Hi Paul,

The use of mercurial eggs for all tool shed mercurial related actions is now 
available in our central repository in change set 7102:c8f4f73e9199.  This will 
be available in the dist repository with the next release, which I believe will 
be coming soon.  If you're tracking the central repository, updating will 
hopefully solve the problems you were seeing.


Greg Von Kuster

On Apr 20, 2012, at 7:39 AM, Paul-Michael Agapow wrote:

> Thanks Greg,
> It's a puzzling one alright. Looking forward to testing the new version, if 
> only because I've run out of ideas on where to look.
> Cheers
> p
> ----
> Paul Agapow (paul-michael.aga...@hpa.org.uk)
> Bioinformatics, Health Protection Agency
> -----Original Message-----
> From: Greg Von Kuster [mailto:g...@bx.psu.edu] 
> Sent: 19 April 2012 22:47
> To: Paul-Michael Agapow
> Cc: 'galaxy-dev@lists.bx.psu.edu'
> Subject: Re: [galaxy-dev] Toolshed initial upload errors
> Paul,
> Sorry to see you're still experiencing problems.  Based on the issues you've 
> encountered (as well as one or two others recently) I've spent some time 
> re-working things to eliminate the need for installing mercurial to use a 
> local tool shed.  We will build eggs for the mercurial package for the 
> various versions of Python supported by Galaxy and include them in the 
> distribution.  
> I'm pretty close to having this finished, so it is likely that this will be 
> available early next week.  
> I'm not sure if this will fix the problems you're seeing, but at least it 
> will eliminate one of the variables.
> Greg Von Kuster
> On Apr 19, 2012, at 5:02 AM, Paul-Michael Agapow wrote:
>> [For those who came in late - I've installed a local toolshed, which allows 
>> me to create repositories, but every time  I attempt to upload files, it 
>> errors out with "TypeError: array item must be char". For those who come 
>> after me, here's what I worked out thus far.]
>> Greg asked:
>>> Since you've tried uploading various files with no success, the problem is 
>>> likely
>>> to be caused by something specific to your environment - possibly the 
>>> version of
>>> the mercurial package you're using.  What version of Python are you 
>>> running, and
>>> what version of the mercurial package do you have installed with it?  Also, 
>>> what
>>> version of Galaxy do you have, and what database / version are you using?
>> We're CentOS, an older flavour (4), but my Mercurial is up to data (2.1.2). 
>> Python 2.6.4, Galaxy is 6799:40f1816d6857 (grabbed it fresh last week for 
>> testing), running it with sqlite. However, the Mercurial is actually 
>> installed local to the account I'm using, so I wonder if the toolshed is 
>> getting confused with another version, although hg doesn't seem to be 
>> installed on the system.
>> Further investigations reveal that the files appear to be in the repo 
>> (database/community_files). The error manifest in the middle of Mercurial, 
>> in manifest.py where it attempts to coerce a Unicode string into a character 
>> array. (As there are some reported issues of Windows file names with Unicode 
>> under Mercurial, and I'm uploading from a Windows machine, I used a Mac to 
>> create a repo and add a file. Nope, same behaviour.) The Cistrome galaxy 
>> fork 
>> (https://bitbucket.org/cistrome/cistrome-harvard/src/e7e2fdd74496/lib/galaxy/webapps/community/controllers/upload.py)
>>  mentions occasional similar errors.
>> I check the Mercurial installation:
>> % hg --version
>> Mercurial Distributed SCM (version 2.1.2+10-4d875bb546dc)
>> ...
>> % hg debuginstall
>> Checking encoding (UTF-8)...
>> Checking installed modules 
>> (/home/f0/paul/Installed/lib/python2.6/site-packages/mercurial)...
>> Checking templates 
>> (/home/f0/paul/Installed/lib/python2.6/site-packages/mercurial/templates)...
>> Checking commit editor...
>> Checking username...
>> No problems detected
>> (Actually, I was missing a username and a user ~/.hgrc file. But making 
>> that, it passes. Error still persists.)
>> Work continues.
>> ----
>> Paul Agapow (paul-michael.aga...@hpa.org.uk)
>> Bioinformatics, Health Protection Agency
>> -----------------------------------------
>> **************************************************************************
>> The information contained in the EMail and any attachments is
>> confidential and intended solely and for the attention and use of
>> the named addressee(s). It may not be disclosed to any other person
>> without the express authority of the HPA, or the intended
>> recipient, or both. If you are not the intended recipient, you must
>> not disclose, copy, distribute or retain this message or any part
>> of it. This footnote also confirms that this EMail has been swept
>> for computer viruses, but please re-sweep any attachments before
>> opening or saving. HTTP://www.HPA.org.uk
>> **************************************************************************
>> ___________________________________________________________
>> 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/

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:


Reply via email to