Where to find moved packages?

[Stikus]

Hello, I'm trying to move our VEP installation from bioperl 1.7.2 to latest 1.7.7. According to VEP test logs I'm missing Bio::Tools::dpAlign:

Error:  Can't locate Bio/Tools/dpAlign.pm in @INC

and it is correct due to this line in Changes:

1.7.3     2019-01-30 13:30:34+00:00 Europe/London

    * The following modules have been removed from the BioPerl
      distribution to be part of a separate distribution.  They have
      been integrated into other module distributions for independent
      development:

          Bio::Align::Graphics
          ...
          Bio::Tools::dpAlign
          ...
          Bio::Variation::*

Where can I find current version of this package? I tried to look at CPAN and github but I cannot find any.

[carandraug]

Looking into the git logs, I've found it was removed with 2ea25ecc4fe5c4d6ed11cf8ba25db62c20a24102 which has this message:

Move modules dependent on Bio::Ext::Align into defunct bioperl-ext

This modules are an interface to Bio::Ext::Align which is part of the
bioperl-ext repo and is now defunct (seems to not be indexed on CPAN
at all).  So move them there so they can all be defunct together.

Are you sure you are using Bio::Tools::dpAlign ? I checked its source again, and indeed it uses Bio::Ext::Align which is not on CPAN.

The repository with all this stuff is at https://github.com/bioperl/bioperl-ext

[Stikus]

As you can see in VEP README:

haplo can make use of a fast compiled alignment algorithm from the bioperl-ext package; this can speed up analysis, particularly in longer transcripts where insertions and/or deletions are introduced. The bioperl-ext package is no longer maintained and requires some tweaking to install.

So yes - package is needed. What you suggest? Use old bioperl build or try to manually install Bio::Tools::dpAlign? According to its code from here:

  use Bio::Tools::dpAlign;
  use Bio::SeqIO;
  use Bio::SimpleAlign;
  use Bio::AlignIO;
  use Bio::Matrix::IO;

Looks like I need all this packages too?

[carandraug]

So yes - package is needed. What you suggest? Use old bioperl build or try to manually install Bio::Tools::dpAlign?

Suppose Bio::Tools::dpAlign was still in core bioperl. To make use of it you'd still need to install bioperl-ext which has been unmaintained for at least 6 years. So I suggest you do whatever VEP suggests you to do to install bioperl-ext. Since bioperl-ext is not on CPAN, I would expect VEP to suggest you to install bioperl-ext from development sources ( https://github.com/bioperl/bioperl-ext ). If you do that, then you should also also get Bio::Tools::dpAlign.

According to its code from here:

 use Bio::Tools::dpAlign;
 use Bio::SeqIO;
 use Bio::SimpleAlign;
 use Bio::AlignIO;
 use Bio::Matrix::IO;

Looks like I need all this packages too?

Besides Bio::Tools::dpAlign, all others seem to still be in bioperl core.

[carandraug]

But to answer the question on this issue, which is "how to find where a module has been moved", I did git log --stat on the repository. The commit message that removed the module makes reference to the repository where the modules were moved to.

[Stikus]

Big thanks for answers, I'll try to get Bio::Tools::dpAlign from bioperl-ext installation. And thanks for git log --stat idea. Closing.