Question: How to set --lineage parameter on BUSCO
gravatar for brandaom
4 months ago by
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*

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 • 111 views
ADD COMMENTlink modified 4 months ago by Jennifer Hillman Jackson23k • written 4 months ago by brandaom0
gravatar for Jennifer Hillman Jackson
4 months ago by
United States
Jennifer Hillman Jackson23k wrote:


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 4 months ago by Jennifer Hillman Jackson23k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 109 users visited in the last hour