How to set --lineage parameter on BUSCO

Question: How to set --lineage parameter on BUSCO

16 months ago by

brandaom • 10 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 • 659 views

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modified 9 months ago • written 16 months ago by brandaom • 10

16 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 (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 COMMENT • link modified 9 months ago • written 16 months ago by Jennifer Hillman Jackson ♦ 25k

9 months ago by

brandaom • 10

brandaom • 10 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/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_fetch_busco/53eec20e8fb6/data_manager_fetch_busco/data_manager/data_manager.py' --out '/export/galaxy-central/database/files/000/dataset_9.dat' --url 'http://busco.ezlab.org/datasets/insecta_odb9.tar.gz' --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 COMMENT • link written 9 months ago by brandaom • 10

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). https://gitter.im/galaxy-iuc/iuc?at=5a85fae8f283b8e54668fa0b

Thanks! Jen, Galaxy team

ADD REPLY • link modified 9 months ago • written 9 months ago by Jennifer Hillman Jackson ♦ 25k

Hi, it's a bit late but here's what I've found while testing:

I launched a 17.09 docker container, installed busco and the data manager, installed some busco datasets using the data manager. At this step I had this problem of empty --lineage option. After restarting the galaxy instance however, the list was ok. Maybe it's a bug in galaxy, I'll try to test on 18.01 to see if it works better

You can also try to refresh the data table in the admin section, "local data", then click on the busco table in "View Tool Data Table Entries", then you have the refresh button at the top.

Hope it helps Anthony

ADD REPLY • link written 8 months ago by abretaud • 20

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