Re: Mira-Assembler: DOESN'T WORK ON GALAXY

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Re: Mira-Assembler: DOESN'T WORK ON GALAXY

Peter Cock
On Fri, Aug 22, 2014 at 9:39 AM, Marija Atanaskovic
<[hidden email]> wrote:

>
> Mira doesn’t work on Galaxy. This is the log message I receive.
>
> Tool: Assemble with MIRA v3.4
> Name: MIRA log
> Created: Fri Aug 22 00:24:38 2014 (UTC)
> Filesize: 0 bytes
> Dbkey: ?
> Format: txt
> Galaxy Tool Version: 0.0.10
> Tool Version: None
> Tool Standard Output: stdout
> Tool Standard Error: stderr
> Tool Exit Code: None
> API ID: d5f55b83db1f410a
> Full Path: /mnt/galaxy/files/000/dataset_326.dat
> ...

What was the stdout and stderr information?

Did you install this from the main tool shed?:
https://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler

> Also I can’t install Mira 4. This is the message I receive.
> Any suggestions.

Getting "Internal Server Error" is unhelpful - I can't
really guess what might be going wrong here :(

I have had problems with the MIRA dependencies when
Bastien has renamed folders on sourceforge... are you
using the Test Tool Shed here (since I have not yet
released the MIRA 4 wrapper on the main ToolShed)?:
https://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler

Regards,

Peter

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Re: Mira-Assembler: DOESN'T WORK ON GALAXY

Peter Cock
On Fri, Aug 22, 2014 at 8:18 PM, Marija Atanaskovic
<[hidden email]> wrote:

> Hi Peter,
>
> I don¹t know what the stdout and stderr information was. I click on it but
> nothing comes up.
>
> I installed from the main toolshed:
> http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
> Yes, I did use the test toolshed for Mira 4.
>
> Regards,
>
> Marija

If stdout and stderr are empty, this is consistent with MIRA never
even starting (as suggested by the next bit of information below).

On Fri, Aug 22, 2014 at 8:20 PM, Marija Atanaskovic
<[hidden email]> wrote:

> Hi Peter,
>
> This is the error in history under MIRA log:
>
>         tool error
> An error occurred with this dataset:Unable to run job due to a
> misconfiguration of the Galaxy job running system.  Please contact a site
> administrator.
>
> Regards,
>
> Marija

That suggests your Galaxy job runner is not properly configured,
and MIRA itself was never started. Are you the site administrator?
Are other Galaxy tools working? Are other Galaxy tools installed
from the ToolShed working?

On Fri, Aug 22, 2014 at 8:22 PM, Marija Atanaskovic
<[hidden email]> wrote:
> Hi Peter,
>
> One more thing. The data that I am trying to analyse are fastq files of
> Ion Torrent reads. I have used them with other assemblers e.g., velvet,
> CLC.
>
> Marija

I have not personally used Ion Torrent, but that ought to be fine.

Peter

P.S. You forgot to CC the mailing list.

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Re: Mira-Assembler: DOESN'T WORK ON GALAXY

Peter Cock
In reply to this post by Peter Cock
On Fri, Aug 22, 2014 at 8:00 PM, Peter Cock <[hidden email]> wrote:
> On Fri, Aug 22, 2014 at 9:39 AM, Marija Atanaskovic
> <[hidden email]> wrote:
>
>> Also I can’t install Mira 4. This is the message I receive.
>> Any suggestions.
>
> Getting "Internal Server Error" is unhelpful - I can't
> really guess what might be going wrong here :(
>

This is a guess, but it could be you need to set the
https_proxy in the /etc/environment file - see this thread:
http://dev.list.galaxyproject.org/Internal-Server-Error-when-trying-to-install-a-tool-from-the-Tool-shed-tt4665361.html

Peter

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Re: Mira-Assembler: DOESN'T WORK ON GALAXY

Marija Atanaskovic
In reply to this post by Peter Cock
Hi Peter,

Thanks for your response and for the advice from the other subscribers. I
am not the site administrator, but I have passed on all the email
correspondence to the administrators. I am a “wet-lab” scientist who
wanted to use the programme for my work. That is why I use Galaxy as the
script writing etc., is taken care of. Galaxy is a great resource for
people like me. I’ll let you know what happens.

Best regards,

Marija

On 23/08/2014 8:48 am, "Peter Cock" <[hidden email]> wrote:

>On Fri, Aug 22, 2014 at 8:18 PM, Marija Atanaskovic
><[hidden email]> wrote:
>> Hi Peter,
>>
>> I don¹t know what the stdout and stderr information was. I click on it
>>but
>> nothing comes up.
>>
>> I installed from the main toolshed:
>> http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
>> Yes, I did use the test toolshed for Mira 4.
>>
>> Regards,
>>
>> Marija
>
>If stdout and stderr are empty, this is consistent with MIRA never
>even starting (as suggested by the next bit of information below).
>
>On Fri, Aug 22, 2014 at 8:20 PM, Marija Atanaskovic
><[hidden email]> wrote:
>> Hi Peter,
>>
>> This is the error in history under MIRA log:
>>
>>         tool error
>> An error occurred with this dataset:Unable to run job due to a
>> misconfiguration of the Galaxy job running system.  Please contact a
>>site
>> administrator.
>>
>> Regards,
>>
>> Marija
>
>That suggests your Galaxy job runner is not properly configured,
>and MIRA itself was never started. Are you the site administrator?
>Are other Galaxy tools working? Are other Galaxy tools installed
>from the ToolShed working?
>
>On Fri, Aug 22, 2014 at 8:22 PM, Marija Atanaskovic
><[hidden email]> wrote:
>> Hi Peter,
>>
>> One more thing. The data that I am trying to analyse are fastq files of
>> Ion Torrent reads. I have used them with other assemblers e.g., velvet,
>> CLC.
>>
>> Marija
>
>I have not personally used Ion Torrent, but that ought to be fine.
>
>Peter
>
>P.S. You forgot to CC the mailing list.


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