Wrapper for Cutadapt v.2.8. This repo supports Python3 and has been tested with Galaxy v.22.01.
In contrast to cutadapt from the toolshed, this wrapper will handle zip files.
Clone this repo in your Galaxy Tools directory:
git clone https://github.com/naturalis/galaxy-tool-cutadapt
Make the python script executable:
chmod 755 galaxy-tool-cutadapt/cutadapt_wrapper.py
Append the file tool_conf.xml:
<tool file="/path/to/Tools/galaxy-tool-cutadapt/cutadapt_primer_trim.xml" />
Depending on your setup the ansible.builtin.git module could be used.
Install the tool by including the following in your dedicated *.yml file:
- repo: https://github.com/naturalis/galaxy-tool-cutadapt
file: cutadapt_primer_trim.xml
version: master
Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.Journal, 17(1), pp. 10-12. doi:http://dx.doi.org/10.14806/ej.17.1.200