Further, it seems that it doesn't manage to get hold of the file specified in 
the input directory as I can see from the output:


    "data_type": "html",
    "deleted": false,
    "download_url": "/csiro/datasets/2faba7054d92b2df/display?to_ext=html",
    "file_name": "/home/galaxy/galaxy-dist/database/files/000/dataset_137.dat",
    "file_size": 194,
    "genome_build": "?",
    "id": "2faba7054d92b2df",
    "metadata_data_lines": null,
    "metadata_dbkey": "?",
    "misc_blurb": "error",
    "misc_info": "Wed May  8 15:07:27 2013\nbashScript is: 
 is: None\ncat: None: No such file or directory\nFailed reading file 
/tmp/tmp.9LWrz6SaLy.nii.gz\nitk::ERROR: PNGImageIO(0x1abdcf0): PNGIma",
    "model_class": "HistoryDatasetAssociation",
    "name": "Extract 2D slice on None",
    "state": "error",
    "visible": true

input_image is: None

Does anybody know why the file may not be getting read? It is being copied from 
the specified input directory to the output directory.

I have set :
allow_library_path_paste = True

and added my user to:

Thanks for any help


From: Burdett, Neil (ICT Centre, Herston - RBWH)
Sent: Wednesday, May 08, 2013 2:46 PM
To: galaxy-dev@lists.bx.psu.edu
Subject: Getting example_watch_folder.py to work...

     I'm trying to get the example_watch_folder.py to run but it seems to fail, 
and I'm not sure why?

I run:

 ./example_watch_folder.py 64f3209856a3cf4f2d034a1ad5bf851c 
http://barium-rbh/csiro/api/ /home/galaxy/galaxy-drop/input 
/home/galaxy/galaxy-drop/output "My API Import" f597429621d6eb2b

I got the workflow Id from :


which gave me:

        "id": "f597429621d6eb2b",
        "name": "extract",
        "url": "/csiro/api/workflows/f597429621d6eb2b"
        "id": "f2db41e1fa331b3e",
        "name": "FULL CTE",
        "url": "/csiro/api/workflows/f2db41e1fa331b3e"

The output I get from the command line is:
{'outputs': ['ba0fa2aed4052bce'], 'history': 'ba03619785539f8c'}

The files I put into /home/galaxy/galaxy-drop/input get copied to 

But nothing else happens.

If I go to http://barium-rbh/csiro/api/histories

I can see:
        "id": "ba03619785539f8c",
        "name": "colin.nii.gz - extract",
        "url": "/csiro/api/histories/ba03619785539f8c"

However when I go to:

I get:
    "contents_url": "/csiro/api/histories/ba03619785539f8c/contents",
    "id": "ba03619785539f8c",
    "name": "colin.nii.gz - extract",
    "state": "error",
    "state_details": {
        "discarded": 0,
        "empty": 0,
        "error": 1,
        "failed_metadata": 0,
        "new": 0,
        "ok": 0,
        "queued": 0,
        "running": 0,
        "setting_metadata": 0,
        "upload": 0

Any ideas much appreciated


Please keep all replies on the list by using "reply all"
in your mail client.  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:

Reply via email to