[Bioperl-l] issue with closing tempfile and bl2seq

[BHurwitz at twt.com]

Hi Ewan,

Thanks so much for the response.  I updated bioperl to 1.2 and
unpacked/installed bioperl-run from the bioperl CVS, but it looks like I am
still missing the WrapperBase.pm module.  Do you know where I can get this?
Is there something I missed?

krispy[~/check_footprint] 10 $ ./footprint_checker.pl -i
40K_TARG_SEQS_FOR_FOOTPRINT_REP -o test
Can't locate Bio/Tools/Run/WrapperBase.pm in @INC (@INC contains:
/home/bhurwitz/perllib /usr/lib/perl5/5.6.1/i386-linux /usr/lib/perl5/5.6.1
/usr/lib/perl5/site_perl/5.6.1/i386-linux /usr/lib/perl5/site_perl/5.6.1
/usr/lib/perl5/site_perl/5.6.0 /usr/lib/perl5/site_perl
/usr/lib/perl5/vendor_perl/5.6.1/i386-linux
/usr/lib/perl5/vendor_perl/5.6.1 /usr/lib/perl5/vendor_perl .) at
/usr/lib/perl5/site_perl/5.6.1/Bio/Tools/Run/StandAloneBlast.pm line 243.
BEGIN failed--compilation aborted at
/usr/lib/perl5/site_perl/5.6.1/Bio/Tools/Run/StandAloneBlast.pm line 243.


-Bonnie




|---------+--------------------------->
|         |           Ewan Birney     |
|         |           <birney at ebi.ac.u|
|         |           k>              |
|         |                           |
|         |           03/05/2003 11:11|
|         |           AM              |
|         |                           |
|---------+--------------------------->
  >-------------------------------------------------------------------------------------------------------------------------------|
  |                                                                                                                               |
  |        To:      BHurwitz at twt.com                                                                                              |
  |        cc:      bioperl-l at bioperl.org                                                                                         |
  |        Subject: Re: [Bioperl-l] issue with closing tempfile and bl2seq                                                        |
  >-------------------------------------------------------------------------------------------------------------------------------|





This is a fix in 1.2 but there is a nasty gotcha which is you also need
WrapperBase to run StandAloneBlast which is in bioperl-run. This
dependency graph is going to be fixed in 1.2.1 and we are also waiting for
the ontology fixes to be done... so... some way off....




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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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