Re: [galaxy-dev] galaxy api documentation
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 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/ > ___ 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/
Re: [galaxy-dev] galaxy api documentation
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/
Re: [galaxy-dev] galaxy api documentation
Thon, Without getting my hands on it, my hunch is that this isn't directly possible out of the box as a 'copy' type operation. That said, it's a fairly straightforward (and sensible) addition if not. Contributions would be welcome, as always. I've added a Trello card for this here: https://trello.com/c/lwBDzAEi That said, my guess is that you could (if file path upload is enabled on your server) specify those options for a library dataset upload. So, via the API, you'd get the file path of the hda's dataset, and then re-enter that in the post to library_contents (https://galaxy-dist.readthedocs.org/en/latest/_modules/galaxy/webapps/galaxy/api/library_contents.html#LibraryContentsController.create). This is a hack, though it would probably work without any additional code changes. -Dannon On Feb 3, 2013, at 4:31 AM, Thon de Boer wrote: > The documentation for the API is looking real nice...Great... > I do have some trouble finding how I move a history item into a data > library... > > Could you give me a few pointers which API call to make for that? > We can assume I have the HDA indentifiers for those objects, just need to > know the command for moving it into a folder of the data library? > > Thanks! > > Thon > > -Original Message- > From: galaxy-dev-boun...@lists.bx.psu.edu > [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Dannon Baker > Sent: Saturday, February 02, 2013 7:57 PM > To: mark.r...@syngenta.com > 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/ > > ___ > 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/ > ___ 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/
Re: [galaxy-dev] galaxy api documentation
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/
Re: [galaxy-dev] galaxy api documentation
The documentation for the API is looking real nice...Great... I do have some trouble finding how I move a history item into a data library... Could you give me a few pointers which API call to make for that? We can assume I have the HDA indentifiers for those objects, just need to know the command for moving it into a folder of the data library? Thanks! Thon -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Dannon Baker Sent: Saturday, February 02, 2013 7:57 PM To: mark.r...@syngenta.com 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/ ___ 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/ ___ 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/
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/ ___ 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/
[galaxy-dev] galaxy api documentation
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/
