[Bioperl-l] Re: [Bioperl-guts-l] Notification: incoming/959

[Peter Schattner]

For what it's worth, the bioperl tutorial (bptutorial.pl) has the following
installation instructions:

"For the external programs (clustal, Tcoffee, ncbi-blast), there is an
extra step:

Set the relevant environmental variable (CLUSTALDIR, TCOFFEEDIR or
BLASTDIR) to the directory holding the executable in your startup
file - eg in .bashrc. (For running local blasts, it is also
necessary that the name of local-blast database directory is known
to bioperl.  This will typically happen automatically, but in case
of difficulty, refer to the documentation for StandAloneBlast.pm)"


If someone suggests wording to make these instructions clearer, I will
gladly edit the install instructions in the tutorial.

- peter

Jason Stajich wrote:

> Would love for that to happen.  Volunteers?  If someone wants to start a
> wiki document with install directions that would be great too.
>
> > Could this be added to the install documentation?  I always forget what
> > these are and then have to do perldoc <module> and scan for the
> > directions for each of them when make test fails.
> > Just wondering, it's not critical.
> >
> > joel
> >
> > On Tue, 15 May 2001, Jason Stajich wrote:
> >
> > > You need to have the following enviroment variable defined
> > > CLUSTALDIR=path to dir containing clustal
> > > TCOFFEEDIR=path to dir containing tcoffee
> > > BLASTDIR=path to dir containing blastall,bl2seq, etc
> > > BLASTDATADIR=path to dir containing blastable dbs
> >
> >