcompare execution chain). Also, Notice that starting version 1.0.2 they've added an option to normalize by either total number of reads or by number of reads that matched the given GTF file. To make matters worse, "cufflinks" defaults to normalizing to total reads, and "cuffdiff" defaults to normalizing by GTF-matching reads. The options are called "--total-hits-norm" and "--compatible-hits-norm". There's no way for users to specify either of those in Galaxy, so running cufflinks/cuffdiff might give unexpected results (not that there are any "expected" results, but still...) Just something to think about when you work on the next version of cufflinks wrappers. -gordon

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Components
by Mariette 08 Jun '11

08 Jun '11

Hi everyone, I'm new in galaxy and I want to create a component, so I have multiple questions. The component executes a script which takes different formats : fasta|fastq|sff. As output it takes a folder, to do so I used the extra_files_path attribute of an output data (--out='$output.extra_files_path'). The result file is stored in this folder with the log file and should be in the same format as the input one. I wrote the xml file and it works just fine, however as it's a folder there is no way to use the result file(s) for further analysis. How can I manage this ? Also it can happen that there is more than 1 file outputted, how can I manage multiple outputs ? An other question about the input format, I have an option to the script to specify the format. I saw there is auto-format detection routines in galaxy, there is a way so I can call them to automatically complete this option ? thx, Jerome

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Adding Link to Sequencing Requests Page
by Joe Cruz 08 Jun '11

08 Jun '11

Hello Everyone, I would like to add a link to the Sequencing Requests page and modify it further in the future but I'm unsure of how to go about doing that, since there is no static html file for the webpage (at least none that I can find) and I'm a newbie when it comes to web application development. I appreciate your help and patience. joe

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New tool shed live?!
by Peter Cock 07 Jun '11

07 Jun '11

Hi all, I thought the new repository based tool shed was still in beta? However, http://community.g2.bx.psu.edu/ and also http://usegalaxy.org/community are both now redirecting to http://toolshed.g2.bx.psu.edu/ and that does seem to be the new version. If so, what happened to the tools I submitted yesterday? e.g. new tool "Rename sequences", file seq_rename.xml etc & "Select sequences by ID", file seq_select_by_id.xml etc. I was worried I would I need to resubmit these, and ask when was the conversion done in case there may be other recently submitted updates missing. However, you're probably going to have to redo the whole import anyway due to this bug: https://bitbucket.org/galaxy/galaxy-central/issue/578/ Regards, Peter

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