[Bioperl-l] error during installation

Fields, Christopher J cjfields at illinois.edu
Tue Jun 19 10:14:09 EDT 2012

This seems specifically like a clustalw problem (the error code is a giveaway).  What version of clustalw is this?  It should run with more recent versions.  

Re: dpalign, is there something that module specifically does that other tools can't provide?   If it proves useful I would rather move it and all related tools into it's own distribution for separate release (so any bugs can be fixed more readily w/o relying on core changes).


On Jun 17, 2012, at 6:16 AM, Du, Peng wrote:

> Sorry for that, actually I am using it, but I forgot to paste the code
> in which I invoked "pairwise_alignment" with dpAlign.
> At the same time, I met another problem regarding "ClustalW". The
> error message was"MSG ClustalW call align crashed -1". It might be
> because of incorrect installation of BioPerl-run. But, I didn't
> encounter any error message while installing it.
> Thank all of you.
> Peng
> On Sun, Jun 17, 2012 at 8:01 PM, Leon Timmermans
> <l.m.timmermans at students.uu.nl> wrote:
>> On Sun, Jun 17, 2012 at 7:37 AM, Du, Peng <du at ibio.jp> wrote:
>>> At present, I want to use dpAlign, I don't know I still need bio-ext
>>> to perform dpAlign or I could modify my code to achieve this without
>>> bio-ext package.
>>> Thank you.
>> Bio::Tools::dpAlign is in the main BioPerl distribution, as can be
>> seen here: https://metacpan.org/module/Bio::Tools::dpAlign. You will
>> need to take out that «use Bio::Ext::Align;», but you don't seem to be
>> using it anyway.
>> Leon
> -- 
> Peng Du
> Graduate School of Information Science and Technology, Hokkaido University
> Kita 14 Nishi 9 Kita-ku, Sapporo, Japan  060-0814
> Email: du at ibio.jp Tel: +81 80 3268 9713

More information about the Bioperl-l mailing list