There were several issues and bugs I encountered getting this script to
work. I've written down some notes for a quickstart for anyone else who
might be following in my footsteps.

1. Create input and output directores where you will drop and emit files.
In my example I used:



2. Edit the galaxy-dist configuration script (universe_wsgi.ini) and set:

allow_library_path_paste = true

3. In, comment out line 30 and replace it with:

#library_id = library[0]['id]      This causes a "key error : 0" -- remove
the indexing

           library_id = library['id']

4. In change the sleep duration on line 59 to 15
seconds. If you're still getting zero byte .dat files, then you'll need to
extend the duration even more.


5. CREATE A SAMPLE Workflow & Dataset:

   1. Start Galaxy
   2. Go to USCS and upload the Exons from chr22 to your clean history file
   3. Use the Text Manipulation tool to select the first 5 lines of the
   gene exon file
   4. Extract the workflow
   5. IMPORTANT: If you don't do the following step you'll get a 500
   Internal Server.
   6. Change the output filename in the workflow and then save the
   7. Test that the workflow is accessable by visiting
   in your browser, and then visit 'http://
   8. Download the exons file to local

6. In your browser go to: http://localhost:8080/api/workflows and identify
the id of the workflow you've just created. Let's assume it is
(4b187121143038ff) and that your api_key for admin is <api_key>

7. Run the script:

./ <api_key> http://localhost:8080/api/
/Users/Rob/Documents/galaxy-drop/output "My API Import" 4b187121143038ff

8. Copy the exons file to /Users/Rob/Documents/galaxy-drop/input when the
process is complete the file will be placed in

9. In your browser go to: http://localhost:8080/api/histories locate the
recently created history and then navigate to:


where <history_id> is the id of the history that was created when you ran
the dataset on the last workflow.

This is my result. The second file is the output file.

        "id": "0d16186aaff7cbfd",
        "name": "Galaxy1-[Exons_chr22].bed",
        "type": "file",
        "url": "/api/histories/2d9035b3fc152403/contents/0d16186aaff7cbfd"
        "id": "81991b32733a4fc4",
        "name": "top200",
        "type": "file",
        "url": "/api/histories/2d9035b3fc152403/contents/81991b32733a4fc4"

10. You can navigate to the JSON description of the file in your browser:


and the output file can be downloaded here:



Rob Leclerc, PhD
<> <!/robleclerc>
P: (US) +1-(917)-873-3037
P: (Shanghai) +86-1-(861)-612-5469
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