I am looking to build and compare the transcriptomes of several plant species. In order to do this, we have obtained the raw reads from Illumina and we are looking to use trinity to put the information together.
We have no local computational power, so we submitted and were granted access to XSEDE's Stampede system. We also requested Blacklight, but didnt seem to be granted access.
In short, I guess I need to know how to prepare a script for the execution of trinity within this system. Blacklight had a very simple, easy-to-follow set of instructions to execute trinity, but stampede has nothing that I can find.
So far, I have the heading information: JobID, defining sterr and stdout, etc. Im am unsure about how to define the number of tasks or the wall time, but I may be able to figure that out.
Essentially I don't know what to do next. I have included 'module load application/version and the command to execute trinity itself. Is there anything else I need? For Blacklight I had to set a few variables and 'cd' into a working directory. I'm not seeing that for Stampede.
Am I missing something, or do I have it so far? I would hate to mess something up and burn through our allocation SUs, because we have several samples to analyze and startup allocation is probably insufficient...
Thanks!
We have no local computational power, so we submitted and were granted access to XSEDE's Stampede system. We also requested Blacklight, but didnt seem to be granted access.
In short, I guess I need to know how to prepare a script for the execution of trinity within this system. Blacklight had a very simple, easy-to-follow set of instructions to execute trinity, but stampede has nothing that I can find.
So far, I have the heading information: JobID, defining sterr and stdout, etc. Im am unsure about how to define the number of tasks or the wall time, but I may be able to figure that out.
Essentially I don't know what to do next. I have included 'module load application/version and the command to execute trinity itself. Is there anything else I need? For Blacklight I had to set a few variables and 'cd' into a working directory. I'm not seeing that for Stampede.
Am I missing something, or do I have it so far? I would hate to mess something up and burn through our allocation SUs, because we have several samples to analyze and startup allocation is probably insufficient...
Thanks!