Update docs
I was testing Zarp by following README and discovered that several instructions should be corrected:
- The virtual environment
install/environment.yml
is not enough if the sample table contains files that should be concatenated. In this caseinstall/environment.dev.yml
is also required (unzip
package?). Possible solution: merging these two.yml
files into one. - In the section "Running the workflow on your own samples", item 4 the
snakemake
command is described. There are two problems. First, the path to theSnakefile
is wrong. It should be../../Snakefile
. Second, for processing real samples on SLURM an additional option--latency-wait 60
is required. With this option the system waits given seconds if an output file of a job is not present after the job finished. This helps if your filesystem suffers from latency (currently, it is the case).
Edited by Alex Kanitz