Open Sebastien-Raguideau opened 3 years ago
+1. I had the same issue using snakemake 5.30 and rule all
after the run failed due to a missing package.
It also got resolved by downgrading to 5.14.
I'll have a go at this. What package was missing for you? I should add it to the conda_env.yaml for install.
thanks! some steps into the pipeline, it took my personal installation of R
instead of the one installed via the conda_env.yaml file (my personal installation was first on my PATH). Therefore dplyr
was missing.
Aouch, this is hard to fix on my end. But I can still try to check installation before running STRONG and inform user of issue. Thanks for feedback :)
with a fresh install and latest version of snakemake, the 2nd step is failing, not going through the rule select_bins_for_strain_analysis. This in turn trip the start of the step 3 when looking for a file which has not been generated. Upon rerun, snakemake throw :
So... snakemake update broke something, unclear what the highest version we can use but the 5.14 is fine.