EUKulele setup database

[slaperriere]

Hello,

I am excited to give EUkulele a try! I am having trouble setting up the database. I downloaded the cleaned MMETSP assemblies, and I also tried having EUkulele download the database. I ran the following:

EUKulele setup --database mmetsp 
EUKulele setup --database mmetsp --reference_dir <path to assemblies>

Both resulted in the following:

Running EUKulele with command line arguments, as no valid configuration file was provided.
METs or MAGs argument (-m/--mets_or_mags) is required with one of 'mets' or 'mags'.

Should the database be set up some other way? I cloned EUkulele from github.

Thanks,
Sarah

[halexand]

Hi Sarah,

Thanks for checking out EUKulele! I think you found an error in our readthedocs site. Thanks so much for posting.

To setup or download a database you can use the following command:

EUKulele download --database mmetsp

This should pull and automatically configure the database for you. There are other ways to point to a database (e.g. by modifying the config file). Also, if you were to run a full fledged EUKulele command (e.g. EUKulele -m mags -o test -s test-files -- database mmetsp) and EUKulele cannot find a reference db locally it will automatically download and configure one for you.

Regardless, thanks for posting an issue. I will fix the readthedocs site.

Best,

Harriet

[halexand]

Also, I think the best way to download and install EUKulele right now (to ensure all dependencies are present) is with bioconda: conda install -c bioconda -c conda-forge eukulele

However, just looking at your error output it looks like it is working... but BUSCO can be a bit pesky downstream so if you run into issues try a conda install.

[slaperriere]

Hi Harriet,

Thanks! EUKulele download worked. Though you were correct, BUSCO gave me an error.

Running busco with 1 simultaneous jobs...
[] is what is in BUSCO directory
BUSCO initial run did not complete successfully.
Please check the BUSCO run log files in the log/ folder.

Originally, I cloned from github because the conda install kept freezing. I tried again and it keeps getting suck on "Solving environment".

Best,
Sarah

[akrinos]

Hi @slaperriere !

For that BUSCO issue, if you prefer not to re-download EUKulele, you might be able to get away with downgrading your BUSCO install to 4.0.6. Unfortunately, there is a bug with EUKulele and the most recent versions of BUSCO. When you download EUKulele with conda, you get 4.0.6, which is why we recommend installing EUKulele via conda. We're hoping to get BUSCO on track with the release of BUSCO 5.

Thanks so much again for your interest in EUKulele!