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:
/Users/Rob/Documents/galaxy-drop/input
/Users/Rob/Documents/galaxy-drop/output
2. Edit the galaxy-dist configuration script (universe_wsgi.ini) and set:
allow_library_path_paste = true
3. In example_watch_folder.py, 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 example_watch_folder.py 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.
time.sleep(15)
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
workflow.
7. Test that the workflow is accessable by visiting
'http://<galaxy_server/api/workflows'
in your browser, and then visit 'http://
<galaxy_server/api/workflows/<workflow_id>
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:
./example_watch_folder.py <api_key> http://localhost:8080/api/
/Users/Rob/Documents/galaxy-drop/input
/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
/Users/Rob/Documents/galaxy-drop/output
9. In your browser go to: http://localhost:8080/api/histories locate the
recently created history and then navigate to:
http://localhost:8080/api/histories/<history_id>/contents
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:
http://localhost:8080/api/histories/2d9035b3fc152403/contents/81991b32733a4fc4
and the output file can be downloaded here:
http:localhost:8080/datasets/81991b32733a4fc4/display?to_ext=data
Cheers!
Rob
Rob Leclerc, PhD
<http://www.linkedin.com/in/robleclerc> <https://twitter.com/#!/robleclerc>
P: (US) +1-(917)-873-3037
P: (Shanghai) +86-1-(861)-612-5469
Personal Email: rob.lecl...@aya.yale.edu
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