[Bioperl-l] Blast stuff

[Ewan Birney]

On Tue, 3 Dec 2002, Hilmar Lapp wrote:

>
> On Tuesday, December 3, 2002, at 12:39 AM, Ewan Birney wrote:
>
> > What about making a new repository - bioperl-retired which you can
> > check
> > out?
>
> You aren't kidding right? As long as it makes legacy code run -
> asking to check out and install another module shouldn't be too
> much. This is also something for the future as more thing may be
> retired over time.


I am not kidding ;) It gives the people f*ck'd systems and bad coding
practices some sort of lifeline but drastically cuts down on the confusion
inside of Bioperl. BLAST or BLAST and BPlite? I vote for just BLAST moving
into "retired".

>
> >
> >
> > Basically for people who have this legacy problem and therefore are not
> > moving forward, isn't the right advice "don't upgrade your Bioperl?".
> >
>
> Well, there may easily be legacy code *and* people who do want to
> move forward in the same place. Only no-one wants to touch that
> legacy code, yet it needs to run because no-one wants to re-write it
> either. I don't think this situation is that rare in industry (it
> may be rare in academia).
>

It is just a sign of so many other bad things that are going wrong that if
people are hoping that Bioperl will magically keep old stuff running *and*
allow them to move into new-exciting-stuff they are... well... wishing on
a star. I don't have that much sympathy for them.


For production systems with static code bases, the recommendation is -
don't upgrade if it works now!


For active development who wants to upgrade to 1.2, then ... yes, people
will need to revisit their BLAST parsers; should not be that hard to do
(yes, I do know that it is just a pain in the arse)


BTW - if people are interested, in Ensembl the route is to internalise
parts of Bioperl (eg, BPlite) when they work-for-us - move the name space
so there is no clash - and then we can work off the internalised version
with no worries and move forward onto newer versions of Bioperl (we hope).


> 	-hilmar
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
>