Re: Missing module in the lwr repository

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Re: Missing module in the lwr repository

John Chilton-4
Hello Dr. Senturk,

  This is the second time I have gotten a question like this one in a week so I am going to cc galaxy-dev mailing in the response so there is a public link I can send out about progress in the future.

  There is some limited caching support so you don't have to re-transfer the same inputs over and over. There is no mechanism for periodically cleaning out this cache however and if the LWR is producing large outputs these need to be transferred back to the Galaxy server and re-uploaded once before they are added to the cache. I have sketched out some plans for improving some of these limitations here - https://trello.com/c/MPlt8DHJ, I consider these important features but I am still not sure how quickly I will be able to get to these issues though.

  If you are interested in testing out caching, I have added some documentation to Galaxy's sample job_conf.xml file how to enable caching on the client ( https://bitbucket.org/galaxy/galaxy-central/commits/d6826c29e15a1f17553ae2fe2b149ef65ac4da9d ) and on the server side you simply need to specify a directory to store cached files by un-commenting the property file_cache_dir in LWR's server.ini configuration file. As experimental as I consider the feature - it was a big help for some particular and large  workflows when I was in my previous position and it allowed us to really scale up what we were doing the LWR and Galaxy.

Hope this helps and thanks for your continued interest in the LWR and Galaxy!
-John



On Thu, May 8, 2014 at 6:54 AM, izzet fatih <[hidden email]> wrote:
Hi John,
I'm new in Galaxy so please correct me if I'm wrong. As far as I understand, Galaxy dispatches jobs by /lib/galaxy/jobs/handler.py one by one even though they are part of a workflow. Consequently, LWR receives them separately. Let's have two consecutive steps to be run by LWR. If the data size is big, this will cause excessive data transfer burden between the steps. Do you have any plans to improve this?

Thanks, 


On Wed, Apr 30, 2014 at 4:14 PM, John Chilton <[hidden email]> wrote:
Doh - sorry about that. It should be fixed with this commit - https://bitbucket.org/jmchilton/lwr/commits/5ebad638537e19b55b7b6c812c49ae9da079480c.

Thanks for your interest in the LWR and let me know if there is anything else I can do to fix it, improve it, etc...

-John


On Wed, Apr 30, 2014 at 1:19 PM, izzet fatih <[hidden email]> wrote:
Hi John,
I've downloaded and configured lwr server and it is great tool thanks for developing it.
When I execute run.sh I got the following error

File "/home/isenturk/src/jmchilton-lwr-bd8d1cc44e75/lwr/managers/base/directory.py", line 13, in <module>
    from ..util.env import env_to_statement
ImportError: No module named env

This exception is thrown from
jmchilton-lwr-bd8d1cc44e75/lwr/managers/base/directory.py
It is trying to use env_to_statement command from ..util.env

If I am not mistaken, the module is supposed to be under jmchilton-lwr-bd8d1cc44e75/lwr/managers/util/
However, it is not there.

Thanks,


--
The Ohio State University
Izzet F Senturk, PhD
Post Doctoral Researcher
College of Medicine SBS-Biomedical Informatics
310-05 Lincoln Tower, 1800 Cannon Drive, Columbus, OH 43210
<a href="tel:6148250565" value="+16148250565" target="_blank">6148250565 Office
[hidden email] http://bmi.osu.edu/hpc/





--
The Ohio State University
Izzet F Senturk, PhD
Post Doctoral Researcher
College of Medicine SBS-Biomedical Informatics
310-05 Lincoln Tower, 1800 Cannon Drive, Columbus, OH 43210
<a href="tel:6148250565" value="+16148250565" target="_blank">6148250565 Office
[hidden email] http://bmi.osu.edu/hpc/



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