'Extract Pairwise MAF Blocks' unable to detect .maf file

Hi all,
I saw that several people have had similar issues with this tool but none of the solutions really clarified what the issue is here. I have BED files with genomic regions that I got using the GRCh38 reference sequence. Because Galaxy only has up to hg19 built in to the Extract Pairwise MAF Blocks tool, I uploaded aligned MAF files to my galaxy history from the UCSC Downloads area to my local computer and then unzipped before uploading to my Galaxy History (the path to the reference: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/vsRheMac8/hg38.rheMac8.synNet.maf.gz).

However, when I open the tool and select my BED file with my genomic intervals, I get an error message pop up that there are no options available for my MAF source. The MAF file is imported in as an MAF and has been labeled as being aligned to GRCh38, so there shouldn’t be any incompatibilities between my MAF and my BED. Does anyone know what’s going on?

Welcome @Maggie_Hassler

Yes, the suite of MAF manipulation tools are a bit older and have some dependencies that are difficult for us to resolve now. Some details here → MAF tools do not find indexed hg19 46-way or 100-way. CVMFS path problem? · Issue #290 · galaxyproject/usegalaxy-playbook · GitHub

The best advice I have for now is to use the tools that accept alignment data from the history. This will exclude the Pairwise MAF tool (since it accepts a native index - only).

There are some updates planned but I don’t have a good way to share details about this yet. I did mark this for an update, but it likely won’t be soon so please don’t wait.

I wish I had a better answer but this is the current state and I still hope the clearer clarifications at least help to understand what is going on! :slight_smile: