Question: How to set --lineage parameter on BUSCO
gravatar for brandaom
7 months ago by
brandaom10 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 • 206 views
ADD COMMENTlink modified 4 days ago • written 7 months ago by brandaom10
gravatar for brandaom
4 days ago by
brandaom10 wrote:

hum... It does not work. I have just migrate to Galaxy docker container and the same problem remains. I am using "Busco assess genome assembly and annotation completeness (Galaxy Version 3.0.2)" install all databases using Data Manager: Busco. It downloads all data but still no lineage parameter. Opening Data Manager: Busco - dataset dowloader I can see this:

python '/shed_tools/' --out '/export/galaxy-central/database/files/000/dataset_9.dat' --url '' --name 'insecta_odb9'

I can see all the data at /galaxy-central/tool-data/busco/ but it does not work!!! How can I circumvent this and make this a working tool? Cheers Marcelo

ADD COMMENTlink written 4 days ago by brandaom10

Hello, Since these are IUC team authored tool wrappers, it is possible to directly communicate with them at Gitter. I asked for help from the team member who worked on this last.

Please follow here and feel free to comment (but you don't need to duplicate what is posted here, I already linked it in).

Thanks! Jen, Galaxy team

ADD REPLYlink modified 4 days ago • written 4 days ago by Jennifer Hillman Jackson24k
gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson24k 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 (probably) 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 modified 4 days ago • written 7 months ago by Jennifer Hillman Jackson24k
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