Dear Leslie,
I solved the problem by using a new python installation (we use the module
system to define PATH, PYTHONPATH, PYTHONUSERBASE and PYTHONHOME), without
any site libraries installed.
Before in the installation I had those packages (in
/software/Python/2.7.9/lib/python2.7/site-packages/) installed:
---
Bio biopython-1.65-py2.7.egg-info
matplotlib pathtools-0.1.2-py2.7.egg
pyparsing.py setuptools
BioSQL curl
matplotlib-1.4.3-py2.7-nspkg.pth pbr
pyparsing.pyc setuptools-18.3.1.dist-info
Cython-0.22-py2.7-linux-x86_64.egg dateutil
matplotlib-1.4.3-py2.7.egg-info pbr-1.8.0.dist-info
pysam singledispatch-3.4.0.3-py2.7.egg
DCC-0.3.1rc0-py2.7.egg
distribute-0.7.3-py2.7.egg-info mock
pip pysam-0.8.2.1-py2.7.egg-info
six-1.9.0-py2.7.egg
DCC-0.3.2-py2.7.egg easy-install.pth
mock-1.3.0.dist-info pip-7.1.2.dist-info
python_dateutil-2.4.2.dist-info sklearn
HTSeq-0.6.1p1-py2.7-linux-x86_64.egg easy_install.py
mpl_toolkits pkg_resources
pytz watchdog-0.8.3-py2.7.egg
MACS2 easy_install.pyc
nose poretools-0.5.1-py2.7.egg
pytz-2015.4.dist-info wget-2.2-py2.7.egg-info
MACS2-2.1.0.20140616-py2.7.egg-info easy_install.pyo
nose-1.3.7.dist-info pybedtools
rpy2-2.5.6-py2.7-linux-x86_64.egg wget.py
MACS2-2.1.0.20150316-py2.7-linux-x86_64.egg funcsigs
numpy
pybedtools-0.6.9-py2.7.egg-info ruffus
wget.pyc
PyYAML-3.11-py2.7-linux-x86_64.egg funcsigs-0.4.dist-info
numpy-1.10.0.dev0_63e8bab-py2.7.egg-info pycurl.so
ruffus-2.6.3-py2.7.egg-info
README
h5py-2.4.0-py2.7-linux-x86_64.egg numpy-1.9.2-py2.7.egg-info
pylab.py scikit_learn-0.16.1-py2.7.egg-info
_markerlib httplib2
pandas pylab.pyc
scipy
argh-0.26.1-py2.7.egg httplib2-0.8-py2.7.egg-info
pandas-0.16.0-py2.7.egg-info pyparsing-2.0.3.dist-info
scipy-0.15.1-py2.7.egg-info
---
I guess setuptools (v 18.3.1) is the cause of the incompatibility with the
distribute package that galaxy_sequencing_utils downloads.
Hope this helps!
Best,
Sven.
On 15 September 2015 at 10:20, Sven E. Templer <sven.templer(a)gmail.com>
wrote:
Hi Leslie,
I face the same problem:
---
Downloading
http://pypi.python.org/packages/source/d/distribute/distribute-0.6.38.tar.gz
Extracting in /tmp/tmplcqzT1
Now working in /tmp/tmplcqzT1/distribute-0.6.38
Building a Distribute egg in
/beegfs/common/galaxy/home/server/database/tmp/tmp-toolshed-mtdqsavtj/galaxy_sequence_utils-1.0.0
Traceback (most recent call last):
File "setup.py", line 248, in <module>
scripts = scripts,
File "/software/Python/2.7.9/lib/python2.7/distutils/core.py", line 111,
in setup
_setup_distribution = dist = klass(attrs)
File "/tmp/tmplcqzT1/distribute-0.6.38/setuptools/dist.py", line 225, in
__init__
_Distribution.__init__(self,attrs)
File "/software/Python/2.7.9/lib/python2.7/distutils/dist.py", line 287,
in __init__
self.finalize_options()
File "/tmp/tmplcqzT1/distribute-0.6.38/setuptools/dist.py", line 257, in
finalize_options
ep.require(installer=self.fetch_build_egg)
File "/tmp/tmplcqzT1/distribute-0.6.38/pkg_resources.py", line 2027, in
require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/tmp/tmplcqzT1/distribute-0.6.38/pkg_resources.py", line 2237, in
requires
dm = self._dep_map
File "/tmp/tmplcqzT1/distribute-0.6.38/pkg_resources.py", line 2466, in
_dep_map
self.__dep_map = self._compute_dependencies()
File "/tmp/tmplcqzT1/distribute-0.6.38/pkg_resources.py", line 2499, in
_compute_dependencies
common = frozenset(reqs_for_extra(None))
File "/tmp/tmplcqzT1/distribute-0.6.38/pkg_resources.py", line 2496, in
reqs_for_extra
if req.marker_fn(override={'extra':extra}):
File "/tmp/tmplcqzT1/distribute-0.6.38/_markerlib/markers.py", line 109,
in marker_fn
return eval(compiled_marker, environment)
File "<environment marker>", line 1, in <module>
NameError: name 'sys_platform' is not defined
/beegfs/common/galaxy/home/server/database/tmp/tmp-toolshed-mtdqsavtj/galaxy_sequence_utils-1.0.0/distribute-0.6.38-py2.7.egg
Traceback (most recent call last):
File "setup.py", line 9, in <module>
use_setuptools()
File
"/beegfs/common/galaxy/home/server/database/tmp/tmp-toolshed-mtdqsavtj/galaxy_sequence_utils-1.0.0/distribute_setup.py",
line 152, in use_setuptools
return _do_download(version, download_base, to_dir, download_delay)
File
"/beegfs/common/galaxy/home/server/database/tmp/tmp-toolshed-mtdqsavtj/galaxy_sequence_utils-1.0.0/distribute_setup.py",
line 132, in _do_download
_build_egg(egg, tarball, to_dir)
File
"/beegfs/common/galaxy/home/server/database/tmp/tmp-toolshed-mtdqsavtj/galaxy_sequence_utils-1.0.0/distribute_setup.py",
line 123, in _build_egg
raise IOError('Could not build the egg.')
IOError: Could not build the egg.
---
It might be an issue that distribute is not maintained any more (v0.6.38
is used, 0.7.3 was latest version in 2013, then migrated to setuptools).
If you probably have updated setuptools (mine is version 18.3.1), it might
cause the error.
I tried to modify setup.py to use version 0.6.49 of distribute, but got
the same error.
Best,
Sven
On 10 September 2015 at 18:33, Leslie Herrera <laherrera(a)ucdavis.edu>
wrote:
> Hello:
>
> My lab is currently in the process of setting Galaxy up on our server. I
> have been installing the appropriate tools, but I am having difficulty
> installing the package_galaxy_utils_1_0. The error message is below. If
> this is something that is occuring on our end, would you please send
> instuctions on how to fix it? If I have sent this email to wrong address
> or you need more information, please let me know. Thank you very much for
> your help.
>
>
> Downloading
>
http://pypi.python.org/packages/source/d/distribute/distribute-0.6.38.tar.gz
> Extracting in /tmp/tmp3dIIS_
> Now working in /tmp/tmp3dIIS_/distribute-0.6.38
>
> Building a Distribute egg in
/scratch/tmp-toolshed-mtdKjroZR/galaxy_sequence_utils-1.0.0
> Traceback (most recent call last):
> File "setup.py", line 248, in <module>
> scripts = scripts,
> File "/usr/lib/python2.7/distutils/core.py", line 111, in setup
> _setup_distribution = dist = klass(attrs)
>
> File "/tmp/tmp3dIIS_/distribute-0.6.38/setuptools/dist.py", line 225, in
__init__
> _Distribution.__init__(self,attrs)
> File "/usr/lib/python2.7/distutils/dist.py", line 287, in __init__
> self.finalize_options()
>
> File "/tmp/tmp3dIIS_/distribute-0.6.38/setuptools/dist.py", line 257, in
finalize_options
> ep.require(installer=self.fetch_build_egg)
>
> File "/tmp/tmp3dIIS_/distribute-0.6.38/pkg_resources.py", line 2027, in
require
> working_set.resolve(self.dist.requires(self.extras),env,installer))
>
> File "/tmp/tmp3dIIS_/distribute-0.6.38/pkg_resources.py", line 2237, in
requires
> dm = self._dep_map
>
> File "/tmp/tmp3dIIS_/distribute-0.6.38/pkg_resources.py", line 2466, in
_dep_map
> self.__dep_map = self._compute_dependencies()
>
> File "/tmp/tmp3dIIS_/distribute-0.6.38/pkg_resources.py", line 2499, in
_compute_dependencies
> common = frozenset(reqs_for_extra(None))
>
> File "/tmp/tmp3dIIS_/distribute-0.6.38/pkg_resources.py", line 2496, in
reqs_for_extra
> if req.marker_fn(override={'extra':extra}):
>
> File "/tmp/tmp3dIIS_/distribute-0.6.38/_markerlib/markers.py", line 109,
in marker_fn
> return eval(compiled_marker, environment)
> File "<environment marker>", line 1, in <module>
> NameError: name 'sys_platform' is not defined
>
>
/scratch/tmp-toolshed-mtdKjroZR/galaxy_sequence_utils-1.0.0/distribute-0.6.38-py2.7.egg
> Traceback (most recent call last):
> File "setup.py", line 9, in <module>
> use_setuptools()
>
> File
"/scratch/tmp-toolshed-mtdKjroZR/galaxy_sequence_utils-1.0.0/distribute_setup.py",
line 152, in use_setuptools
> return _do_download(version, download_base, to_dir, download_delay)
>
> File
"/scratch/tmp-toolshed-mtdKjroZR/galaxy_sequence_utils-1.0.0/distribute_setup.py",
line 132, in _do_download
> _build_egg(egg, tarball, to_dir)
>
> File
"/scratch/tmp-toolshed-mtdKjroZR/galaxy_sequence_utils-1.0.0/distribute_setup.py",
line 123, in _build_egg
> raise IOError('Could not build the egg.')
> IOError: Could not build the egg.
> --
> Leslie A Herrera
> Starr Lab Junior Specialist
> MCB, 139 Briggs Hall
> University of California, Davis
> laherrera(a)ucdavis.edu
>
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