Questions tagged [galaxy]

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Using galaxy tool htseq_count for lncRNA in wheat reference genome

My group wants to use Galaxy's htseq_count to map reads from a BAM file onto the IWGSC v1.0 lncRNA GFF file however we have encountered several difficulties. Specifically, there are many lines for ...
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29 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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Could I create assembly by unicycler for ion torrent output?

I have ubam files from ion torrent machine, I convert it to fastq by samtools bam2fq tool, then I use galaxy platform to assembly the genome by Unicycler. At the end I get a fasta file. My question ...
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What Galaxy tools can annotate a de novo assembly RNA seq plant transcripts?

What Galaxy tools can annotate a de novo assembly RNA seq plant transcripts? How to do it using Python API?
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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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galaxy output bam file sorted

I included a new tool in galaxy and I get the following debug msg: ...
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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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96 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 ...