New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

bioperl-run LVB.pm and LVB.t require updates for LVB version 2.3 #24

Open
cjfields opened this Issue Oct 8, 2015 · 2 comments

Comments

Projects
None yet
1 participant
@cjfields
Member

cjfields commented Oct 8, 2015


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


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

This comment has been minimized.

Show comment
Hide comment
@cjfields

cjfields Oct 8, 2015

Member

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


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

Member

cjfields commented Oct 8, 2015


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


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

@cjfields

This comment has been minimized.

Show comment
Hide comment
@cjfields

cjfields Oct 8, 2015

Member

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


(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

Member

cjfields commented Oct 8, 2015


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


(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

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment