[Bioperl-l] StandAloneBlast troubles
Jason Stajich
jason@chg.mc.duke.edu
Thu, 23 Aug 2001 14:56:33 -0400
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RE: [Bioperl-l] StandAloneBlast troublesI assume it is similar to UNIX =
style, I believe you can see examples in your autoexec.bat. Something =
like
set VARNAME=3DVALUE
=20
An alternative way to set the env variable is was explained =
before,adding the following to your script will set the env variable for =
the life of your script.
BEGIN {
$ENV{'VARIABLENAME'} =3D 'a value';
}
It was reported that way paths are constructed to the executable in this =
module are too UNIX centric to work on Windows so a windows user will =
have to debug this and report back. We need someone to use the =
File::Spec->catdir method instead of what is hardcoded.
There should be a bug reported submitted by someone close to the problem =
so a developer can be assigned to it.
-jason
----- Original Message -----=20
From: Ngo, Viet=20
To: Jason Stajich=20
Sent: Thursday, August 23, 2001 11:46 AM
Subject: RE: [Bioperl-l] StandAloneBlast troubles
How do you set said environmental variable???=20
-----Original Message-----=20
From: Jason Stajich [mailto:jason@chg.mc.duke.edu]=20
Sent: Tuesday, August 21, 2001 6:16 PM=20
To: Ngo, Viet=20
Cc: bioperl-l@bioperl.org=20
Subject: Re: [Bioperl-l] StandAloneBlast troubles=20
Have you set the environment variable BLASTDIR to point to the =
directory=20
where blastall executable is located? This should be in the =
documentation=20
but we probably need to do a better job making it more prominent.=20
--Volunteers to help improve POD and install documentation are =
welcomed!--=20
You can also add the following to your code which should work:=20
BEGIN {=20
$ENV{'BLASTDIR'} =3D 'C:\path\to\blast';=20
}=20
-jason=20
On Tue, 21 Aug 2001, Ngo, Viet wrote:=20
> I can't seem to get this module installed correctly -- it keeps =
saying BLAST=20
> isn't installed on my system, even though it is. I'm running =
ActivePerl=20
> 5.6.1 and BioPerl 0.7.1 on a Windows NT 4.0 machine.=20
>=20
> Viet Ngo=20
>=20
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<DIV><FONT face=3DArial size=3D2>I assume it is similar to UNIX =
style, I=20
believe you can see examples in your autoexec.bat. Something=20
like</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>set VARNAME=3DVALUE</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=3DArial size=3D2>An alternative way to set the env =
variable is was=20
</FONT><FONT face=3DArial size=3D2>explained before,adding the following =
to your=20
script will set the env variable for the life of your =
script.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>BEGIN {</FONT></DIV>
<DIV><FONT face=3DArial size=3D2> $ENV{'VARIABLENAME'} =3D 'a=20
value';</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>}</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>It was reported that way paths are =
constructed to=20
the executable in this module are too UNIX centric to work on Windows so =
a=20
windows user will have to debug this and report back. We need =
someone to=20
use the File::Spec->catdir method instead of what is =
hardcoded.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>There should be a bug reported =
submitted by someone=20
close to the problem so a developer can be assigned to it.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>-jason</FONT></DIV>
<DIV>----- Original Message ----- </DIV>
<BLOCKQUOTE=20
style=3D"PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; =
BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
<DIV=20
style=3D"BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: =
black"><B>From:</B>=20
<A title=3DVNgo@coh.org href=3D"mailto:VNgo@coh.org">Ngo, Viet</A> =
</DIV>
<DIV style=3D"FONT: 10pt arial"><B>To:</B> <A =
title=3Djason@chg.mc.duke.edu=20
href=3D"mailto:jason@chg.mc.duke.edu">Jason Stajich</A> </DIV>
<DIV style=3D"FONT: 10pt arial"><B>Sent:</B> Thursday, August 23, 2001 =
11:46=20
AM</DIV>
<DIV style=3D"FONT: 10pt arial"><B>Subject:</B> RE: [Bioperl-l] =
StandAloneBlast=20
troubles</DIV>
<DIV><BR></DIV>
<P><FONT size=3D2>How do you set said environmental variable???</FONT> =
</P>
<P><FONT size=3D2>-----Original Message-----</FONT> <BR><FONT =
size=3D2>From: Jason=20
Stajich [<A=20
=
href=3D"mailto:jason@chg.mc.duke.edu">mailto:jason@chg.mc.duke.edu</A>]</=
FONT>=20
<BR><FONT size=3D2>Sent: Tuesday, August 21, 2001 6:16 PM</FONT> =
<BR><FONT=20
size=3D2>To: Ngo, Viet</FONT> <BR><FONT size=3D2>Cc: <A=20
href=3D"mailto:bioperl-l@bioperl.org">bioperl-l@bioperl.org</A></FONT> =
<BR><FONT=20
size=3D2>Subject: Re: [Bioperl-l] StandAloneBlast troubles</FONT> =
</P><BR>
<P><FONT size=3D2>Have you set the environment variable BLASTDIR to =
point to the=20
directory</FONT> <BR><FONT size=3D2>where blastall executable is =
located? =20
This should be in the documentation</FONT> <BR><FONT size=3D2>but we =
probably=20
need to do a better job making it more prominent.</FONT> </P>
<P><FONT size=3D2>--Volunteers to help improve POD and install =
documentation are=20
welcomed!--</FONT> </P><BR>
<P><FONT size=3D2>You can also add the following to your code which =
should=20
work:</FONT> </P>
<P><FONT size=3D2>BEGIN {</FONT> <BR><FONT size=3D2> =
$ENV{'BLASTDIR'} =3D=20
'C:\path\to\blast';</FONT> <BR><FONT size=3D2>}</FONT> </P>
<P><FONT size=3D2>-jason</FONT> <BR><FONT size=3D2>On Tue, 21 Aug =
2001, Ngo, Viet=20
wrote:</FONT> </P>
<P><FONT size=3D2>> I can't seem to get this module installed =
correctly -- it=20
keeps saying BLAST</FONT> <BR><FONT size=3D2>> isn't installed on =
my system,=20
even though it is. I'm running ActivePerl</FONT> <BR><FONT =
size=3D2>> 5.6.1=20
and BioPerl 0.7.1 on a Windows NT 4.0 machine.</FONT> <BR><FONT =
size=3D2>>=20
</FONT><BR><FONT size=3D2>> Viet Ngo</FONT> <BR><FONT size=3D2>> =
</FONT></P><BR><BR></BLOCKQUOTE></BODY></HTML>
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