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
----------------------------------------- ************************************************************************** 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: