Re: [galaxy-dev] Is dynamic associated information per dataset possible?
Duddy, John wrote: The sample tracking system looks interesting. It looks like this is designed to have the sequencers modeled in Galaxy, have Galaxy pull the data from the sequencers, and might assume 1-1 pairing between sequencing run and samples. I'd like to be able to support pushing files from a central location and variably multiplexed runs, all via the API (or extensions to the API). Is there any up-to-date documentation on this feature? The sample tracking system is undergoing a bunch of changes, so I'm thinking the documentation will be rewritten after that. --nate John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jdu...@illumina.com -Original Message- From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: Thursday, May 26, 2011 2:18 AM To: Duddy, John Cc: galaxy-dev Subject: Re: [galaxy-dev] Is dynamic associated information per dataset possible? In addition to Data Library templates, which are useful after the sequencer data has arrived in a Galaxy Data Library, Galaxy's sample tracking system includes sample run templates which are very similar to the Data Library templates, but are associated with a sample as it progresses through it's sequence run lifecycle in the facility. Sample run details templates are defined by the facility administrator. They can be created in the Admin view via the Manage form definitions menu link. ___ 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] thanks for the conference; presentations availbale?
A wiki page is available here: http://wiki.g2.bx.psu.edu/GCC2011 On Mon, May 30, 2011 at 4:20 AM, Martin Senger martin.sen...@gmail.comwrote: I really enjoyed the recent conference. Many thanks for the splendid logistics and, of course, the content. I wonder if the slides presented there will be available for downloading perhaps? Cheers, Martin -- Martin Senger email: martin.sen...@gmail.com,martin.sen...@kaust.edu.sa skype: martinsenger ___ 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] Is dynamic associated information per dataset possible?
Duddy, John wrote: The sample tracking system looks interesting. It looks like this is designed to have the sequencers modeled in Galaxy, have Galaxy pull the data from the sequencers, and might assume 1-1 pairing between sequencing run and samples. I'd like to be able to support pushing files from a central location and variably multiplexed runs, all via the API (or extensions to the API).Is there any up-to-date documentation on this feature? The sample tracking system is undergoing a bunch of changes, so I'm thinking the documentation will be rewritten after that. There's some code from Brad Chapman at https://github.com/chapmanb/bcbb/tree/master/nextgen/scripts that specifically addresses some of your downstream use cases and more. Currently involves deep galaxy introspection into the sequencing system. As Nate said, that's undergoing replumbing, so that interface part will need changes - but the rest is likely a great starting point for putting together your own local common tasks like (eg) splitting and analysing a multiplexed lane and calling variants and other routine core lab kinds of operations. ___ 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] Implemented adding tools via admin console
Peter,
if you were just interested in having a dynamic refresh it was posted long
time ago and we have it operational. It comes as a tool in your tool list and
refreshes all from the tool_conf.xml. Not the loc filtes though! As far as i
remember it doesn't kill running jobs.
It requires two lines of code in galaxy source and the addition of a tool to
the tools section.
I pasted it from my archive below. But it is quite self explanatory.
Alex
Galaxy source adapt for tool refresh
Changes to Galaxy to add refresh toolbox ability:
1. change the execute method of the class tool in
lib/galaxy/tools/__init__.py to
def execute( self, trans, incoming={}, set_output_hid=True ):
Execute the tool using parameter values in `incoming`. This just
dispatches to the `ToolAction` instance specified by
`self.tool_action`. In general this will create a `Job` that
when run will build the tool's outputs, e.g. `DefaultToolAction`.
#
#add code to verify if user has administrative privileges
#added by sumedha ganjoo, sganjoo at uga.edu: line 1104 to 1109 - to
refresh toolbox
if self.id == 'REFRESH_ID':
self.app.refreshToolBox()
#
return self.tool_action.execute( self, trans,
incoming=incoming, set_output_hid=set_output_hid )
2. add refreshToolBox method (find below) to UniverseApplication class
in lib/galaxy/app.py
###
# added by sumedha ganjoo,sganjoo at uga.edu, line 86-90
def refreshToolBox( self):
self.toolbox = tools.ToolBox( self.config.tool_config,
self.config.tool_path, self )
###
3. Add Refresh tool. Attached.
Thanks,
Sumedha
tool id=REFRESH_ID name=Refresh Version=1.0.0 description
:Refresh Galaxy/description command interpreter=python
refreshTool.py
$input
$output
/command
inputs
param name=input type=select display=radio size=250
label=Execute this tool by clicking on Execute button
option value=refreshRefresh Galaxy/option
/param
/inputs
outputs
data format=tabular name=output /
/outputs
tests
/tests
help
**Click on Galaxy on the top left corner of this window to refresh
the page.**
/help
/tool
Van: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu]
namens Peter Cock [p.j.a.c...@googlemail.com]
Verzonden: maandag 30 mei 2011 21:09
Aan: Vossen, Bodo
CC: galaxy-dev@lists.bx.psu.edu
Onderwerp: Re: [galaxy-dev] Implemented adding tools via admin console
On Mon, May 30, 2011 at 9:54 AM, Vossen, Bodo wrote:
Hi Peter,
thanks a lot for your comments.
Hi Bodo,
No problem :)
I think it is more comfortable to be able to upload tools and xml via the
webbrowser than to open a terminal and copy them, that was the idea
behind my work. Especially for our institute this is very useful.
For me the command vs the web interface is not important.
What I was excited about was adding a tool to Galaxy without
having to restart Galaxy and interrupt any users.
You're right about the check_argument methods. I wasn't sure to add this
kind of functionality in the first place, because it can become very tricky.
What I did should just be the very first step for someone who wants to
continue the work (if this makes sense).
That's why I added a checkbox that disable this check, so that you still
can upload your tool/xml even the argument test would fail.
It might be useful then.
Do you have some comments about the other parts ? Is this something
you would be interested in using ?
I've not had a chance to try the code yet, but it could be useful.
Peter
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Re: [galaxy-dev] Implemented adding tools via admin console
On Mon, May 30, 2011 at 10:42 PM, Bossers, Alex wrote: Peter, if you were just interested in having a dynamic refresh it was posted long time ago and we have it operational. It comes as a tool in your tool list and refreshes all from the tool_conf.xml. I'd like to see something like this functionality built into Galaxy, on the admin page next to reload a single tool. Having an extra standard tool (if world visible) is not an ideal solution. If that is what you meant? I'll have to try it and see. Not the loc filtes though! Reloading loc files is also on my wish list :) As far as i remember it doesn't kill running jobs. Good - because otherwise you might as well restart Galaxy. It requires two lines of code in galaxy source and the addition of a tool to the tools section. I pasted it from my archive below. But it is quite self explanatory. Alex Thanks, now I have two solutions to play with ;) Peter ___ 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/
