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Running assemble_trinity takes just one command. The script automatically generates the launcher scripts and submits them for you. There's no need to put assemble_trinity inside a launcher script (in fact, that won't work). To run a plain vanilla Trinity assembly without and special options, run this command at your command prompt:
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assemble_trinity -a <your_allocation> --no-ram-disk -l <R1_reads.fq> -r <R2_reads.fq> -o <output_directory>
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If you want to use Trinity options that assembly_trinity doesn't support yet, you can still use assemble_trinity to generate the list of launchers necessary to submit to TACC, then edit the *.sgeslurm files to add your desired options to the assembly. Just add the --no-run option to the assemble_trinity command. This will generate all the launchers, but will not submit them. Make any changes you desire, then submit all the launchers in sequence by simply running submit_launchers submission.list. (The file submission.list is a simple text list of the launcher files, and the submit_launchers script reads the list and submits the jobs in order, with commands to hold each job until the previous finishes.)
As of now (early November), assemble_trinity is only supported on Lonestar. It will probably work on Stampede, but we need to make some changes to take full advantage of Stampede.