How to stop writing to read-only home directory

[erinyoung]

I am unsure why pangolin is trying to write to my home directory, but I need it to NOT write there (it's read only).

This is my command (I'm using tempdir here because I thought it would help) :

pangolin        --threads 4       --outdir pangolin       --tempdir temp    ultimate_fasta.fasta 

The error I got:

  Traceback (most recent call last):
    File "/opt/conda/envs/pangolin/lib/python3.8/site-packages/snakemake/__init__.py", line 587, in snakemake
      workflow = Workflow(
    File "/opt/conda/envs/pangolin/lib/python3.8/site-packages/snakemake/workflow.py", line 242, in __init__
      self.sourcecache = SourceCache()
    File "/opt/conda/envs/pangolin/lib/python3.8/site-packages/snakemake/sourcecache.py", line 358, in __init__
      os.makedirs(self.cache, exist_ok=True)
    File "/opt/conda/envs/pangolin/lib/python3.8/os.py", line 213, in makedirs
      makedirs(head, exist_ok=exist_ok)
    File "/opt/conda/envs/pangolin/lib/python3.8/os.py", line 213, in makedirs
      makedirs(head, exist_ok=exist_ok)
    File "/opt/conda/envs/pangolin/lib/python3.8/os.py", line 213, in makedirs
      makedirs(head, exist_ok=exist_ok)
    [Previous line repeated 1 more time]
    File "/opt/conda/envs/pangolin/lib/python3.8/os.py", line 223, in makedirs
      mkdir(name, mode)
  OSError: [Errno 30] Read-only file system: '/home/eriny'

[aineniamh]

Hi @erinyoung, I'm not sure why this is happening- what's your current working directory when running pangolin?

[erinyoung]

/Volumes/IDGenomics_Nas/testing

(A mounted directory)

[aineniamh]

Hmm, what happens if you give full paths for the temp and outdir? Those should be the only two places written to, so i think something is happening with them. It could be to do with the mounting, I've not tested really on mounted directories!

[theosanderson]

Looking over this log (sorry, randomly watching this repo. not a pangolin dev!) it looks like this might be a built in Snakemake feature to cache source code. Try setting the XDG_CACHE_HOME environmental variable e.g. export XDG_CACHE_HOME=/tmp/mycache, or maybe refer to https://github.com/snakemake/snakemake/issues/1593

[erinyoung]

Thank you @theosanderson ! XDG_CACHE_HOME=/tmp appears to have fixed things.