Questions tagged [galaxy]

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

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use Kallisto in galaxy

I want to use Kallisto for sequence alignment in Galaxy. Its description is: a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target ...
Zahrae's user avatar
  • 63
1 vote
1 answer
117 views

How to identify index sequences for cutadapt for atac-seq

I am just starting on my atac-seq analysis (not very experienced, so my apologies for a stupid question), and I am wanting to trim the adapters of off my paired-end reads. I am following the galaxy ...
Faleevs's user avatar
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1 vote
2 answers
172 views

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, ...
jack's user avatar
  • 13
1 vote
1 answer
59 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 ...
aerijman's user avatar
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1 vote
1 answer
146 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 ...
Varuna Peiris's user avatar
1 vote
0 answers
8 views

Where is the galaxy results file path?

I want to wrap galaxy into a docker image, and I want to delete files that are older than a certain date on a regular basis, so I want to know how to generate the files and where to store them.
huangzj's user avatar
  • 63
1 vote
0 answers
52 views

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?
gl00ten's user avatar
  • 249
1 vote
0 answers
197 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....
Najeha Mohamed's user avatar
0 votes
1 answer
99 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?
aerijman's user avatar
  • 645
0 votes
1 answer
71 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 ...
aerijman's user avatar
  • 645
0 votes
1 answer
20 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?
player777's user avatar
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Do you need galaxy.yml when you start creating galaxy?

First question: I found that there is no galaxy.yml in the config directory of the running version of docker galaxy, only galaxy.yml.sample file and galaxy.yml.interactivatetools file, so do I need to ...
huangzj's user avatar
  • 63