Hi all,
I’m facing a python package conflict (statsmodels 0.12.1 instead of 0.11.* and python-dateutil 2.7.2 instead of 2.7.3, cf. ".command.log"at the end of this message)…but I though that kind of problem would not append using a singularity container (everything embedded inside it) . Does I forget something ?
(Rq : Process goes well on my personal computer but not on my office computer ;-((( ---->>> So this is not due to input data )
I would really appreciate any help or clarification about setting-up installation and tractoflow …
Romain
Here is the command used :
nextflow run tractoflow-2.1.1/main.nf --root data_4_tractoflow/ --dti_shells “0 1000” --fodf_shells “0 2000 3000” -with-singularity tractoflow_2.1.1_650f776_2020-07-15.img
My configuration under ubuntu 20.04 :
python --version : Python 3.7.6
java -version: openjdk version “11.0.9.1” 2020-11-04
nextflow -version : version 20.10.0 build 5430
singularity --version 2.6.1-dist
singularity image container : tractoflow_2.1.1_650f776_2020-07-15.img
cat work/c6/827d7a39828ba2db1fcaa0e97aa549/.command.log
nxf-scratch-dir woody:/tmp/nxf.Q3Jby9fMtI
Traceback (most recent call last):
File “/usr/local/lib/python3.7/dist-packages/pkg_resources/init.py”, line 584, in _build_master
ws.require(requires)
File “/usr/local/lib/python3.7/dist-packages/pkg_resources/init.py”, line 901, in require
needed = self.resolve(parse_requirements(requirements))
File “/usr/local/lib/python3.7/dist-packages/pkg_resources/init.py”, line 792, in resolve
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (statsmodels 0.12.1 (/home/romain/.local/lib/python3.7/site-packages), Requirement.parse(‘statsmodels==0.11.*’), {‘scilpy’})During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/usr/local/bin/scil_extract_b0.py”, line 4, in
import(‘pkg_resources’).run_script(‘scilpy==0.2.dev0’, ‘scil_extract_b0.py’)
File “/usr/local/lib/python3.7/dist-packages/pkg_resources/init.py”, line 3258, in
@_call_aside
File “/usr/local/lib/python3.7/dist-packages/pkg_resources/init.py”, line 3242, in _call_aside
f(*args, **kwargs)
File “/usr/local/lib/python3.7/dist-packages/pkg_resources/init.py”, line 3271, in _initialize_master_working_set
working_set = WorkingSet._build_master()
File “/usr/local/lib/python3.7/dist-packages/pkg_resources/init.py”, line 586, in _build_master
return cls._build_from_requirements(requires)
File “/usr/local/lib/python3.7/dist-packages/pkg_resources/init.py”, line 599, in _build_from_requirements
dists = ws.resolve(reqs, Environment())
File “/usr/local/lib/python3.7/dist-packages/pkg_resources/init.py”, line 792, in resolve
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (python-dateutil 2.7.2 (/usr/local/lib/python3.7/dist-packages), Requirement.parse(‘python-dateutil>=2.7.3’), {‘pandas’})