I am trying to use the qiime2 docker container you provide but I can’t get past the demux step. I was able to successfully import the example data from the website, and a proper .qza file was generated. But when I try to run the qiime demux step I get this error:
qiime demux emp-single --i-seqs emp-single-end-sequences.qza --m-barcodes-file sample-metadata.tsv --m-barcodes-category BarcodeSequence --o-per-sample-sequences demux.qza
Traceback (most recent call last):
File “/opt/conda/bin/qiime”, line 11, in
sys.exit(qiime())
File “/opt/conda/lib/python3.5/site-packages/click/core.py”, line 722, in call
return self.main(*args, **kwargs)
File “/opt/conda/lib/python3.5/site-packages/click/core.py”, line 697, in main
rv = self.invoke(ctx)
File “/opt/conda/lib/python3.5/site-packages/click/core.py”, line 1061, in invoke
cmd_name, cmd, args = self.resolve_command(ctx, args)
File “/opt/conda/lib/python3.5/site-packages/click/core.py”, line 1100, in resolve_command
cmd = self.get_command(ctx, cmd_name)
File “/opt/conda/lib/python3.5/site-packages/q2cli/commands.py”, line 77, in get_command
plugin = self._plugin_lookup[name]
File “/opt/conda/lib/python3.5/site-packages/q2cli/commands.py”, line 53, in _plugin_lookup
import q2cli.cache
File “/opt/conda/lib/python3.5/site-packages/q2cli/cache.py”, line 302, in
CACHE = DeploymentCache()
File “/opt/conda/lib/python3.5/site-packages/q2cli/cache.py”, line 58, in init
self._cache_dir = self._get_cache_dir()
File “/opt/conda/lib/python3.5/site-packages/q2cli/cache.py”, line 85, in _get_cache_dir
os.makedirs(cache_dir, exist_ok=True)
File “/opt/conda/lib/python3.5/os.py”, line 231, in makedirs
makedirs(head, mode, exist_ok)
File “/opt/conda/lib/python3.5/os.py”, line 231, in makedirs
makedirs(head, mode, exist_ok)
File “/opt/conda/lib/python3.5/os.py”, line 241, in makedirs
mkdir(name, mode)
PermissionError: [Errno 13] Permission denied: ‘/.config’
I’m pretty sure the issue is that qiime is trying to setup a config file at:
/.config
but I don’t have permission to write in that directory. Is there a way I can tell qiime to restrict itself to the local namespace in which I am running it?
