[Bioperl-l] Lagan environment variable

Nathan S. Haigh n.haigh at sheffield.ac.uk
Wed Oct 25 09:16:16 EDT 2006


Sendu Bala wrote:
> 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.
>
Ah, OK! :-[  teach me for speak up about something I know nothing about!
:-)

FYI, I've been busy this morning installing as much Bioperl-run external
software as I could (those that have tests). Will be posting results shorty.

Nath



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