Those prior tools are no longer available at http://usegalaxy.org (the Trinity suite). Perhaps the tools in NGS: Du Novo will meet your needs. Or if the goal is to create RNA-seq assembled transcripts for expression analysis (note: this is not true assembly in the sense of creating in fasta contigs), tools in the group NGS: RNA Analysis might be what you are looking for (Cufflinks, Sailfish). If not, the Tool Shed has other assembly tool options for use in a local or cloud Galaxy - review the category "Assembly". Should your ideal target tool not be yet wrapped for Galaxy, it could be, if you have resource to do that.
The link-outs from the wiki above include many more details for Admin functions, including how to set up a local instance to install tools (and the tools used to create built-in data indexes, e.g. Data Managers) from the Tool Shed. The ability to install tools configured by default on a Cloudman instance plus includes a basic set of the most popular genomes already indexed for many tools.
And just in case it is of interest, the 101 help and tutorials linked from the top of this page can aid in learning Galaxy from a scientific perspective. https://wiki.galaxyproject.org/Support
Take care, Jen, Galaxy team