svn commit: r370220 - in head/biology: . ncbi-blast

[John Marino]

On 12/28/2014 18:22, Dag-Erling Smørgrav wrote:
> John Marino <marino at FreeBSD.org> writes:
>> Log:
>>   Add new port biology/ncbi-blast
>>   
>>   PR:		190854
>>   Submitted by:	Jason Bacon
>>   
>>   The Basic Local Alignment Search Tool (BLAST) finds regions of local
>>   similarity between sequences. The program compares nucleotide or protein
>>   sequences to sequence databases and calculates the statistical
>>   significance of matches. BLAST can be used to infer functional and
>>   evolutionary relationships between sequences as well as help identify
>>   members of gene families.
> 
> I wish I had caught this in time.
> 
> This is wrong.  The port you committed installs BLAST+, not BLAST.
> These are two significantly different programs which implement the same
> algorithm.  While the former is intended as a successor to the latter,
> they are not interchangeable.  Many applications which use BLAST have
> not yet been, and may never be, ported to BLAST+, and this port stands
> in the way of a BLAST port.
> 
> Since the authors, in their infinite stup^H^H^H^Hwisdom, decided to
> start numbering BLAST+ versions where BLAST left off, there is no way to
> fix this without either a) bumping PORTEPOCH or b) naming the BLAST port
> blast-legacy or something similar, while renaming this one to blast+ or
> blast-plus.

It's a brand new port with a unique name.  Why is "bumping PORTEPOCH"
considered necessary?  Why is the existence of this port blocking the
introduction of a new BLAST port?  AFAIK, this port was not claiming to
be a drop-in replacement for the blast port that was removed; no
dependencies of other ports changed to this port.

It seems that all that is needs is to update the pkg-descr file to
specify it's the blast+ implementation.

John