Re: [galaxy-dev] Changing job command line.
On Feb 14, 2013, at 7:26 AM, James wrote: Hi Nate, Thanks for your reply, I guess the idea is that the job is prepared in the interface which lets a user select the grid. This is currently located in my galaxy instance as a if statement in the default job dispatcher. Just before it sends it to the job runner and all the preparation is done there. But regarding the command line you are probably right, it would just mean that every job runner on our instance will have to be patched to include this if statement as to whether the command line needs to be reassigned. Hi James, In this case, either method seems fine. You are going to have to modify the way that Galaxy prepares jobs regardless of the way you do it. Another simple question regarding adding UI options to toolform.mako. Could i parse them to my module using javascript. Although I feel the best approach would be to add these options to the job model and then they would remain tracked in the database. There have been various requests in the past to allow for inclusion of a global parameter set in tool forms, for this exact purpose. I thought there was a bitbucket issue or trello card for it, but I'm having trouble locating it now. --nate Cheers James. On 2/14/2013 4:20 AM, Nate Coraor wrote: On Feb 4, 2013, at 6:03 PM, James Boocock wrote: Hi All, I am currently working on a clustering interface for galaxy that will hopefully enable users to pick the grid in the tool form. With tools that need access to files within the galaxy directory, I have an idea to create a symlinked fake galaxy root with all the files the tools needs for galaxy. This is done currently in my own xml format for each grid. Problem is when parsing a tool_wrapper variable I need to prepare the job and add my additional commands to the command line so that the fake galaxy dir is created with the symlinked databases. Is it bad practice to disable preparation in each tool runner if the job has come from my clustering module or is there a better way to do this. Will the job runners wrapper.prepare() overwrite any of my changes to the command-line when the job makes its way to the runner say local.py. Hi James, You'll probably need to make the changes to the command line after the command line has been assembled in prepare(). Can you do this later in prepare()? --nate Cheers James. ___ 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] Changing job command line.
Hi Nate, Thanks for your reply, I guess the idea is that the job is prepared in the interface which lets a user select the grid. This is currently located in my galaxy instance as a if statement in the default job dispatcher. Just before it sends it to the job runner and all the preparation is done there. But regarding the command line you are probably right, it would just mean that every job runner on our instance will have to be patched to include this if statement as to whether the command line needs to be reassigned. Another simple question regarding adding UI options to toolform.mako. Could i parse them to my module using javascript. Although I feel the best approach would be to add these options to the job model and then they would remain tracked in the database. Cheers James. On 2/14/2013 4:20 AM, Nate Coraor wrote: On Feb 4, 2013, at 6:03 PM, James Boocock wrote: Hi All, I am currently working on a clustering interface for galaxy that will hopefully enable users to pick the grid in the tool form. With tools that need access to files within the galaxy directory, I have an idea to create a symlinked fake galaxy root with all the files the tools needs for galaxy. This is done currently in my own xml format for each grid. Problem is when parsing a tool_wrapper variable I need to prepare the job and add my additional commands to the command line so that the fake galaxy dir is created with the symlinked databases. Is it bad practice to disable preparation in each tool runner if the job has come from my clustering module or is there a better way to do this. Will the job runners wrapper.prepare() overwrite any of my changes to the command-line when the job makes its way to the runner say local.py. Hi James, You'll probably need to make the changes to the command line after the command line has been assembled in prepare(). Can you do this later in prepare()? --nate Cheers James. ___ 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] Changing job command line.
On Feb 4, 2013, at 6:03 PM, James Boocock wrote: Hi All, I am currently working on a clustering interface for galaxy that will hopefully enable users to pick the grid in the tool form. With tools that need access to files within the galaxy directory, I have an idea to create a symlinked fake galaxy root with all the files the tools needs for galaxy. This is done currently in my own xml format for each grid. Problem is when parsing a tool_wrapper variable I need to prepare the job and add my additional commands to the command line so that the fake galaxy dir is created with the symlinked databases. Is it bad practice to disable preparation in each tool runner if the job has come from my clustering module or is there a better way to do this. Will the job runners wrapper.prepare() overwrite any of my changes to the command-line when the job makes its way to the runner say local.py. Hi James, You'll probably need to make the changes to the command line after the command line has been assembled in prepare(). Can you do this later in prepare()? --nate Cheers James. ___ 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/
