[Bioperl-pipeline] Requirements for pipeline installation

[Andy Nunberg]

Basically we are running blast searches against several databases. We would
like to keep track of the hits
(possible top 3 from each database).
I'd like to add GeneScan or whatever is the most appropriate gene-finding
algorithim in plants.

I would like to set up an ensembl database to house the annotations

We were looking at the code some more and getting more comfortable with
what is going on.
The reason why I was asking about mySQL databases for input sequences is
because I looked like
the actual sequence is not stored in the input object and that it would
have to go and grab it at some point.
So somehow it has to find it, I am thinking even and indexed fasta file
would suffice..correct? 

Sorry for all the e-mails, yesterday was just one of those days where
nothing made sense :)

For me i like to have a basic understanding of what scripts are doing what,
so that is why I am looking at the code.  I plan on making the first
test/attempt on a local machine ( I dont want to even think about talking
to our queuing system)! :)

I guess i only need info on how to set up reading in  flat files and
setting up a simple database to store results

Thanks for everything
Andy

At 04:26 PM 8/27/2002 +0800, you wrote:
>> We are a company so that point is mute :)
>
>I understand that, was just trying to help, what I really wanted to know
>which is usually not top secret, is just the series of programs you want
>to run. Usually what makes workflows secret is the data that is being
>flowed, not the flow itself, because the flow itself is quite standard,
>almost every company I've seen at the end of the day uses more or less a
>slice of very common tools and programs....
>
>Elia
>
>********************************
>* http://www.fugu-sg.org/~elia *
>* tel:    +65 6874 1467        *
>* mobile: +65 9030 7613        *
>* fax:    +65 6779 1117        *
>********************************
>

*******************************************************************
Andy Nunberg, Ph.D
Computational Biologist
Orion Genomics, LLC 
(314) 615-6989
http://www.oriongenomics.com