This bug has been fixed in galaxy-central but, as per one of the threads you 
found, has not made it to galaxy-dist yet.

Try this:
1. assuming you haven't made any changes to datatypes_conf.xml, copy 
datatypes_conf.xml.sample to datatypes_conf.xml
2. visit the custom builds page (User tab --> Custom Builds) and see if the 
Page loads properly; if it does, your custom build should work and everything 
should be fine.
3. this is a user-specific problem, so you can always create a new user and you 
should be good to go. If you want to continue to use the problematic account 
and the above doesn't work, you'll need to manually--via SQL--delete the user 
preferences for the problematic user.

Best,
J.

On Feb 13, 2012, at 10:30 AM, Joachim Jacob wrote:

> For completeness: this is a local galaxy instance running for few months now, 
> updated recently (27 Jan 'release').
>> Hello Joachim,
>>> After a quick try with visualising track in Trackster (importing one 
>>> chromosome of hg19 - which did not succeed BTW), none of the tools in my 
>>> local galaxy appear to work.
>> What are the steps you're taking to produce this issue?
>> 
> I had a BAM file that I wanted to test to view with Trackster. I clicked that 
> icon in the dataset . In the next screen: save in new visualation, which I 
> called test. And I selected there 'Add a custom build'. Next I could select 
> which fasta from my history containing the reference: selected the correct 
> one. I named it "hg19_chrom21". But then, clicking OK, gave an error.
> 
> From then on, all tools give the error: Error executing tool: 'hg19'. The 
> point is, I cannot recreate that BAM file, since the required tools are not 
> working anymore... Basically, my Galaxy has become useless. Before I dig up 
> my backup, I hope somebody can help me?
>>> They all send this error message:
>>> 
>>> Error executing tool: 'hg19'
>> Are you seeing this error in failed datasets? If not, where are you seeing 
>> this error?
> This error appears in the middle pane, after clicking execute.
> 
> 
>> 
>>> This bug has been reported before, but I was wondering if somebody suggest 
>>> a fix for this?
>> Can you provide a link to the thread/issue where this has been reported?
> http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg04216.html
> http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg03995.html
> 
>> Thanks,
>> J.
> Thank for looking into this.


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