I think this error most commonly occurs when a virtualenv is used with a different python than the one it was created with. Is the cluster also running Ubuntu 14.04? If not, you can create a separate virtualenv for running tools using the instructions at:
https://docs.galaxyproject.org/en/master/admin/framework_dependencies.html#managing-dependencies-manually Once created, your tools can use it by setting `<param id="GALAXY_VIRTUAL_ENV">/path/to/venv</param>` on the destination in job_conf.xml --nate On Thu, Jan 18, 2018 at 1:50 PM, Cao Tang <charlietan...@gmail.com> wrote: > You can try to install: > > https://pypi.python.org/pypi/hashlib > > On Thu, Jan 18, 2018 at 1:22 PM, John Letaw <le...@ohsu.edu> wrote: > >> Thanks for the response Peter. I currently have this instance installed >> on a lustre fs, that is visible on an Ubuntu 14.04 vm. So, there very well >> may be mismatches between directories on the VM, and those on the lustre >> cluster. This would mean the python installation on the VM needs to >> exactly match that which is on the cluster? What else will need to match >> to ensure success? >> >> Thanks, >> John >> >> On 1/18/18, 1:50 AM, "Peter Cock" <p.j.a.c...@googlemail.com> wrote: >> >> I *think* this is a problem with your copy of Python 2.7 and a >> standard library (hashlib) normally present. Do you know how this >> Python was installed? If it was compiled from source, then it may have >> been missing a few dependencies, and thus you have ended up with >> missing a few normally present Python modules. >> >> Peter >> >> On Wed, Jan 17, 2018 at 11:15 PM, John Letaw <le...@ohsu.edu> wrote: >> > Hi all, >> > >> > >> > >> > I have been trying to finish up a production cluster Galaxy >> installation, >> > and am having trouble with the below error. In the past, when >> seeing >> > something along these lines, I usually can adjust environmental >> variables >> > either in startup scripts, or by including a script for Galaxy to >> source >> > before it sends out a job. I have tried all of these different >> methods, but >> > I can’t seem to get rid of this error message in any tool >> invocation. I >> > currently have “embed_metadata_in_job” set to False in my >> job_conf.xml file. >> > This removes a “No module named galaxy_ext.metadata.set_metadata” >> error, but >> > this hashlib error remains. If I could understand a little more >> about the >> > steps that are taken when sending out a job, perhaps I could better >> diagnose >> > this? >> > >> > >> > >> > “”” >> > >> > Could not find platform dependent libraries >> > >> > Consider setting $PYTHONHOME to [:] >> > >> > Traceback (most recent call last): >> > >> > File "~/galaxydev/galaxy/tools/data_source/upload.py", line 14, >> in >> > >> > import tempfile >> > >> > File "/usr/lib64/python2.7/tempfile.py", line 35, in >> > >> > from random import Random as _Random >> > >> > File "/usr/lib64/python2.7/random.py", line 49, in >> > >> > import hashlib as _hashlib >> > >> > File "/usr/lib64/python2.7/hashlib.py", line 116, in >> > >> > import _hashlib >> > >> > ImportError: No module named _hashlib >> > >> > “”” >> > >> > >> > >> > Thanks, >> > >> > John >> > >> > >> > ___________________________________________________________ >> > 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/ >> > >> > To search Galaxy mailing lists use the unified search at: >> > http://galaxyproject.org/search/ >> >> >> ___________________________________________________________ >> 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/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/ > > > > ___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ >
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