[Bioperl-pipeline] RE: Install fails
Wiepert, Mathieu
Wiepert.Mathieu@mayo.edu
Mon, 19 Aug 2002 11:32:01 -0500
Hi,
I got an update, most tests fail, but they all relate to DBI not being able to connect. I don't have the db set up properly and was looking for documentation as to setting up the pipeline tables ( I haven't looked yet). I liked seeing the model recently posted, thanks for that, it is very helpful.
Thanks,
-Mat
> -----Original Message-----
> From: Shawn [mailto:shawnh@fugu-sg.org]
> Sent: Monday, August 19, 2002 6:06 PM
> To: Wiepert, Mathieu
> Cc: bioperl-pipeline mailing list
> Subject: Re: Install fails
>
>
> 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
> > > >
> > > >
> > > >
> > >
> > >
> >
>
>