Richard, For specifying or changing species, you may want to inspect the input via the API (api/histories/<id>/contents/<id>/) and snag the "genome_build" attribute that way. Or am I missing the issue you're running into?
As an aside, I'd love to look at the runtime parameter specification changes you've made for potential inclusion. This is a feature I've wanted to add for some time. Thanks! Dannon On Apr 4, 2012, at 4:17 PM, Richard Park wrote: > Hi Dannon, > Thank for the pointers from before, I have a version of galaxy that is able > to change runtime parameters through the API when running a workflow. > > Format: param=<tool name>=<tool parameter>=<value> > > # example execution: (currently changing 2 parameters: 1) bowtie, > suppressHeader parameter 2) Chip-seq peakcalling, aligner change > python workflow_execute.py api_key http://localhost:8080/api/workflows > workflow_galaxy_id 'Test API' '69=ld=a799d38679e985db' > '70=ld=33b43b4e7093c91f' 'param=peakcalling_spp=aligner=arachne' > 'param=bowtie_wrapper=suppressHeader=True' > > However, I was wondering if you had any pointers on how to deal w/ changing > species or chromosome lengths? > > # example workflow: bowtie tool > "tool_id": "bowtie_wrapper", > "tool_state": "{\"suppressHeader\": \"\\\"False\\\"\", > \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": > \\\"dm3\\\", \\\"__current_case__\\\": 0}\", \"__page__\": 0, \"chromInfo\": > \"\\\"/data/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/dm3.len\\\"\", > \"singlePaired\": \"{\\\"sInput1\\\": null, \\\"sParams\\\": > {\\\"sMismatchSeed\\\": \\\"2\\\", \\\"sUnmappedFile\\\": \\\"False\\\", > \\\"sTrimH\\\": \\\"0\\\", \\\"sTrimL\\\": \\\"0\\\", \\\"sSuppressAlign\\\": > \\\"1\\\", \\\"sSettingsType\\\": \\\"full\\\", \\\"sSeed\\\": \\\"-1\\\", > \\\"sMismatchQual\\\": \\\"70\\\", \\\"sMaqSoapAlign\\\": \\\"-1\\\", > \\\"sAlignLimit\\\": \\\"-1\\\", \\\"sTryHard\\\": \\\"noTryHard\\\", > \\\"sRounding\\\": \\\"round\\\", \\\"__current_case__\\\": 1, \\\"sSkip\\\": > \\\"0\\\", \\\"sBestOption\\\": {\\\"snMaxBacktracks\\\": \\\"125\\\", > \\\"sBest\\\": \\\"noBest\\\", \\\"__current_case__\\\": 0}, > \\\"sAllValAligns\\\": \\\"noAllValAligns\\\", \\\! "sOffrate\\\": \\\"-1\\\", \\\"sSeedLen\\\": \\\"28\\\", \\\"sValAlign\\\": \\\"1\\\", \\\"sMaxFile\\\": \\\"False\\\"}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}", > "tool_version": "1.1.2", > "type": "tool", > "user_outputs": [] > > Is there a way to configure bowtie in galaxy to use the species automatically > associated with input file? I am currently having troubles dealing w/ > parameters that are defined in sub dictionaries defined in the tool state. > Any general approaches would be appreciated. > > Thanks! > Richard > > > > On Mon, Dec 5, 2011 at 6:32 PM, Dannon Baker <dannonba...@me.com> wrote: > > Richard, > > > > You're correct in that currently the workflow API affords no method for > > runtime modification of tool parameters, other than inputs. Depending on > > your needs, it might be feasible to have a few static workflows that you > > reuse often via the workflow API. If that isn't the case, and you think > > it'd be likely that you'll want to, say, programmatically modify parameters > > at runtime based on input data heuristics, then the API does need to be > > extended. The first place to look at would be > > lib/galaxy/web/controllers/workflow.py (run() method), to see the general > > approach to running workflows and providing parameters in the existing > > infrastructure. Then, see the API version at > > lib/galaxy/web/api/workflows.py (create() method) for a comparison. > > > > Let me know if you need any help with this at all. Once it's done, if > > you're willing, we'd certainly like to merge the changes back in and > > include the functionality in the base galaxy distribution. > > > > -Dannon > > > > > > > > > > On Dec 5, 2011, at 5:10 PM, Richard Park wrote: > > > >> Hello, > >> I was wondering what would be the best way to extend Galaxy's API > >> functionality to allow for runtime modification of tool parameters? > >> > >> I have successfully been able to run workflows programmatically using > >> the API, following the basic steps in: > >> scripts/api/execute_workflow.py. > >> scripts/api/example_watch_folder.py > >> > >> However, it is unclear to me, what would be the best way to run > >> workflows through API with specific parameters at various steps. > >> Should I generate new workflows for every workflow that requires > >> different parameters and upload this to galaxy? Or would it be better > >> to extend the API to allow for runtime parameter configuration? If > >> this is the case, any pointers on how to extend this would be greatly > >> appreciated. > >> > >> Thank you, > >> Richard Park > >> ___________________________________________________________ > >> 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/
