Re: [galaxy-dev] WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
It turned out this error was caused by the python installation on the computer node, I reinstalled Python 2.7.3 on the computer node and then fetch_eggs.py doesn't generate any problem, however when I submit a job in Galaxy and the job fails with the following error: Traceback (most recent call last): File "./scripts/set_metadata.py", line 24, in import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers File "/home/galaxy/galaxy-dist/lib/galaxy/model/__init__.py", line 13, in import galaxy.datatypes.registry File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py", line 5, in import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks, chrominfo, binary, assembly, ngsindex, wsf, hmm ImportError: Bad magic number in /home/galaxy/galaxy-dist/lib/galaxy/datatypes/wsf.pyc On Wed, Jan 23, 2013 at 3:48 PM, Luobin Yang wrote: > Hi, Nate, > > It seems fetch_eggs.py does not run correctly on the compute node, which > runs Ubuntu 12.04.1 LTS and Python 2.7.3. After I ran "python > scripts/fetch_eggs.py", I got the following errors: > > Traceback (most recent call last): > File "scripts/fetch_eggs.py", line 30, in > c.resolve() # Only fetch eggs required by the config > File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, > in resolve > egg.resolve() > File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, > in resolve > return self.version_conflict( e.args[0], e.args[1] ) > File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 226, > in version_conflict > r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), > env, egg.fetch ) > File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 584, in > resolve > raise DistributionNotFound(req) > pkg_resources.DistributionNotFound: docutils==0.7 > Error in sys.excepthook: > Traceback (most recent call last): > File "/usr/lib/python2.7/dist-packages/apport_python_hook.py", line 66, > in apport_excepthook > from apport.fileutils import likely_packaged, get_recent_crashes > ImportError: No module named apport.fileutils > > Original exception was: > Traceback (most recent call last): > File "scripts/fetch_eggs.py", line 30, in > c.resolve() # Only fetch eggs required by the config > File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, > in resolve > egg.resolve() > File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, > in resolve > return self.version_conflict( e.args[0], e.args[1] ) > File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 226, > in version_conflict > r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), > env, egg.fetch ) > File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 584, in > resolve > raise DistributionNotFound(req) > pkg_resources.DistributionNotFound: docutils==0.7 > > > > On Wed, Jan 23, 2013 at 2:48 PM, Nate Coraor wrote: > >> On Jan 23, 2013, at 4:09 PM, Luobin Yang wrote: >> >> > Hi, >> > >> > I ran into this error and I found the following thread discussing the >> problem, interestingly, for my system, the computer node runs the same >> Python version as the head node, but with a newer OS version, but it also >> generates this error. Does this mean the Galaxy system requires the >> computer nodes in a cluster to have the same version of OS and the same >> version of Python? >> > >> > http://comments.gmane.org/gmane.science.biology.galaxy.devel/3188 >> > >> > Luobin >> >> Hi Luobin, >> >> If you remove the galaxy-dist/eggs/ directory and then run: >> >> galaxy-dist% python ./scripts/fetch_eggs.py >> >> On both the galaxy server and the cluster, the output should reveal the >> differences in what platforms are being detected. It's not required that >> they be the same OS or Python version, but if they differ they will both >> need to acquire platform-specific eggs. Normally missing eggs are fetched >> automatically, but there are a few cases where you have to run >> fetch_eggs.py by hand. >> >> --nate >> >> > ___ >> > 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: >> > >> > http://lists.bx.psu.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: http://lists.bx.psu.edu/
Re: [galaxy-dev] WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
Hi, Nate, It seems fetch_eggs.py does not run correctly on the compute node, which runs Ubuntu 12.04.1 LTS and Python 2.7.3. After I ran "python scripts/fetch_eggs.py", I got the following errors: Traceback (most recent call last): File "scripts/fetch_eggs.py", line 30, in c.resolve() # Only fetch eggs required by the config File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, in resolve return self.version_conflict( e.args[0], e.args[1] ) File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 226, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 584, in resolve raise DistributionNotFound(req) pkg_resources.DistributionNotFound: docutils==0.7 Error in sys.excepthook: Traceback (most recent call last): File "/usr/lib/python2.7/dist-packages/apport_python_hook.py", line 66, in apport_excepthook from apport.fileutils import likely_packaged, get_recent_crashes ImportError: No module named apport.fileutils Original exception was: Traceback (most recent call last): File "scripts/fetch_eggs.py", line 30, in c.resolve() # Only fetch eggs required by the config File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, in resolve return self.version_conflict( e.args[0], e.args[1] ) File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 226, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 584, in resolve raise DistributionNotFound(req) pkg_resources.DistributionNotFound: docutils==0.7 On Wed, Jan 23, 2013 at 2:48 PM, Nate Coraor wrote: > On Jan 23, 2013, at 4:09 PM, Luobin Yang wrote: > > > Hi, > > > > I ran into this error and I found the following thread discussing the > problem, interestingly, for my system, the computer node runs the same > Python version as the head node, but with a newer OS version, but it also > generates this error. Does this mean the Galaxy system requires the > computer nodes in a cluster to have the same version of OS and the same > version of Python? > > > > http://comments.gmane.org/gmane.science.biology.galaxy.devel/3188 > > > > Luobin > > Hi Luobin, > > If you remove the galaxy-dist/eggs/ directory and then run: > > galaxy-dist% python ./scripts/fetch_eggs.py > > On both the galaxy server and the cluster, the output should reveal the > differences in what platforms are being detected. It's not required that > they be the same OS or Python version, but if they differ they will both > need to acquire platform-specific eggs. Normally missing eggs are fetched > automatically, but there are a few cases where you have to run > fetch_eggs.py by hand. > > --nate > > > ___ > > 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: > > > > http://lists.bx.psu.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: http://lists.bx.psu.edu/
Re: [galaxy-dev] WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
On Jan 23, 2013, at 4:09 PM, Luobin Yang wrote: > Hi, > > I ran into this error and I found the following thread discussing the > problem, interestingly, for my system, the computer node runs the same Python > version as the head node, but with a newer OS version, but it also generates > this error. Does this mean the Galaxy system requires the computer nodes in a > cluster to have the same version of OS and the same version of Python? > > http://comments.gmane.org/gmane.science.biology.galaxy.devel/3188 > > Luobin Hi Luobin, If you remove the galaxy-dist/eggs/ directory and then run: galaxy-dist% python ./scripts/fetch_eggs.py On both the galaxy server and the cluster, the output should reveal the differences in what platforms are being detected. It's not required that they be the same OS or Python version, but if they differ they will both need to acquire platform-specific eggs. Normally missing eggs are fetched automatically, but there are a few cases where you have to run fetch_eggs.py by hand. --nate > ___ > 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: > > http://lists.bx.psu.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: http://lists.bx.psu.edu/
