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.
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@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@ucdavis.edu
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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@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@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@ucdavis.edu
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
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galaxy-dev@lists.galaxyproject.org
-
Leslie Herrera -
Sven E. Templer