First, thanks. I just created a new user, and I am ready to go with that user. FYI, the reset of the datatypes_conf.xml did not do the trick: following error appears on the custom builds page: NoConverterException: "Conversion from 'fasta' to 'len' not possible"


Thanks,
Joachim

On 02/13/2012 06:02 PM, Jeremy Goecks wrote:
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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