Hey Peter, Hopefully Nate will have some wisdom, all I have is a workaround (I have fought with this on multiple forks and this is the best I have come up with).
Check out a clean version of the tools branch somehow (it seems like the working contents can get stuck in an invalid state that update and checkout cannot recover from). Once you are back to a good state, it works when you merge in two steps. hg checkout tools hg merge -r ee389d2 hg ci -m "Partial merge." # Not sure if this step is needed. hg merge default -John On Thu, Apr 11, 2013 at 10:47 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > (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 > (nothing) > > 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 > 'static/june_2007_style' > > 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: > /mnt/galaxy/galaxy-central/static/style/blue/base.css > > Advice from an hg guru would be appreciated. > > Thanks, > > Peter > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
