Hi Nate, Ah, I like this answer, let me see if I can make it work. The way I currently have the instance set up is inside an Ubuntu 14.04 VM, that has been configured to accept lustre mounts. The galaxy code is installed in a lustre directory, which I mainly did to avoid any issues with the cluster seeing important files. I figure the installation may need to be moved to a local VM directory, with the Galaxy files visible in a lustre directory. Anyways, the cluster itself is based on CentOS 7. If you have any other suggestions for this type of setup, please let me know before I go too deep in the rabbit hole!
Cao – I can see hashlib in all of the correct places, but I will try to mess with the installation if the virtualenv method doesn’t help me. Thanks so much! From: Nate Coraor <[email protected]> Date: Thursday, January 18, 2018 at 1:12 PM To: Cao Tang <[email protected]> Cc: John Letaw <[email protected]>, galaxy-dev <[email protected]> Subject: Re: [galaxy-dev] Cluster Install Path Errors 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 <[email protected]<mailto:[email protected]>> wrote: You can try to install: https://pypi.python.org/pypi/hashlib On Thu, Jan 18, 2018 at 1:22 PM, John Letaw <[email protected]<mailto:[email protected]>> 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" <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> 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/
___________________________________________________________ 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/
