Hello Kevyin,

As you stated, the build directory was not being tracked in your 
fastq_groomer_parallel repository in the tool shed - running hg status on your 
repository produced this:

%hg status
? build/README
? build/fastq_groomer_parallel.py
? build/fastq_groomer_parallel.xml
? build/ipython/IPython/__init__.py
? build/ipython/IPython/config/__init__.py
? build/ipython/IPython/config/application.py
? build/ipython/IPython/config/configurable.py
...

Since it was not tracked, I just deleted the directory and it's contents from 
disk, so your repository contents now look like this.  I hope this is what you 
intended, but if not, let me know and I'll help with what's needed.

Contents:
fastq_groomer_parallel
README
fastq_groomer_parallel.py
fastq_groomer_parallel.xml

Thanks,

Greg Von Kuster


On Sep 18, 2012, at 7:44 PM, kevyin wrote:

> Hi Greg,
> Thanks for the toolshed links I'll make sure to go over them.
> 
> I think when the upload failed, mercurial didn't get to the point of tracking 
> the build folder. 
> From a mercurial point of view there seems to be no issue, pulling/cloning or 
> even installing is fine because it's not tracked.
> 
> But the folder seems to be there when I go to "Browse or delete repository 
> tip files" via the web interface.
> 
> From a user and our point of view this is isn't causing any usability issues 
> at the moment, though it is weird.
> 
> Hope this clarifies things and thanks for the help!
> Kevin.
> 
> On Wed, Sep 19, 2012 at 4:41 AM, Greg Von Kuster <g...@bx.psu.edu> wrote:
> Hello Kevin,
> 
> 
> On Sep 14, 2012, at 3:48 AM, kevyin wrote:
> 
>> Hi,
>> I have a tool on the main galaxy toolshed called fastq_groomer_parallel.
>> During an update, with a new tar.gz upload I accidentally included in an 
>> unrelated big folder of stuff under the folder build/
>> 
>> The upload failed (with no helpful error message, only to turn on debug mode)
>> I went and browsed the files via the web interface and the folder is there, 
>> but when I tried to delete it it says "No changes to repository. "
>> Everything is normal, ie I can install this from a galaxy instance and the 
>> build/ folder is not there.
>> when I hg pull and push etc the folder is not there. 
> 
> I'm not sure how you were seeing anything related to a large folder named 
> "build".  Looking at you change log, I see the following changeset revisions, 
> none of which include this folder.
> 
> Description: First upload 0.3.0
> Commit: 0:18a08d476d5e
> added: 
> README 
> fastq_groomer_parallel.py 
> fastq_groomer_parallel.xml
> 
> 
> Description: Deleted selected files
> Commit: 1:2f394cd7db91
> removed: 
> README 
> fastq_groomer_parallel.py 
> fastq_groomer_parallel.xml
> 
> 
> Description: Uploaded
> Commit: 2:cac848910bd8
> added: 
> README 
> fastq_groomer_parallel.py 
> fastq_groomer_parallel.xml
> 
> 
>> 
>> I have another question with versioning. So far with my experimentation on 
>> the testtoolshed, The version is only bumped when I upload via an archive 
>> not when I push to the repo.
>> Is this meant to be the case?
> 
> This is probably not the case.  A new change set is created every time you 
> make a change to the repository, either by uploading something new or by 
> deleting one or more files.  Whenever a new change set is produced, it is 
> associated with a revision number and string.  The following sections of the 
> tool shed wiki may provide more clarification.
> 
> http://wiki.g2.bx.psu.edu/Tool%20Shed#The_mercurial_repository_change_log
> http://wiki.g2.bx.psu.edu/Tool%20Shed#Repository_revisions:_uploading_a_new_version_of_an_existing_tool
> http://wiki.g2.bx.psu.edu/Tool%20Shed#Repository_revisions:_valid_tool_versions
> 
> 
> 
>> Also "Get Updates" to a toolshed tool as a galaxy Admin. doesnt seem to 
>> work, I basically have to install a new instance again, is this normal?
> 
> It depends - the following section of the tool shed wiki should clarify this:
> 
> http://wiki.g2.bx.psu.edu/Tool%20Shed#Getting_updates_for_tool_shed_repositories_installed_in_a_local_Galaxy_instance
> 
> Greg Von Kuster
> 
> 
>> 
>> Regards,
>> Kevin.
>> 
>> 
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