I created a conda environment and installed snakemake and the PyYAML in the environment. Then I git cloned the pipeline repository. All this is in a CentOS cluster.
When I run the command - snakemake --use-conda -j 50 all
I get the following error:
WorkflowError in line 5 of /workingdirectory/Snakefile:
Config file is not valid JSON and PyYAML has not been installed. Please install PyYAML to use YAML config files.
File "/workingdirectory/Snakefile", line 5, in
When I try to install PyYAML after seeing this message, I get the information that PyYAML is already installed.
I created a conda environment and installed snakemake and the PyYAML in the environment. Then I git cloned the pipeline repository. All this is in a CentOS cluster.
When I run the command - snakemake --use-conda -j 50 all I get the following error:
WorkflowError in line 5 of /workingdirectory/Snakefile: Config file is not valid JSON and PyYAML has not been installed. Please install PyYAML to use YAML config files. File "/workingdirectory/Snakefile", line 5, in
When I try to install PyYAML after seeing this message, I get the information that PyYAML is already installed.
Any help will be appreciated.
Thanks, Kaushik