issues with seqlinkage installation

[valecipriani]

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

[gaow]

@valecipriani could you confirm that there is this switch -v /tmp:/tmp in the alias you specified? What if you add to it: -v /tmp/PYTHON_EGG_CACHE:/tmp/PYTHON_EGG_CACHE, and try on your Ubuntu WSL, mkdir -p /tmp/PYTHON_EGG_CACHE, then run the command -- does it help? Please remember to load the bash configuration after you modify it to activate the change.

[valecipriani]

Fantastic. It works. I should have asked you much earlier instead of wasting hours. Thanks!
vcipriani@DESKTOP-UI2KNDV:~$ seqlink -h
usage: seqlink [--bin FLOAT] [-b FILE] [--single-markers] --fam FILE --vcf
FILE [--build STRING] [--freq INFO] [--freq_by_fam INFO]
[--mle] [--rvhaplo] [--recomb_max INT] [--recomb_cross_fam]
[--include_vars FILE] [-c P] [--chrom-prefix STRING] [-o Name]
[-f FORMAT [FORMAT ...]] [-K FLOAT] [--moi STRING] [-W FLOAT]
[-M FLOAT] [--theta-max FLOAT] [--theta-inc FLOAT]
[--run-linkage] [--output-entries N] [-h] [-j N]
[--tempdir PATH] [--cache] [-q]

    SEQLinkage, linkage analysis using sequence data
    [1.1.0]

Collapsed haplotype pattern method arguments:
--bin FLOAT Defines theme to collapse variants. Set to 0 for
"complete collapsing", 1 for "no collapsing", r2 value
between 0 and 1 for "LD based collapsing" and other
integer values for customized collapsing bin sizes.
Default to 0.8 (variants having r2 >= 0.8 will be
collapsed).
-b FILE, --blueprint FILE
Blueprint file that defines regional marker (format:
"chr startpos endpos name avg.distance male.distance
female.distance").
--single-markers Use single variant markers. This switch will overwrite
"--bin" and "--blueprint" arguments.

Input / output options:
--fam FILE Input pedigree and phenotype information in FAM
format.
--vcf FILE Input VCF file, bgzipped.
--build STRING Reference genome version for VCF file.
--freq INFO Info field name for allele frequency in VCF file.
--freq_by_fam INFO Per family info field name for allele frequency in VCF
file.
--mle Estimate allele frequency using MERLIN's MLE method.
--rvhaplo Only using rare variants for haplotyping
--recomb_max INT Maximum recombination events allowed per region.
--recomb_cross_fam Code sub-regions with cross family recombination
events; otherwise sub-regions are generated on per
family basis.
--include_vars FILE Variants to be included in CHP construction
-c P, --maf-cutoff P MAF cutoff to define "common" variants to be excluded
from analyses.
--chrom-prefix STRING
Prefix to chromosome name in VCF file if applicable,
e.g. "chr".
-o Name, --output Name
Output name prefix.
-f FORMAT [FORMAT ...], --format FORMAT [FORMAT ...]
Output format. Default to LINKAGE.

LINKAGE options:
-K FLOAT, --prevalence FLOAT
Disease prevalence.
--moi STRING Mode of inheritance, AD/AR: autosomal
dominant/recessive.
-W FLOAT, --wt-pen FLOAT
Penetrance for wild type.
-M FLOAT, --mut-pen FLOAT
Penetrance for mutation.
--theta-max FLOAT Theta upper bound. Default to 0.5.
--theta-inc FLOAT Theta increment. Default to 0.05.
--run-linkage Perform Linkage analysis using FASTLINK program.
--output-entries N Write the highest N LOD/HLOD scores to output tables.
Default to 10.

Runtime arguments:
-h, --help Show help message and exit.
-j N, --jobs N Number of CPUs to use.
--tempdir PATH Temporary directory to use.
--cache Load cache data for analysis instead of starting from
scratch.
-q, --quiet Disable the display of runtime MESSAGE.

    Copyright (c) 2013 - 2014 Gao Wang <[email protected]>
    Distributed under GNU General Public License
    Home page: http://bioinformatics.org/seqlink

I can try use the software now. Hopefully I will not encounter any other issues! :-)