Thanks Peter. You guessed correctly, I tried
https://toolshed.g2.bx.psu.edu/view/clustalomega/clustalomega ... I'm back
to using the command line ;-)

cheers,

Isabelle



On 10/7/14 1:45 AM, "Peter Cock" <p.j.a.c...@googlemail.com> wrote:

>On Tue, Oct 7, 2014 at 1:47 AM, Isabelle Phan
><isabelle.p...@seattlebiomed.org> wrote:
>> Hello,
>>
>> I installed clustalomega from the galaxy main toolshed using the admin
>> interface of our local galaxy install.
>>
>> When I run the tool, I get this message:
>>
>>
>> Dataset generation errors
>>         Dataset 55: co_alignment.fasta
>>
>>
>>                 Tool execution generated the following error message:
>>                     Error invoking command:
>> clustalo --force --threads=1 --maxnumseq=300000 --maxseqlen=15000 -o
>> /opt/galaxy-dist/database/files/000/dataset_158.dat -l
>> /opt/galaxy-dist/database/files/000/dataset_159.dat -v -i
>> /opt/galaxy-dist/database/files/000/dataset_153.dat
>>
>> [Errno 2] No such file or directory
>>
>>
>>
>> I've tried reloading my input file, reloading the tool's configuration,
>> resetting the metadata on the clustalomega repository, deleting the tool
>> completely and re-installing. No luck. If I try to rerun the job again,
>>I
>> get non-sensical errors that seem to originate from other tools, as if
>>the
>> database was completely garbled. Each of those tools work fine. Only
>> clustalomega behaves oddly.
>>
>> I have no access to our galaxy server, so any solution would have to be
>> implemented from the admin interface.
>>
>> thanks for any hints,
>>
>>
>> Isabelle
>
>Hi Isabelle,
>
>I am guessing you used this ToolShed repository:
>
>https://toolshed.g2.bx.psu.edu/view/clustalomega/clustalomega
>
>As far as I can see, this does not automatically install the clustalo
>binary, which would explain "[Errno 2] No such file or directory".
>The (incomplete and out of date) README file suggests you are
>expected to manually compile it from the bundled copy of the
>Clustal Omega source code.
>
>If the only access you have to modify the server is via the Galaxy
>admin interface, you will not be able to fix this.
>
>As it stands right now, this ToolShed repository would not get a
>gold star approval rating :(
>
>Peter


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