[Bioperl-pipeline] Re: Install fails

[Shawn]

Hi Mat :)

yeah thanks for catching that. Someone committed an erroneous pod fix
that was failing the tests. Also something trivial but just remember to
set the Perl5lib env variable too :)
let me know how it works out.


shawn

On Mon, 2002-08-19 at 21:39, Wiepert, Mathieu wrote:
> Not sure why this came through now, an old post.  But, it spurred me to install and test.  Had 100% failure ;-)  I am sure it has something to do with not having any db set up, no?  
> 
> The temp dirs all point to /tmp, which is writable on my system.  No load balancer.  
> 
> I'll go poke around for the tests and see why they fail, and move on from there.
> 
> -Mat
> 
> Mathieu Wiepert
> Medical Information Resources
> Mayo Foundation
> (507) 266-2317 Fax (507)-284-0360
> wiepert.mathieu@mayo.edu 
> 
> 
> > -----Original Message-----
> > From: Shawn [mailto:shawnh@fugu-sg.org]
> > Sent: Tuesday, August 06, 2002 7:23 AM
> > To: Wiepert, Mathieu
> > Cc: bioperl-pipeline mailing list; Bob Freimuth (E-mail)
> > Subject: [Bioperl-pipeline] RE: bioperl-pipeline for the small lab
> > 
> > 
> > Hi Mat,
> > one can subscribe to the list at:
> > 
> > http://bioperl.org/mailman/listinfo/bioperl-pipeline
> > 
> > I think most your questions were captured in Elia's mail.
> > 
> > >I have mySQL loaded (should I move to postgres?  
> > >Chris Mungall seemed to say that it was better, haven't 
> > heard other endorsements one way or the other yet)  
> > 
> > I have no experience with postgres, mysql works great for us. I think
> > what Chris pointed out was that postgres allowed certain programmatic
> > queries which reduces some latency without having to do multiple
> > queries.
> > 
> > > In the meantime, I think me getting the infrastructure ready for the
> > pipeline will be good, maybe testing something out?  
> > 
> > yup sounds good. I will commit a blast pipeline then u can try it out.
> > You will need to have the bioperl-run package as well.
> > 
> > In the mean time, you can run the pipeline tests to see whether it
> > passes.
> > 
> > Do this for the first time:
> > perl Makefile.PL
> > make
> > 
> > Then run:
> >  make test 
> > and see whether it runs
> > 
> > Before doing this you will need to modify 
> > bioperl-pipeline/Bio/Pipeline/PipeConf.pm
> > 
> > Ensure that NFSTMP_DIR  writes to a dir that is accessible
> > Ensure that BATCH_MOD is correct either LSF/PBS. Hmm. I remember now,
> > you don't have a load sharing software right? You will need something
> > like this unless there is some way you can submit the jobs from one
> > machine. THen you can encapsulate that in a BatchSubmission object.
> > But the tests will skip if u don't so its ok for now.
> > 
> > > I don't have your slides (will you be posting them at the 
> > OBF or bioperl-site), but any other servers needed?  Apache
> > 
> > attach are my slides, yeah..I will pass it to Chris D for the bioperl
> > site.
> > 
> > >:, tomcat (guess not, no java?)  Can I go check cvs for an 
> > ERD? (Already have BioSQL loaded, but what of GFD
> > 
> > Nope, only mysql needed. ERD? hehe.. good idea...we might come up with
> > one.
> > 
> > 
> > 
> > shawn
> > 
> > 
> > On Tue, 2002-08-06 at 04:53, Wiepert, Mathieu wrote:
> > > Hi Shawn,
> > > 
> > > Glad you got the list started.  I have a friend down at 
> > Wustl, who is interested in this as well.
> > 
> >   It was his research that generated the process for us.
> > 
> >   If you could add him to the list, or else give me the url 
> > to have him enroll, that would be great.(rfreimut@im.wustl.edu)
> > > 
> > > We will have to flesh this out re the cron job.  I see that 
> > aspect as taking a normal pipeline job and then just cron'ing 
> > it, which I think is what you are saying?  So a cron wrapper 
> > on an already existing pipeline path?
> > > 
> > > Regarding 2, I can help with trying to write first passes 
> > at any runnable that I might need (it sounds simple enough), 
> > but will wait for Martin's attempt to define the interface as 
> > you suggest.
> > > 
> > 
> > 
> > 
> > 
> > I have been updating the bioperl-pipeline code from anonymous cvs.  
> > 
> > > 
> > > oe?O=
> > > 
> > > BTW, I didn't get this except as direct from you, nothing 
> > from a bioperl-pipeline list.  Just FYI...
> > > 
> > > Thanks,
> > > -Mat
> > > 
> > > -----Original Message-----
> > > From: Shawn [mailto:shawnh@fugu-sg.org]
> > > Sent: Monday, August 05, 2002 8:41 PM
> > > To: Wiepert, Mathieu
> > > Cc: Elia Stupka; kiran; bioperl-pipeline@bioperl.org
> > > Subject: Re: bioperl-pipeline for the small lab
> > > 
> > > 
> > > Hi Mat,
> > > 	great to hear from you. We are most interested to see 
> > how we can help
> > > you out. We want to encourage as much use of the pipeline 
> > as possible
> > > and that will give us tremendous support in terms of validating our
> > > design and incorporating new features as new requirements arise.
> > > >From your mail, I will try and summarize what you propose
> > > 
> > > 1) The daemon pipeline which I can see as a cron job is 
> > essentially a
> > > one stage pipeline. But we might have one or more runnables for the
> > > logic of doing the diffs and annotating your database based 
> > on new hits
> > >  etc. Yup, its interesting to me to develop this 
> > functionality which is
> > > very generalizable.
> > > 
> > > 2) The second pipeline is seems like a series of blast 
> > pipelines running
> > > in parallel. Then using the hits to run framesearch and 
> > TFASTA. We can
> > > write bioperl wrapper for those or you could help out too 
> > :) Wait for
> > > the proposal of a new Bio::Tools::Run::Analysis interfaceI 
> > think that
> > > Martin Senger is proposing for writing these wrappers which 
> > should be
> > > quite nice and clean  . Outputs can be dumped to database 
> > or csv as you
> > > wish :) In terms of GFD, it seems that we are mostly storing
> > > hits/featurepairs for your searches which is now doable and we are
> > > refining. You prolly also want to store your genes in the 
> > db as well.
> > > For your sequences you may want to store them in BioSQL.
> > > 
> > > When I get back, we can come up with more concrete plans, I 
> > will try and
> > > write up some configurations for your pipeline :)
> > > 
> > > its looks like an interesting start. FYI, we just created a
> > > bioperl-pipeline mailing list and hope u don't mind I have 
> > cc'ed this 
> > > mail to the list. 
> > > 
> > > >I can write some sort of docs for you on how to do this 
> > for the small
> > > lab? 
> > > :) we will definitely take u up on that
> > > 
> > > are u still at ISMB? lets talk some more if you want 
> > > great mail.
> > > 
> > > cheers,
> > > shawn
> > > 
> > > 
> > > 
> > 
> > 
>