It looks like the problem may have to do with the file I am using ??? It is a *.nii.gz file. Does galaxy try to uncompress ? do something to *.gz files when using the api (as it tries to do in ~/galaxy-dist/tools/data_source/upload.py Does anyone know of where in the code I can edit so my mile can be uploaded? Thanks Neil From: Burdett, Neil (ICT Centre, Herston - RBWH) Sent: Wednesday, 8 May 2013 3:15 PM To: galaxy-dev@lists.bx.psu.edu Subject: RE: Getting example_watch_folder.py to work... 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: http://barium-rbh/csiro/api/histories/964b37715ec9bd22/contents/2faba7054d92... { "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: /home/galaxy/galaxy-dist/tools/visualization/extractSlice-wrapper.sh\ninput_image 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: admin_users Thanks for any help Neil ________________________________ From: Burdett, Neil (ICT Centre, Herston - RBWH) Sent: Wednesday, May 08, 2013 2:46 PM To: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> Subject: Getting example_watch_folder.py to work... Hi, 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 : http://barium-rbh/csiro/api/workflows 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 /home/galaxy/galaxy-drop/output 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: http://barium-rbh/csiro/api/histories/ba03619785539f8c 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 Thanks Neil