[Bioperl-l] Re: Bioperl-l digest, Vol 1 #611 - 14 msgs
Gong Cheng
cheng_gong@yahoo.com
Thu, 7 Feb 2002 13:21:55 -0800 (PST)
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> Today's Topics:
>
> 1. help for installation bioperl Reahat linux
> (Yong Jiang)
> 2. Re: help for installation bioperl Reahat
> linux (Jason Stajich)
> 3. oracle and bioperl/ensembl (Tania Oh)
> 4. Flash Website Builder (Mark)
> 5. Substitution matrix format for Bio::Tools::pSW
> (Wise2) (Benjamin Berman)
> 6. Re: oracle and bioperl/ensembl (Lincoln Stein)
> 7. Re: Bio::Graphics (Lincoln Stein)
> 8. Re: oracle and bioperl/ensembl (Elia Stupka)
> 9. Re: Substitution matrix format for
> Bio::Tools::pSW
> (Wise2) (Ewan Birney)
> 10. RE: oracle and bioperl/ensembl (Fulton, Tim J)
> 11. [Fwd: [Biohackathon] Re: bibliography stuff in
> perl] (Heikki Lehvaslaiho)
> 12. (no subject) (Andrew Hynes)
> 13. ID line parsing in swiss.pm (Emmanuel Mongin)
>
> --__--__--
>
> Message: 1
> Date: Wed, 06 Feb 2002 10:11:26 -0800
> From: Yong Jiang <yjiang@ucsd.edu>
> Organization: UCSD
> To: bioperl-l@bioperl.org
> Subject: [Bioperl-l] help for installation bioperl
> Reahat linux
>
> Hello, I am trying to install the bioperl 0.7.2 in
> my linux system, it
> reminded me the there is no clustalw installed on my
> platform, actually
> the clustalw1.82 is in my computer and it works
> well. Also I got a
> message that no string is installed, the BIO::DB
> won't work. Can someone
> tell me how this happen and how to solve it?
> Thanks in advance.
> yong
>
>
> --__--__--
>
> Message: 2
> Date: Wed, 6 Feb 2002 14:09:17 -0500 (EST)
> From: Jason Stajich <jason@cgt.mc.duke.edu>
> To: Yong Jiang <yjiang@ucsd.edu>
> cc: <bioperl-l@bioperl.org>
> Subject: Re: [Bioperl-l] help for installation
> bioperl Reahat linux
>
> On Wed, 6 Feb 2002, Yong Jiang wrote:
>
> > Hello, I am trying to install the bioperl 0.7.2 in
> my linux system, it
> > reminded me the there is no clustalw installed on
> my platform, actually
> > the clustalw1.82 is in my computer and it works
> well. Also I got a
>
>
> See the documentation in
> Bio::Tools::Run::Alignment::Clustalw.
> You will need to set the env variable CLUSTALDIR to
> point to the dir
> where your clustalw is installed. I have fixed the
> logic for this in the
> later 0.9.3 release to be a little bit smarter if it
> can find the exe in
> your path but setting CLUSTALDIR env variable will
> get you what you need
> in 0.7.2.
>
> > message that no string is installed, the BIO::DB
> won't work. Can someone
> > tell me how this happen and how to solve it?
>
> You need to install the package IO::String from
> CPAN.
>
> > Thanks in advance.
> > yong
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
>
> --
> Jason Stajich
> Duke University
> jason@cgt.mc.duke.edu
>
>
> --__--__--
>
> Message: 3
> From: "Tania Oh" <taniaoh@yahoo.com>
> To: "Ensembl-Dev" <ensembl-dev@ebi.ac.uk>
> Cc: "Bioperl" <bioperl-l@bioperl.org>
> Date: Thu, 7 Feb 2002 09:14:36 +0800
> Subject: [Bioperl-l] oracle and bioperl/ensembl
>
>
> Hi all,
>
> the new group I'm in now is interested in using
> ensembl only if there is an
> oracle -> bioperl/ensembl DBAdaptor.
>
> I remember reading on the list sometime back that
> there was some development
> going on in providing an oracle port?
> is that development still going on or is there some
> other list I can get on
> for more information?
>
> any suggestions / comments about using
> bioperl/ensembl with an oracle DB is
> appreciated, esp. since it'll boost my argument
> about the advantages of
> using bioperl/ensembl for annotation!!!
>
> thanks in advance,
>
> Tania Oh
>
> Genomic Institute of Singapore
> http://www.genomeinstitute.org/
>
>
>
> --__--__--
>
> Message: 4
> Date: Wed, 6 Feb 2002 18:57:24 -0500
> From: Mark <maltman@onestepbeyond.com>
> To: bioperl-l@bioperl.org
> Subject: [Bioperl-l] Flash Website Builder
>
> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01
> Transitional//EN">
>
> <html>
> <head>
> <title>123Turnkey.com</title>
> </head>
>
> <body bgcolor="#ffffff" link="#006699" leftmargin=0
> topmargin=0>
> <table cellspacing="0" align="center"
> cellpadding="0" border="0" width="752">
> <tr>
> <td width="752">
> <table cellspacing="0" cellpadding="0" border="0">
> <tr>
> <td rowspan="2" valign="top"><A
> href="http://www.123turnkey.com/?cid=G1"
> target="_new"><IMG alt="" border=0
> src="http://www.123turnkey.com/images/logo.jpg"
> target"=_new"></A></td>
> <td><A href="http://www.123turnkey.com/?cid=G1"
> target="_new"><IMG alt="" border=0 name=tour
>
src="http://www.123turnkey.com/images/tour.gif"></A></td>
> <td><A href="http://www.123turnkey.com/?cid=G1"
> target="_new"><IMG alt="" border=0 name=start
>
src="http://www.123turnkey.com/images/start.gif"></A></td>
> <td><A href="http://www.123turnkey.com/?cid=G1"
> target="_new"><IMG alt="" border=0 name=questions
>
src="http://www.123turnkey.com/images/questions.gif"></A></td>
> <td><A href="http://www.123turnkey.com/?cid=G1"
> target="_new"><IMG alt="" border=0 name=members
>
src="http://www.123turnkey.com/images/members.gif"></A></td>
> </tr><tr>
> <td colspan="4" valign="top"><IMG alt="" border=0
>
src="http://www.123turnkey.com/images/topbanner2.gif"></td>
> </tr>
> <tr>
>
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