To whom may it concern;
We are writing to inquire on the possibility of contributing to the Galaxy pool of tools.
At the outset, we thank the Galaxy community for all the hard work on the wonderful platform, which is of a big value to the scientific community.
We are participants of the Open Life Science Project-2 (OLS-2) and are mentored by Dr. Mallory Freeberg, who is also CCed in this email. Our project is about creating a single pipeline integrating metagenomics tools for taxonomic classification. The pipeline would ease the work of those interested in metagenomic studies, especially those who do not have IT background or enough computational resources. We also want to include a visualization tool (Krona) to illustrate the output, since the standard output is typically a txt file. The selected tools for the taxonomic classification are Kraken2, Centrifuge and Clark, which are widely used and identified as the state of the art based on our literature review.
Last week, we presented our work to Dr Berenice Batut (who is also CCed herein), who is an expert in the field. Thanks to her feedback and advice and that of Dr Mallory, we want to explore the prospect of porting our project onto the Galaxy platform, to benefit the wider community. We have checked both the Galaxy servers (https://usegalaxy.eu/ and https://usegalaxy.org), as well as the ToolShed to see if the tools that we want to deploy are already available on Galaxy.
Kraken2 is available and is ready for use with various DB's. On the other hand, we were not able to find Centrifuge on the tools search section, although it appears in the ToolShed ( https://toolshed.g2.bx.psu.edu/view/jvolkening/centrifuge/be7bba8229c6), whereas Clark (http://clark.cs.ucr.edu/) is not available on the platform.
Thus, we hope that you could import these tools on Galaxy so that we can port our pipeline(workflow) on the Galaxy platform.
Thank you, Muhammet