Temporary directory for downloading packages

[nirwan1265]

I am using an HPC server that does not allow me to download anything in the home directory. Is there a way I can change the directory for the downloads. This is the error i get:

more stderr.2525 50 Traceback (most recent call last): File "/usr/local/usrapps/maize/ntanduk/kgwasflow/lib/python3.11/site-packages/snakemake/init.py", line 584, in snakemake workflow = Workflow( ^^^^^^^^^ File "/usr/local/usrapps/maize/ntanduk/kgwasflow/lib/python3.11/site-packages/snakemake/workflow.py", line 242, in init self.sourcecache = SourceCache() ^^^^^^^^^^^^^ File "/usr/local/usrapps/maize/ntanduk/kgwasflow/lib/python3.11/site-packages/snakemake/sourcecache.py", line 358, in init self.runtime_cache = tempfile.TemporaryDirectory(dir=runtime_cache_parent) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/usrapps/maize/ntanduk/kgwasflow/lib/python3.11/tempfile.py", line 854, in init self.name = mkdtemp(suffix, prefix, dir) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/usrapps/maize/ntanduk/kgwasflow/lib/python3.11/tempfile.py", line 368, in mkdtemp _os.mkdir(file, 0o700) OSError: [Errno 122] Disk quota exceeded: '/home/ntanduk/.cache/snakemake/snakemake/source-cache/runtime-cache/tmpui67fttu' ERROR:root:Error running Snakemake: Command '['snakemake', '--use-conda', '--conda-frontend', 'conda', '--cores', '16', '--snakefile', '/usr/local/usrapps/maize/ntanduk/ kgwasflow/lib/python3.11/site-packages/workflow/Snakefile', '--configfile', '/usr/local/usrapps/maize/ntanduk/kgwasflow/lib/python3.11/site-packages/workflow/test/config _ecoli/config.yaml', '--dryrun', '--rerun-triggers', 'mtime', 'params', 'input', 'software-env', 'code']' returned non-zero exit status 1.

[akcorut]

Hi @nirwan1265,

You can define a new working directory when you initialize and also when you run the pipeline with --work-dir option. For example:

# Initializing a new kgwasflow working dir
kgwasflow init --work-dir path/to/your/work_dir 

# Run kGWASflow with user defined working directory:
 kgwasflow run -t 16 --work-dir path/to/work_dir

For more information: https://github.com/akcorut/kGWASflow/wiki/Running-kGWASflow#running-kgwasflow-with-kgwasflow-run

[akcorut]

Closing this issue due to the lack of activity. Feel free to reopen if this issue persists.