bioperl-run LVB.pm and LVB.t require updates for LVB version 2.3

[cjfields]

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Author Name: Daniel Barker (Daniel Barker)
Original Redmine Issue: 3125, https://redmine.open-bio.org/issues/3125
Original Date: 2010-07-28
Original Assignee: Bioperl Guts

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The user interface to LVB has changed. From LVB 2.3, the user is no longer asked whether the analysis should be ‘fast’ or ‘slow’.

This change is not yet reflected in “lib/Bio/Tools/Run/Phylo/LVB.pm”. The DURATION parameter (and its action) should be removed. “t/LVB.t” will also require minor change.

Would someone like to make these changes? I just tried to update things myself, from trunk (“svn checkout http://svn.github.com/bioperl/bioperl-run.git”). However, even the previous version (LVB 2.2) fails tests, before I’ve modified anything. Last time I looked - some years ago - LVB 2.2 passed all its tests. Probably I’m doing something wrong.

Thank you very much,

Daniel

[cjfields]

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Original Redmine Comment
Author Name: Chris Fields
Original Date: 2010-07-30T00:31:18Z

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Not sure when we can get to this; all depends on how difficult it will be to update it.

[cjfields]

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Original Redmine Comment
Author Name: Daniel Barker
Original Date: 2010-07-30T12:16:56Z

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(In reply to comment #1)

Dear Chris,

Thank you for your rapid reply.

Not sure when we can get to this; all depends on how difficult it will be to
update it.

If someone were able to get the tests passing for LVB 2.2 again (or I am doing something wrong that makes them fail?), I could adapt them to LVB 2.3. Alternatively: would you be able to remove LVB.pm and LVB.t from BioPerl?

The old version of LVB required stdin as follows:

i|s
u|f
integer 0 to 900000000 | blank line
f|s
integer 1 to 1000000 | blank line

The new version requires one less line:

i|s
u|f
integer 0 to 0 to 900000000 or blank line
integer 1 to 1000000 or blank line

For example, this would be valid stdin for LVB 2.2:

=begin quote=
i
u

s

=end quote=

The corresponding stdin for LVB 2.3 would be:

=begin quote=
i
u

=end quote=

Best wishes,

Daniel