Syntax issue with rake

[14zac2]

Hello!

I'm having trouble getting flo started. I was hoping you might be able to help me out. To set up flo, I installed all dependencies using apt-get or conda (conda create -n flo -c mvdbeek -c conda-forge parallel genometools ucsc_tools). I set up my data as requested, and am now getting the following error:

rake aborted! SyntaxError: /path/to/dir/opts_example.yaml:16: syntax error, unexpected ':', expecting end-of-input

Often I encounter errors because my directory has spaces in it (can't change this), but I don't think this is the problem, here. In my opts file, the line throwing the error is as such:

:source_fa: '/path/to/genome/genome.fa'

Do you have any idea what might be going on here? Some sort of version error, perhaps?

Thanks, Zoe

[yeban]

It looks like you are running flo something like rake -f /path/to/dir/opts_example.yaml when it should be rake -f /path/to/flo/Rakefile.

• Rakefile is the pipeline script that comes with flo.
• flo will automatically look for config file, specifically called flo_opts.yaml in the directory you run the above command in.

[14zac2]

Perfect, that was my misunderstanding! Thanks for clarifying, it works now! :)