User: d.hand

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d.hand0
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Posts by d.hand

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Answer: A: Snippy does not recognize my genbank reference file
... NCBI has an option to download genomes in genbank format .gbk. This is how I got my annotations for snippy. ...
written 4 months ago by d.hand0
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Answer: A: Quast not installing correctly
... Actually I have found out all tools I have installed recently have command not found errors. Is this indicative of anything? how do I check them manually? I resized my galaxy partition recently so I'm not sure if this has anything to with it. ...
written 4 months ago by d.hand0
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Answer: A: Quast not installing correctly
... Thanks it is iuc quast. ...
written 4 months ago by d.hand0
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Quast not installing correctly
... I'm having an issue installing the latest version of quast on my 17.09 galaxy cluster. in the history I get: /mnt/galaxy/tmp/job_working_directory/004/4494/tool_script.sh: line 9: quast: command not found WARNING:galaxy.model:Datatype class not found for extension 'tex' WARNING:galaxy.model:D ...
quast local install admin dependencies written 4 months ago by d.hand0
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Answer: A: Using filename as a tool variable
... Is there any conceivable workaround for renaming a single fasta header with the inputfile? other than making my own tool? ...
written 5 months ago by d.hand0
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Answer: A: Using filename as a tool variable
... Is there any conceivable workaround for renaming a single fasta header with the inputfile? other than making my own tool? ...
written 5 months ago by d.hand0
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Answer: A: Setting default files for workflow
... Thank you for your help. ...
written 5 months ago by d.hand0
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Setting default files for workflow
... For some of my workflows I have reference files such as .fasta, .bed and .tab. They are used everytime the workflow is used. I was wondering if it was possible to force their use in the workflow and if it is also possible to "save them" to the workflow so they don't need to be uploaded with the in ...
inputs galaxy static preset workflow written 5 months ago by d.hand0
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Using filename as a tool variable
... I know you can use #{input} in the workflow editor to change the name of the output files, however is it possible to feed this into the tools as well? I've tried to use it in the tool options such as graph label:"#{input}" or name:"#{input}", but this doesn't work. I assume this is because galaxy ...
dataset wrapper name variable tool written 5 months ago by d.hand0
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Comment: C: Kraken run time
... So i modified job_conf.xml, but I don't think this is the problem. With "squeue" I get: JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 11 main g464_kra galaxy R 49:46 1 w1 And a r3.8xlarge worker node is started, but i think ...
written 8 months ago by d.hand0

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