Can you confirm that the following lines are in your datatypes_conf.xml file?
<datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta"
<converter file="fasta_to_2bit.xml" target_datatype="twobit"/>
<converter file="fasta_to_len.xml" target_datatype="len"/>
If so, the other issue is that you'll need to restart Galaxy in order for the
changes to take hold. Apologies for not mentioning this step previously.
On Feb 14, 2012, at 3:18 AM, Joachim Jacob wrote:
> 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"
> 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.
>> 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
>>> 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?
>>> Thank for looking into this.
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