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2 votes
Accepted

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

Each Galaxy tool uses its own (typically conda-based) environment, which will normally not use the same python as Galaxy itself (note that Galaxy can run under python 3). An example of this is ...
Devon Ryan's user avatar
  • 19.7k
2 votes

How to identify index sequences for cutadapt for atac-seq

The sequence to trim for ATAC-seq is CTGTCTCTTATACACATCT. It's the Nextera adapter sequence. The sequence is the reverse complement of the 3' ends of your primers, ...
ATpoint's user avatar
  • 1,440
1 vote
Accepted

Help with MinION sequencing data species identification

There are a number of useful metagenomics tools out there, including Centrifuge and Kraken2, as @gringer has mentioned. Also, FWIW, the WIMP tool from ONT, a Centrifuge based metageonomic classifier, ...
Scot's user avatar
  • 782
1 vote

use Kallisto in galaxy

You have to click on the dropdown menu and select "Use transcriptome from history", which will allow you to specify your own file. I suspect the default will be built-in human transcriptome....
Kamil S Jaron's user avatar
1 vote

Add new tool to galaxy

The .main and .sample file files usually come with default installations and may have been removed by whoever setup this Galaxy instance. You can look at the originals online and just base your own ...
Devon Ryan's user avatar
  • 19.7k
1 vote

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

You best bet is bioblend, since it's a more convenient wrapper around the Galaxy API, but if you really want to you could use that directly. I should note that large files should probably still be ...
Devon Ryan's user avatar
  • 19.7k
1 vote

Including Picard tool in galaxy

Picard, like most tools, prints logs to stderr. It should be in the Galaxy history. Are you using a version of picard from the toolshed (if so, which one)? You might set ...
Devon Ryan's user avatar
  • 19.7k
1 vote

Create galaxy local toolshed using Planemo

--shed_target local will only work if you're running a Galaxy toolshed on your local computer, since it's reading the .shed.yaml ...
Devon Ryan's user avatar
  • 19.7k

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