[BUG] SyntaxError in line 84 of /home/josephus/ncov/Snakefile: invalid syntax

[gwangjinkim]

Something is wrong with the Snakefile.

In ubuntu do:

sudo apt install snakemake
snakemake --version
4.3.1

OR do in a conda environment

conda install -c bioconda snakemake
snakemake --version
5.3.0

git clone this repo

cd
git clone https://github.com/nextstrain/ncov.git
cd ncov

# then do:
snakemake -p
# SyntaxError in line 84 of /home/josephus/ncov/Snakefile:
# invalid syntax

# this is the error!

So, something is wrong with the Snakefile! But what? line 84 is

checkpoint partition_sequences:

I really don't get it why there is an invalid syntax ...

(I tried using the docker version etc. - nothing helped. I realized, this is a Snakefile and snakemake problem).

[brianpardy]

Hi @gwangjinkim, do you have the ability to install a newer version of snakemake? It appears from the snakemake changelog that the checkpoint keyword was added in release 5.4.0 of snakemake. The Snakefile processes cleanly without errors on my system running snakemake 5.10.0.

[gwangjinkim]

@brianpardy Thank you so much! And sorry that I answer right now. A newer version of snakemake did it. I am now stuck on some other error but will try to find a way first. Thank you so much that you answered quickly!