Hi Tobias,
this is a shortcoming of the installation method back in the time. We
changed this a while back to the more stable one in:
https://github.com/galaxyproject/galaxy/blob/ef417464c7cf25b5c9a4526ed31817d80553420a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py#L1638
So the only advice I can give you is, to upgrade your Galaxy instance.
It's really worth it. 15.05 is really old!
Ciao,
Bjoern
Hello,
I'm having a problem with the installation of the
"deeptools_bam_compare" tool (Revision: d5d57b40b29a). The
installation of the requirements (package_python_2_7_deeptools_2_2_2)
fails. The command which fails is the following (stderr output is
located in
/ceph/galaxy/tool_dependencys/deepTools/2.2.2/iuc/package_python_2_7_deeptools_2_2_2/0e67aa094608/INSTALLATION.log):
...
easy_install --no-deps --install-dir
/galaxy/tool_dependencys/deepTools/2.2.2/iuc/package_python_2_7_deeptools_2_2_2/0e67aa094608
--script-dir
/galaxy/tool_dependencys/deepTools/2.2.2/iuc/package_python_2_7_deeptools_2_2_2/0e67aa094608/bin
deeptools_2.2.2_src_all.tar.gz
STDERR
Traceback (most recent call last):
File "/usr/bin/easy_install", line 5, in <module>
from pkg_resources import load_entry_point
File
"/ceph/galaxy/tool_dependencys/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/site-packages/pkg_resources/__init__.py",
line 3084, in <module>
@_call_aside
File
"/ceph/galaxy/tool_dependencys/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/site-packages/pkg_resources/__init__.py",
line 3070, in _call_aside
f(*args, **kwargs)
File
"/ceph/galaxy/tool_dependencys/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/site-packages/pkg_resources/__init__.py",
line 3097, in _initialize_master_working_set
working_set = WorkingSet._build_master()
File
"/ceph/galaxy/tool_dependencys/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/site-packages/pkg_resources/__init__.py",
line 653, in _build_master
return cls._build_from_requirements(__requires__)
File
"/ceph/galaxy/tool_dependencys/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/site-packages/pkg_resources/__init__.py",
line 666, in _build_from_requirements
dists = ws.resolve(reqs, Environment())
File
"/ceph/galaxy/tool_dependencys/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/site-packages/pkg_resources/__init__.py",
line 839, in resolve
raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'setuptools==3.3' distribution
was not found and is required by the application
...
The problem seems to be the missing / wrong version of setuptools. The
next step for me was to check the missing tool dependencies error
reports. All tool dependencies (deepTools, pysam, matplotlib,
bx-python, scipy, pybigwig and numpy) show the same error with the
missing setuptools.
Only the package_python_2_7_10 dependency is installed correct. I
checked the setuptools version in the python dependency
(/ceph/galaxy/tool_dependencys/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/site-packages/setuptools/version.py)
and it's version 18.2 (__version__ = '18.2'). This might be the
problem here?
I am using Galaxy release_15.05.
Thanks,
Tobias
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