User: d.hand

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d.hand0
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Posts by d.hand

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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 10 days 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 10 days ago by d.hand0
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Answer: A: Setting default files for workflow
... Thank you for your help. ...
written 28 days 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 28 days 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 28 days 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 3 months ago by d.hand0
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Comment: A: Kraken run time
... Hi thanks for the response, actually i still have a job running now for 24 hours! I have set the master to not do any jobs. So the job is running on one r3.8xlarge, I'm not sure How I can get much larger than this! ...
written 3 months ago by d.hand0
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Kraken run time
... I have been running 0.2-2M 150 bp kraken jobs on the bacterial database on a private cloudman cluster with one c3.large master node (set to not do jobs) and 0-10 r3.8xlarge worker nodes (32 cores, 244 gb memory). The problem is that the jobs are taking between 6-13+ hours with the bacterial databas ...
kraken written 3 months ago by d.hand0

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