We also have a python library for dealing with the API, the documentation is available at http://bioblend.readthedocs.org/ The library source code also contains an example very similar to what you're trying to achieve: imports a workflow, imports data, and runs the workflow. Here's that script: https://github.com/afgane/bioblend/blob/master/docs/examples/run_imported_workflow.py
On Mon, Feb 4, 2013 at 2:38 AM, Dannon Baker <dannonba...@me.com> wrote: > Sure, automated data import and workflow execution is certainly possible. > In addition to the documentation there are several example scripts in the > /scripts/api directory of your galaxy install. In particular, for your use > case, you may want to have a look at example_watch_folder.py. This script > watches a specified folder for any new files, uploads them to a galaxy data > library, and then triggers the execution of a predefined workflow on the > data. I wouldn't implement your pipeline exactly like in that script, but > it's designed to illustrate a few specific examples without being overly > complicated. > > -Dannon > > On Feb 3, 2013, at 10:22 AM, mark.r...@syngenta.com wrote: > > > Hey Dannon > > > > Thanks, the web page I was finding earlier was mostly just an outline. > This is much better. At this point I'm just interested in learning what > general capabilities the API can provide. I'm sure after I read this and > think more about it I'll have questions. One thing I am thinking about is > what role the API might play in automatically analyzing data coming off an > Illumina MiSeq. This would seem to be attractive in that it might proceed > in a timely way, offer the possibility of a greater variety of analyses > than come onboard the MiSeq, and place the results in a history that might > readily be shared with multiple users. Does this seem possible? Do you > know of anyone doing this now? > > > > Thanks again for your help > > > > Mark > > > > -----Original Message----- > > From: Dannon Baker [mailto:dannonba...@me.com] > > Sent: Saturday, February 02, 2013 10:57 PM > > To: Rose Mark USRE > > Cc: galaxy-dev@lists.bx.psu.edu > > Subject: Re: [galaxy-dev] galaxy api documentation > > > > Mark, > > > > There's documentation currently available here: > https://galaxy-dist.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html > > > > Is there anything else in particular you're looking for? > > > > -Dannon > > > > > > On Feb 2, 2013, at 9:15 PM, mark.r...@syngenta.com wrote: > > > >> Hi All > >> > >> When is it anticipated that the documentation for the API will be > available? > >> > >> Thanks > >> > >> Mark > >> > >> > >> This message may contain confidential information. If you are not the > >> designated recipient, please notify the sender immediately, and delete > >> the original and any copies. Any use of the message by you is > >> prohibited. > >> ___________________________________________________________ > >> 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: > >> > >> http://lists.bx.psu.edu/ > > > > > > > > > > > > This message may contain confidential information. If you are not the > designated recipient, please notify the sender immediately, and delete the > original and any copies. Any use of the message by you is prohibited. > > > > ___________________________________________________________ > 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: > > http://lists.bx.psu.edu/ >
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