Problems installing pbs_python from scramble.
Hello All, I am trying to setup job submission to pbs server running on our cluster. I have python 2.7 installed in /usr/local along with easy_install. But when trying to compile pbs_python I am getting following error: [galaxy@galaxy galaxy-dist]$ LIBTORQUE_DIR=/usr/lib python scripts/scramble.py -e pbs_python fetch_one(): Trying to fetch: http://eggs.galaxyproject.org/pbs_python/pbs_python-4.3.5.tar.gz fetch_one(): Fetched to: /home/galaxy/galaxy-dist/scripts/scramble/archives/pbs_python-4.3.5.tar.gz unpack_source(): Unpacked to: /home/galaxy/galaxy-dist/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python copy_build_script(): Using build script /home/galaxy/galaxy-dist/scripts/scramble/scripts/pbs_python.py run_scramble_script(): Beginning build run_scramble_script(): Executing in /home/galaxy/galaxy-dist/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python: /home/galaxy/galaxy-python/python scramble.py Traceback (most recent call last): File "scramble.py", line 14, in <module> from scramble_lib import * File "../../../lib/scramble_lib.py", line 146, in <module> from setuptools import * File "build/bdist.linux-x86_64/egg/setuptools/__init__.py", line 11, in <module> File "build/bdist.linux-x86_64/egg/setuptools/extension.py", line 8, in <module> File "build/bdist.linux-x86_64/egg/setuptools/dist.py", line 21, in <module> AttributeError: 'module' object has no attribute 'packaging' Traceback (most recent call last): File "scripts/scramble.py", line 50, in <module> egg.scramble() File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/scramble.py", line 57, in scramble self.run_scramble_script() File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/scramble.py", line 210, in run_scramble_script raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" % ( sys._getframe().f_code.co_name, self.name, self.version ) ) galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build failed for pbs_python 4.3.5 I also tried setuptools-18.0.1 installed in user's local path but I am still getting the same error. It is Centos 6.6 OS. Any help would be appreciated. -- Regards, -- Zuzanna K. Filutowska, HPC Systems Administrator Poznan Supercomputing and Networking Center Institute of Bioorganic Chemistry Polish Academy of Sciences Seize the day boys! Make your lifes extraordinary! --John Keating
Dnia 2015-07-29, śro o godzinie 12:35 +0200, Zuzanna K. Filutowska pisze: It is worth to add that I installed pip, and tried to install pbs_python using pip or easy_install and these seems to work fine. -- Pozdrawiam, -- Zuzanna K. Filutowska, HPC Systems Administrator Poznan Supercomputing and Networking Center Institute of Bioorganic Chemistry Polish Academy of Sciences Seize the day boys! Make your lifes extraordinary! --John Keating
Hi Zuzanna, You can temporarily relocate the 'pkg_resources.py' that ships with Galaxy (and delete the corresponding .pyc file) to get around this error. Let me know if this doesn't work for you, though, and I can help debug some more. We're hoping to swap to new dependency management code that should resolve this error in a coming release. -Dannon On Wed, Jul 29, 2015 at 7:25 AM, Zuzanna K. Filutowska < platyna@man.poznan.pl> wrote:
Dnia 2015-07-29, śro o godzinie 12:35 +0200, Zuzanna K. Filutowska pisze:
It is worth to add that I installed pip, and tried to install pbs_python using pip or easy_install and these seems to work fine.
--
Pozdrawiam,
-- Zuzanna K. Filutowska, HPC Systems Administrator Poznan Supercomputing and Networking Center Institute of Bioorganic Chemistry Polish Academy of Sciences Seize the day boys! Make your lifes extraordinary! --John Keating
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Dnia 2015-07-29, śro o godzinie 18:43 -0400, Dannon Baker pisze:
Hi Zuzanna,
You can temporarily relocate the 'pkg_resources.py' that ships with Galaxy (and delete the corresponding .pyc file) to get around this error. Let me know if this doesn't work for you, though, and I can help debug some more.
We're hoping to swap to new dependency management code that should resolve this error in a coming release.
Dear Dannon, this solution worked fine. However despite the fact I copied this file back before starting Galaxy I have: [galaxy@galaxy ~]$ Some eggs are out of date, attempting to fetch... Warning: pbr (a dependent egg of sqlalchemy-migrate) cannot be fetched setuptools 18.0.1 couldn't be downloaded automatically. You can try building it by hand with: python scripts/scramble.py -c config/galaxy.ini -e setuptools Fetch failed. I have systemtools 18.0.1 and pbr installed by pip2.7 on the system, why can't Galaxy use these? Also pbr is not in eggs.ini and setuptools will not compile using scramble, even if the files lib/pkg_resources.* are not there: creating dist creating 'dist/setuptools-18.0.1-py2.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Traceback (most recent call last): File "scripts/scramble.py", line 50, in <module> egg.scramble() File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/scramble.py", line 60, in scramble raise ScrambleFailure( self, "%s(): Egg build for %s did not appear to fail, but no egg found to copy from expected path:\n %s" % ( sys._getframe().f_code.co_name, self.name, new_egg ) ) galaxy.eggs.scramble.ScrambleFailure: scramble(): Egg build for setuptools did not appear to fail, but no egg found to copy from expected path: /home/galaxy/galaxy-dist/scripts/scramble/build/py2.7-linux-x86_64-ucs4/setuptools/dist/setuptools-18.0.1-py2.7-linux-x86_64-ucs4.egg Full output: http://www.wklej.org/id/1765369/ -- Pozdrawiam, -- Zuzanna K. Filutowska, HPC Systems Administrator Poznan Supercomputing and Networking Center Institute of Bioorganic Chemistry Polish Academy of Sciences Seize the day boys! Make your lifes extraordinary! --John Keating
participants (2)
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Dannon Baker -
Zuzanna K. Filutowska