Join GitHub today
GitHub is home to over 28 million developers working together to host and review code, manage projects, and build software together.Sign up
bioperl-run LVB.pm and LVB.t require updates for LVB version 2.3 #24
Author Name: Daniel Barker (Daniel Barker)
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,
Original Redmine Comment
(In reply to comment #1)
Thank you for your rapid reply.
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:
The new version requires one less line:
For example, this would be valid stdin for LVB 2.2:
The corresponding stdin for LVB 2.3 would be: