Question: How to set --lineage parameter on BUSCO
0
gravatar for brandaom
9 weeks ago by
brandaom0
brandaom0 wrote:

Hello there I have just installed BUSCO on Galaxy. But I haven't found a way to configure the (--lineage) parameter it keeps showing me "No options available" I heve tryed to edit all busco.loc files that I have found using:

find ./galaxyuser/* -iname *busco.loc*
./tool-data/toolshed.g2.bx.psu.edu/repos/iuc/busco/87983967544b/busco.loc
./tool-data/busco.loc.sample
./tool-data/busco.loc

I add the following line to it:

eukaryota_odb9 eukaryota_odb9 eukaryota (odb9) /home/galaxyuser/busco_db/eukaryota_odb9/

But no success :( Someone have any idea how to make this work properly? Thanks!!!!

busco rna-seq lineage • 67 views
ADD COMMENTlink modified 9 weeks ago by Jennifer Hillman Jackson22k • written 9 weeks ago by brandaom0
0
gravatar for Jennifer Hillman Jackson
9 weeks ago by
United States
Jennifer Hillman Jackson22k wrote:

Hello,

The format of the .loc file appears to be correct. However, Galaxy is looking for this configuration file in another location, specifically under ./tool-data. Try moving it there to see if the problem resolves. And/or check the tool_data_table_conf.xml file to see where Galaxy is looking for the data and modify it as needed.

This assumes that the genome eukaryota_odb9 was installed in a way that creates a new dbkey (and the associated .len file) using Data Managers (also from the Tool Shed) and that tool_data_table_conf.xml points to the .locs correctly. Starting with this one is best: data_manager_fetch_genome_dbkeys_all_fasta. Then create these other important indexes/.loc files (as needed) for Samtools, Picard, and 2bit if you have not done that already to avoid other problems.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 9 weeks ago by Jennifer Hillman Jackson22k
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