Wrapper for FLASH v.1.2.11. This repo uses Pyhton3 and has been tested with Galaxy v.22.01
(using a Terraform/Ansible install on the new Naturalis OpenStack). Although FLASH is also
available from the Toolshed, this wrapper fits better in our pipeline because it can handle zip files.
Clone this repo in your Galaxy Tools directory:
git clone https://github.com/naturalis/galaxy-tool-flash
Make the python script executable:
chmod 755 galaxy-tool-flash/flash_wrapper.py
Append the file tool_conf.xml:
<tool file="/path/to/Tools/galaxy-tool-flash/flash.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-flash
file: flash.xml
version: master
FLASH: Fast length adjustment of short reads to improve genome assemblies. T. Magoc and S. Salzberg. Bioinformatics 27:21 (2011), 2957-63 https://ccb.jhu.edu/software/FLASH/