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a-ludi / dentist

Close assembly gaps using long-reads at high accuracy.
https://a-ludi.github.io/dentist/
MIT License
47 stars 6 forks source link

Missing Snakefile from example test dataset #23

Closed davidjstudholme closed 3 years ago

davidjstudholme commented 3 years ago

I believe this is a distinct issue from https://github.com/a-ludi/dentist/issues/21 as it pertains to the Snakefile rather than the .yml files that you helpfully signposted. I am using the https://github.com/a-ludi/dentist-example/releases/download/v1.0.2-2/dentist-example.tar.gz example dataset.

When I execute (base) ubuntu@bio-xanthomonas:~/dentist-example$ snakemake --configfile=snakemake.yml --use-singularity --cores=all I get this error message: Error: no Snakefile found, tried Snakefile, snakefile, workflow/Snakefile, workflow/snakefile.

So, I guessed the obvious thing to do was to download this Snakefile: https://github.com/a-ludi/dentist/blob/develop/snakemake/Snakefile.

However, when I try again to execute the above command line, with this Snakefile in the current directory, I get:

IndentationError in line 113 of <tokenize>:
unindent does not match any outer indentation level (<tokenize>, line 113)
 File "/usr/lib/python3.8/tokenize.py", line 512, in _tokenize

I suspect, that this might be because I am not using the correct Snakefile?

a-ludi commented 3 years ago

I suspect, that this might be because I am not using the correct Snakefile?

I agree. Try this Snakefile. It is the one that should be included in the tarball.

davidjstudholme commented 3 years ago

The link in your message above is: https://raw.githubusercontent.com/a-ludi/dentist/d85a86fda8da241b0de3d3b8d3b02cf9e3405302/snakemake/cluster.yml. This is file called 'cluster.yml' not 'Snakefile'. Is this intended?

a-ludi commented 3 years ago

This was a copy&paste mishap. Sorry. Correct link: https://raw.githubusercontent.com/a-ludi/dentist/d85a86fda8da241b0de3d3b8d3b02cf9e3405302/snakemake/Snakefile

davidjstudholme commented 3 years ago

Thanks, Arne.

However, with this file I now get this error message:

SyntaxError in line 896 of /home/djs217/dentist-example/Snakefile:
Unexpected keyword container in rule definition (Snakefile, line 896)
davidjstudholme commented 3 years ago

Possibly this is an issue with snakemake version used?

$ snakemake --version
5.10.0
davidjstudholme commented 3 years ago

The offending line 896 seems to be:

container: dentist_container
a-ludi commented 3 years ago

Possibly this is an issue with snakemake version used? Yes, please update to v5.32.1.

davidjstudholme commented 3 years ago

Thanks, Arne. So, I think the original issue is now resolved since the the missing file is available at: https://raw.githubusercontent.com/a-ludi/dentist/d85a86fda8da241b0de3d3b8d3b02cf9e3405302/snakemake/Snakefile