[Bioperl-l] Lagan environment variable

Sendu Bala bix at sendu.me.uk
Wed Oct 25 12:12:00 UTC 2006

Nathan S. Haigh wrote:
> Sendu Bala wrote:
>> Notification to say I'm changing the environmental variable that 
>> Bio::Tools::Run::Alignment::Lagan expects to define the location of the 
>> lagan executables from LAGANDIR to LAGAN_DIR, since the latter is the 
>> default variable that the lagan installation and scripts themselves look 
>> for.
>> I hope this isn't too much of a burden, but it seems like the sensible 
>> approach to getting Bio::Tools::Run::Alignment::Lagan to actually work.
> Woudn't it make more sense to change the test? That is what I've just
> done for t/Genscan.t

For Genscan.t, the test script looked at the wrong environment variable.

Here I'm talking about lagan itself (the thing you get from 
http://lagan.stanford.edu/lagan_web/citing.shtml, nothing to do with 
Bioperl) needing the environment variable LAGAN_DIR to be set in order 
to work.

Since you need to set LAGAN_DIR to make lagan work, it makes sense that 
the Bioperl front-end to lagan also use the same variable.

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