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.temp...@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 <laherr...@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
>> laherr...@ucdavis.edu
>>
>> ___________________________________________________________
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>
>
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