problem running Augustus

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problem running Augustus

Claudio Slamovits
Hello,

I am trying to use the genome Annotation tool Augustus on my locally installed copy of Galaxy. After loading the data file, all analyses stop and deliver the following:

error
an error occurred with this dataset: /bin/sh:1:augustus: not found python: can't open file: '/extract_features.py': [Errno 2] No such file or directory

Python is installed on my system (Ubuntu 12.04, Python 2.7.3)

It must be something very basic I'm missing, but more basic are my linux skills…

Thanks a lot

Claudio



~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^
Claudio Slamovits,
Canadian Institute for Advanced Research
Department of Biochemistry and Molecular Biology
Dalhousie University
5850 College Street, Halifax, Nova Scotia
B3H 4R2, Canada

Lab Webpage: http://slamo.biochem.dal.ca
Lab: (902) 494 7894
Office: (902) 494 8825
Fax: (902) 494 1355
^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~


"Reality is what it is, not what you want it to be." 
- Frank Zappa 


___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
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Re: problem running Augustus

Björn Grüning-2
Hi Claudio,

I will have a look at it, at latest tomorrow, promised.

Cheers,
Bjoern (Augustus wrapper developer)

>
>
> I am trying to use the genome Annotation tool Augustus on my locally
> installed copy of Galaxy. After loading the data file, all analyses
> stop and deliver the following:
>
>
> error
> an error occurred with this dataset: /bin/sh:1:augustus: not found
> python: can't open file: '/extract_features.py': [Errno 2] No such
> file or directory
>
>
> Python is installed on my system (Ubuntu 12.04, Python 2.7.3)
>
>
> It must be something very basic I'm missing, but more basic are my
> linux skills…
>
>
> Thanks a lot
>
>
> Claudio
>
>
>
> ~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^
> Claudio Slamovits,
> Canadian Institute for Advanced Research
> Department of Biochemistry and Molecular Biology
> Dalhousie University
> 5850 College Street, Halifax, Nova Scotia
> B3H 4R2, Canada
>
> Lab Webpage: http://slamo.biochem.dal.ca
> Lab: (902) 494 7894
> Office: (902) 494 8825
> Fax: (902) 494 1355
> ^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~
>
>
> "Reality is what it is, not what you want it to be."
> - Frank Zappa
>
>
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
>   http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>
>   http://galaxyproject.org/search/mailinglists/



___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/
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Re: problem running Augustus

Björn Grüning
In reply to this post by Claudio Slamovits
Hi Claudio,

did you installed Augustus with the ToolShed?
The env variable $AUGUSTUS_SCRIPT_PATH need to be set and point to the
augustus wrapper folder containing the extract_features.py script.

Hope that helps!
Bjoern

> Hello,
>
>
> I am trying to use the genome Annotation tool Augustus on my locally
> installed copy of Galaxy. After loading the data file, all analyses
> stop and deliver the following:
>
>
> error
> an error occurred with this dataset: /bin/sh:1:augustus: not found
> python: can't open file: '/extract_features.py': [Errno 2] No such
> file or directory
>
>
> Python is installed on my system (Ubuntu 12.04, Python 2.7.3)
>
>
> It must be something very basic I'm missing, but more basic are my
> linux skills…
>
>
> Thanks a lot
>
>
> Claudio
>
>
>
> ~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^
> Claudio Slamovits,
> Canadian Institute for Advanced Research
> Department of Biochemistry and Molecular Biology
> Dalhousie University
> 5850 College Street, Halifax, Nova Scotia
> B3H 4R2, Canada
>
> Lab Webpage: http://slamo.biochem.dal.ca
> Lab: (902) 494 7894
> Office: (902) 494 8825
> Fax: (902) 494 1355
> ^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~
>
>
> "Reality is what it is, not what you want it to be."
> - Frank Zappa
>
>
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
>   http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>
>   http://galaxyproject.org/search/mailinglists/



___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/