(Apologies if this comes twice - it seems I didn't press send when I wrote
the draft earlier in the week)

On Tue, Feb 19, 2013 at 5:38 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Tue, Feb 19, 2013 at 5:26 PM, Nate Coraor <n...@bx.psu.edu> wrote:
>> On Feb 19, 2013, at 12:18 PM, Peter Cock wrote:
>> Nate wrote:
>>>> Hi Peter,
>>>> This is due to the annoying way in which Mercurial handles symlinks.  We're
>>>> going to graft the changesets that caused this up to stable shortly, but 
>>>> in the
>>>> meantime, you can do:
>>>> % rm static/june_2007_style
>>>> % hg update stable --clean
>>>> This would remove any uncommitted local changes, if you had any, so it's
>>>> not safe for all scenarios.  But it's fine here since you're working on a 
>>>> fresh
>>>> clone with no changes.
>>> Cheers Nate, that trick seems to work.
>>> I'm guessing this recent commit (11 days ago) is part of the issue:
>>> https://bitbucket.org/galaxy/galaxy-central/commits/506484344db3a370f8ae24096041d38557d1967e
>> Indeed, that, and the previous commit.
>>> I hope this won't require any 'grafting' for those of us working from the
>>> default branch? Will I be safe merging the 'default' into my own branch,
>>> or should I wait while you guys sort out whatever you need to do first?
>> It shouldn't require you to do anything.  The only complications that
>> should arise will be if you have changes to files under 
>> static/june_2007_style/
> I've not touched that, so that's all good news - thank you :)
> Peter

It seems I've not updated my 'tools' development branch with the
'default' branch changes since this sym link issue.

So I've switched to the default branch, done a pull, and this is
now all up to date.

$ hg checkout default --clean
0 files updated, 0 files merged, 0 files removed, 0 files unresolved

$ hg update --clean
0 files updated, 0 files merged, 0 files removed, 0 files unresolved

$ hg tip
changeset:   10037:ce3143a06f21
tag:         tip
user:        jeremy goecks <jeremy.goe...@emory.edu>
date:        Fri Apr 05 09:39:05 2013 -0400
summary:     Implement a reference-based compression approach for
encoding aligned reads' sequence and cigar. Move cigar functions into
own file.

$ hg diff

At this point I would normally do: hg checkout tools,  hg merge default

$ hg checkout tools
abort: path 'static/june_2007_style/Makefile' traverses symbolic link

So, trying the trick from before:

$ rm static/june_2007_style
$ hg checkout tools
abort: crosses branches (merge branches or use --clean to discard changes)
$ hg checkout tools --clean
769 files updated, 0 files merged, 413 files removed, 0 files unresolved

And now, the stumbling block:

$ hg merge default
merging datatypes_conf.xml.sample
merging lib/galaxy/datatypes/registry.py
merging lib/galaxy/jobs/__init__.py
merging run.sh
merging static/june_2007_style/blue/base.css and
static/style/blue/base.css to static/style/blue/base.css
merging tool_conf.xml.sample
merging tools/filters/cutWrapper.pl
abort: No such file or directory:

Advice from an hg guru would be appreciated.


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