I installed FSL/5.0.11 on our system at Indiana University on Wednesday, and have discovered we have the same problem. the same three files are missing from our installation:
< imcp
< imglob
< immv
I tried the command you suggested:
[hbrokaw@h1 fsl]$ $FSLDIR/fslpython/bin/conda env create -f $FSLDIR/etc/fslconf/fslpython_environment.yml
But I am getting undefined symbol errors. We have 2 python 2.7's on our system. 2.7.3 and 2.7.9. What version is needed to successfully run the above conda build?
Error encountered with python 2.7.9 was:
Collecting SPARQLWrapper==1.7.6 (from -r /N/soft/rhel6/fsl/5.0.11/etc/fslconf/condaenv.tm2wsoiz.requirements.txt (line 1))
Downloading https://files.pythonhosted.org/packages/92/4f/e44f10d2d2a4c66c01f0f47e1aa1fe8addeedaf050e7cbcfa3a5ebce6f14/SPARQLWrapper-1.7.6.tar.gz
Exception:
Traceback (most recent call last):
File "/N/soft/rhel6/python/2.7.9/lib/python2.7/site-packages/pip/basecommand.py", line 215, in main
status = self.run(options, args)
File "/N/soft/rhel6/python/2.7.9/lib/python2.7/site-packages/pip/commands/install.py", line 335, in run
wb.build(autobuilding=True)
File "/N/soft/rhel6/python/2.7.9/lib/python2.7/site-packages/pip/wheel.py", line 749, in build
self.requirement_set.prepare_files(self.finder)
File "/N/soft/rhel6/python/2.7.9/lib/python2.7/site-packages/pip/req/req_set.py", line 380, in prepare_files
ignore_dependencies=self.ignore_dependencies))
File "/N/soft/rhel6/python/2.7.9/lib/python2.7/site-packages/pip/req/req_set.py", line 634, in _prepare_file
abstract_dist.prep_for_dist()
File "/N/soft/rhel6/python/2.7.9/lib/python2.7/site-packages/pip/req/req_set.py", line 129, in prep_for_dist
self.req_to_install.run_egg_info()
File "/N/soft/rhel6/python/2.7.9/lib/python2.7/site-packages/pip/req/req_install.py", line 412, in run_egg_info
self.setup_py, self.name,
File "/N/soft/rhel6/python/2.7.9/lib/python2.7/site-packages/pip/req/req_install.py", line 387, in setup_py
import setuptools # noqa
File "/N/soft/rhel6/python/2.7.9/lib/python2.7/site-packages/setuptools/__init__.py", line 11, in <module>
from setuptools.extension import Extension
File "/N/soft/rhel6/python/2.7.9/lib/python2.7/site-packages/setuptools/extension.py", line 8, in <module>
from .dist import _get_unpatched
File "/N/soft/rhel6/python/2.7.9/lib/python2.7/site-packages/setuptools/dist.py", line 19, in <module>
import pkg_resources
File "/N/soft/rhel6/python/2.7.9/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1696, in <module>
register_loader_type(importlib_bootstrap.SourceFileLoader, DefaultProvider)
AttributeError: module 'importlib._bootstrap' has no attribute 'SourceFileLoader'
CondaValueError: pip returned an error
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