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. Thanks! 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.agapow@hpa.org.uk) Bioinformatics, Health Protection Agency
-----Original Message----- From: Greg Von Kuster [mailto:greg@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/...) 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.agapow@hpa.org.uk) Bioinformatics, Health Protection Agency
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