Ok, so that confirms that you definitely have local customizations we'll want to make sure to keep. What I'd do before we go any further is this: `hg diff -p > local_changes.patch` This will save all of your current changes to a patch, should we have to recreate them (though I don't expect this). `hg ci -m "Local changes to cleanup_datasets and various tools"` Which will commit your local changes to your local repository. At this point, hopefully, you can just 'hg update', possibly needing to merge as well. For IRC: Just join the "Freenode" network shown in XChat, and then Join Channel should pop up a box you can put #galaxyproject in On Jan 29, 2013, at 1:52 PM, "Waldron, Michael H" <mwaldron@email.unc.edu> wrote:
Here is hg st output:
$ hg st M scripts/cleanup_datasets/delete_datasets.sh M scripts/cleanup_datasets/delete_datasets_main.sh M scripts/cleanup_datasets/delete_userless_histories.sh M scripts/cleanup_datasets/delete_userless_histories_main.sh M scripts/cleanup_datasets/purge_datasets.sh M scripts/cleanup_datasets/purge_datasets_main.sh M scripts/cleanup_datasets/purge_folders.sh M scripts/cleanup_datasets/purge_folders_main.sh M scripts/cleanup_datasets/purge_histories.sh M scripts/cleanup_datasets/purge_histories_main.sh M scripts/cleanup_datasets/purge_libraries.sh M scripts/cleanup_datasets/purge_libraries_main.sh M scripts/cleanup_datasets/update_metadata.sh M tools/peak_calling/macs_wrapper.xml M tools/plotting/boxplot.xml M tools/sr_mapping/bfast_wrapper.xml M tools/sr_mapping/bowtie2_wrapper.xml M tools/sr_mapping/bowtie_color_wrapper.xml M tools/sr_mapping/bowtie_wrapper.xml M tools/sr_mapping/bwa_color_wrapper.xml M tools/sr_mapping/bwa_wrapper.xml ? contrib/galaxy-init ? galaxy_cleanup.log ? galaxy_cleanup.sh ? migrated_tools_conf.xml.110712 ? paster.pid ? scripts/cleanup_datasets/delete_userless_histories.log ? scripts/cleanup_datasets/purge_datasets.log ? scripts/cleanup_datasets/purge_folders.log ? scripts/cleanup_datasets/purge_histories.log ? scripts/cleanup_datasets/purge_libraries.log ? static/UNC_galaxy_mirror_housekeeping_notes.pdf ? tool-data/bwa_index.loc.sample ? tool-data/bwa_index_color.loc.sample ? tool-data/tool_data_table_conf.xml.sample ? tool_conf.xml.110212 ? tool_conf.xml.new ? tool_data_table_conf.xml.030112 ? tools/plotting/boxplot.xml.012512 ? typescript
The hg diff output is quite long.
It turns out I didn't connect to the IRC channel. I have XChat IRC client, but not familiar with using it. How to I connect to the irc.freenode.net server to access the #galaxyproject channel?
Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill
________________________________________ From: Dannon Baker [dannonbaker@me.com] Sent: Tuesday, January 29, 2013 1:48 PM To: Waldron, Michael H Cc: Paul Boddie; James Taylor; Greg Von Kuster; galaxy-dev@bx.psu.edu Dev Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository
I don't know why I thought we'd already checked this, but --
'hg st' will tell you which files have been modified in your local repository, and 'hg diff' will tell you exactly what changes have taken place
I'm not sure of the exact state of your repository at the moment, so this *might* display all changes from the pull as well, which wouldn't be particularly useful. Worth trying, though.
Don't see you in #galaxyproject yet, sure it's working?
On Jan 29, 2013, at 1:42 PM, "Waldron, Michael H" <mwaldron@email.unc.edu> wrote:
The hg update --check command reports the following:
$ hg update --check abort: uncommitted local changes
I just connected to the #galaxyproject IRC channel.
Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill
________________________________________ From: Dannon Baker [dannonbaker@me.com] Sent: Tuesday, January 29, 2013 1:37 PM To: Waldron, Michael H Cc: Paul Boddie; James Taylor; Greg Von Kuster; galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository
So that's interesting. My best guess was that this was caused by swapping from galaxy-dist to galaxy-central in the situation where galaxy-dist has had changesets applied directly and then ported to galaxy-central out of order, combined with your oder version of mercurial. That parent, however, would have been before that happened.
Anyway, at this point, does `hg update --check` actually work?
And, lastly, If you want -- hop on IRC (irc.freenode.net #galaxyproject, http://wiki.galaxyproject.org/Get%20Involved#IRC_Channel) and it might be faster to iterate through what we need to do to get your repository back in shape.
On Jan 29, 2013, at 1:32 PM, "Waldron, Michael H" <mwaldron@email.unc.edu> wrote:
Forgot to also include the hg parents output.
$ hg parents changeset: 7986:12fcd068b12e user: Daniel Blankenberg <dan@bx.psu.edu> date: Thu Oct 18 11:22:12 2012 -0400 summary: Do not hide failed datasets with HideDatasetAction post job action.
Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill
________________________________________ From: Waldron, Michael H Sent: Tuesday, January 29, 2013 1:28 PM To: Paul Boddie; James Taylor Cc: Greg Von Kuster; galaxy-dev@bx.psu.edu Subject: RE: [galaxy-dev] Error trying to add tools from tool shed respository
As it turns out, it was fairly simple to install a newer hg version (2.4.2).
So now running hg merger --preview and hg heads returns:
$ hg merge --preview abort: branch 'default' has one head - please merge with an explicit rev (run 'hg heads' to see all heads) [galaxy@galaxy galaxy-dist]$ hg heads changeset: 8677:22788c1262a2 tag: tip user: jeremy goecks <jeremy.goecks@emory.edu> date: Mon Jan 28 16:36:02 2013 -0500 summary: Language improvements for tophat wrappers.
Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill
________________________________________ From: Paul Boddie [paul.boddie@biotek.uio.no] Sent: Tuesday, January 29, 2013 12:01 PM To: James Taylor Cc: Waldron, Michael H; Greg Von Kuster; galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository
On 29/01/13 17:33, James Taylor wrote:
Wasn't sure of the order, those are definitely after running the update. Dannon's advice makes a good point, upgrading to the latest mercurial should help.
If upgrading Mercurial will involve introducing another detour, you could potentially check which version of the Galaxy code you're using now as defined by the "parent" revisions:
hg parents
This (or these in certain cases) might not be a repository "head" and thus won't appear in "hg heads". If you have the graphlog extension enabled, running the following might be informative as it should show you where you are (with a "@" symbol) in the code history:
hg glog | more
If you don't want to risk your working directory, you could first clone it to make something that you can then experiment with:
hg clone . ../galaxy-dist-test
Then, you'd move into this clone:
cd ../galaxy-dist-test
You might need to update to the version previously printed by "hg parents" above:
hg update <revision>
One might then assume that any desirable update would involve getting to the "tip", and so you could try a merge with that:
hg merge tip
If all of this works reasonably, you should be able to do the same merge on your real working directory (and can thus delete the test directory). The result of any merge will need to be committed:
hg commit
Anyway, these are just some thoughts. The crucial point is that you can clone the repository and then work with the clone, discarding it if your experiments go wrong. Doing this might be quicker than having to get a more recent Mercurial version installed.
Paul
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