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.
Mark,
There's documentation currently available here: https://galaxy-dist.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api....
Is there anything else in particular you're looking for?
-Dannon
On Feb 2, 2013, at 9:15 PM, mark.rose@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:
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-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Dannon Baker Sent: Saturday, February 02, 2013 7:57 PM To: mark.rose@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.rose@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:
___________________________________________________________ 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:
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...). 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 thondeboer@me.com 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-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Dannon Baker Sent: Saturday, February 02, 2013 7:57 PM To: mark.rose@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.rose@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:
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:
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:dannonbaker@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....
Is there anything else in particular you're looking for?
-Dannon
On Feb 2, 2013, at 9:15 PM, mark.rose@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:
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.
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.rose@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:dannonbaker@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....
Is there anything else in particular you're looking for?
-Dannon
On Feb 2, 2013, at 9:15 PM, mark.rose@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:
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.
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_wo...
On Mon, Feb 4, 2013 at 2:38 AM, Dannon Baker dannonbaker@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.rose@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:dannonbaker@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....
Is there anything else in particular you're looking for?
-Dannon
On Feb 2, 2013, at 9:15 PM, mark.rose@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:
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:
galaxy-dev@lists.galaxyproject.org
-
Dannon Baker -
Enis Afgan -
mark.rose＠syngenta.com -
Thon de Boer