Questions tagged [galaxy]

A framework for doing bioinformatics in a GUI, on the cloud. Free.

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Help with MinION sequencing data species identification

Hi I'm new to bioinformatics and have just completed my first run on the MinION (long read sequencing Oxford Nanopore Technologies). I was hoping someone could direct me towards R packages, workflow, ...
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0answers
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In Galaxy, using the bracken tool, how do I get a Kmer distribution?

As you can see in the image, the Kmer distribution field is empty: "No options available" What am I missing? Is there another tool I must use first to generate a Kmer distribution?
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use Kallisto in galaxy

I want to use kalisto for sequence alignment in Galaxy. i found this field empty: there is no option available for the reference transcriptome. how I can get one? Can I let the other configuration by ...
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0answers
71 views

FastQC and Trimmomatic in Galaxy?

I am independently working on data retrieved SRA database, paired-end data as separate inputs. The proceedure I followed is, After running FastQC using Galaxy, the majority of the modules have failed....
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1answer
63 views

run a tool with python>=3.6 on galaxy-project instance that runs on python2.7

I am developing a wrapper for a bioinformatics tool writen in python3. The native Galaxy-project runs on python2.7. How can I the tool that requires python3 in a galaxy-project instance?
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1answer
47 views

Add new tool to galaxy

I am trying to include a new tool to the galaxy main menu, following these instructions. tool_conf.xml doesn't exists only ...
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1answer
19 views

How to upload and process a data set to Galaxy instance and retrieve results programmatically?

How to upload and process (de novo assembly pipe) a data set to Galaxy instance and retrieve the results programmatically? Are there any packages beyond BioBlend?
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0answers
135 views

galaxy output bam file sorted

I included a new tool in galaxy and I get the following debug msg: ...
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1answer
41 views

Including Picard tool in galaxy

I am running the Picard tool CollectSequencingArtifactMetrics in galaxy (locally in my pc). The output files are saved into disk and not passed to stdout and (I guess) they can't be passed as output ...
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1answer
123 views

Create galaxy local toolshed using Planemo

I tried to create galaxy local toolshed using planemo. I used command as follows, create virtual env virtualenv .venv; .venv/bin/activate Install planemo ...