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issues with seqlinkage installation #22
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@valecipriani could you confirm that there is this switch |
Fantastic. It works. I should have asked you much earlier instead of wasting hours. Thanks!
Collapsed haplotype pattern method arguments: Input / output options: LINKAGE options: Runtime arguments:
I can try use the software now. Hopefully I will not encounter any other issues! :-) |
Hi I am using Ubuntu for Windows 10.
I believe I correctly run the command:
docker pull gaow/seqlink
If I run: docker images
I obtain:
REPOSITORY TAG IMAGE ID CREATED SIZE
gaow/seqlink latest e4fdb25d85ab 9 months ago 2.66GB
Now, when I run: seqlink -h
I get the following:
Traceback (most recent call last):
File "/opt/miniconda2/bin/seqlink", line 4, in
import('pkg_resources').run_script('SEQLinkage==1.1.0', 'seqlink')
File "/opt/miniconda2/lib/python2.7/site-packages/pkg_resources/init.py", line 666, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/opt/miniconda2/lib/python2.7/site-packages/pkg_resources/init.py", line 1469, in run_script
exec(script_code, namespace, namespace)
File "/opt/miniconda2/lib/python2.7/site-packages/SEQLinkage-1.1.0-py2.7.egg/EGG-INFO/scripts/seqlink", line 9, in
File "build/bdist.linux-x86_64/egg/SEQLinkage/Core.py", line 11, in
File "build/bdist.linux-x86_64/egg/faulthandler.py", line 7, in
File "build/bdist.linux-x86_64/egg/faulthandler.py", line 4, in bootstrap
File "/opt/miniconda2/lib/python2.7/site-packages/pkg_resources/init.py", line 1145, in resource_filename
self, resource_name
File "/opt/miniconda2/lib/python2.7/site-packages/pkg_resources/init.py", line 1743, in get_resource_filename
self._extract_resource(manager, self._eager_to_zip(name))
File "/opt/miniconda2/lib/python2.7/site-packages/pkg_resources/init.py", line 1806, in _extract_resource
manager.extraction_error()
File "/opt/miniconda2/lib/python2.7/site-packages/pkg_resources/init.py", line 1192, in extraction_error
raise err
pkg_resources.ExtractionError: Can't extract file(s) to egg cache
The following error occurred while trying to extract file(s)
to the Python egg cache:
[Errno 2] No such file or directory: '/tmp/Python-Eggs'
The Python egg cache directory is currently set to:
/tmp/Python-Eggs
Perhaps your account does not have write access to this directory?
You can change the cache directory by setting the PYTHON_EGG_CACHE
environment variable to point to an accessible directory.
--
I am not sure whether it is a problem of simply updating PYTHON_EGG_CACHE (I tried but not successfully)
or another rather a python issue.
Any ideas please?
Many thanks
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