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
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
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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:
To search Galaxy mailing lists use the unified search at:
participants (3)
-
Bjoern Gruening -
Björn Grüning -
Claudio Slamovits