[Bioperl-l] Can't find Bio::ext::Align on CPAN

[Warren Gallin]

I am trying to use the Bio::Tools::dpAlign module, but the run fails with a message:\

The C-compiled engine for Smith Waterman alignments (Bio::Ext::Align) has not been installed.
Please install the bioperl-ext package

I can not find this package.

Am I dealing with a no-longer-functional module, or am I missing a pathway to a resource?

All advice appreciated.

Warren Gallin

[Mark Jensen]

Warren - this is an old module and not currently maintained, but it should still work. You can find it at https://github.com/bioperl/bioperl-ext
There are some details on installation there. Your mileage may vary, but post to the list if you run into trouble.

Mark Jensen

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[Fields, Christopher J]

Correct, quite a few of the tools in that package have not been maintained.  We have discussed releasing some of these as separate packages in the past, but no one has taken this up.

 

chris

 

From: Bioperl-l <bioperl-...@bioperl.org> on behalf of Mark Jensen <m...@fortinbras.us>
Date: Thursday, March 11, 2021 at 9:39 PM
To: Warren Gallin <wga...@ualberta.ca>
Cc: BioPerl List <Biop...@lists.open-bio.org>
Subject: Re: [Bioperl-l] Can't find Bio::ext::Align on CPAN

Warren - this is an old module and not currently maintained, but it should still work. You can find it at https://urldefense.com/v3/__https://github.com/bioperl/bioperl-ext__;!!DZ3fjg!uSvOF9SuI7pDulK8EWVNYLGvFzexZNOGo8D4-QUVZXWuLtXUoAXqcFQPD2qZMRBq8sA$

There are some details on installation there. Your mileage may vary, but post to the list if you run into trouble.

Mark Jensen

> On Mar 11, 2021, at 5:43 PM, Warren Gallin <wga...@ualberta.ca> wrote:
>
> I am trying to use the Bio::Tools::dpAlign module, but the run fails with a message:\
>
> The C-compiled engine for Smith Waterman alignments (Bio::Ext::Align) has not been installed.
> Please install the bioperl-ext package
>
> I can not find this package.
>
> Am I dealing with a no-longer-functional module, or am I missing a pathway to a resource?
>
> All advice appreciated.
>
> Warren Gallin_______________________________________________
> Bioperl-l mailing list
> Biop...@bioperl.org

> https://urldefense.com/v3/__https://mailman.open-bio.org/mailman/listinfo/bioperl-l__;!!DZ3fjg!uSvOF9SuI7pDulK8EWVNYLGvFzexZNOGo8D4-QUVZXWuLtXUoAXqcFQPD2qZmrVcpvI$

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