Mira source files can be found at /home/scott/Downloads/mira-3.2.1; these include demos (see the "minidemo" directory).
Visit Mira's sourceforge documentation.
Running mira is a bit odd - you use either "condensed" or "extensive" command line switches, but you never specify input files. Input files must follow a prescribed naming convention, set by the job name (which you pick) and the type of data ("454", "solexa", "solid", etc.)
If you're assembling 454 data (ESPECIALLY mate-pair data), you must use the sff_extract utility to convert the sff data into the format mira likes. Note that ALL your 454 reads must be in one file set (.fasta/.fasta.qual). If you have multiple library sizes, you must create an xml traceinfo file to specify each read's insert size.
Installation notes for the future:
On installation, mira required BOOST installed as: sudo ./bootstrap.sh --with-libraries=all --prefix=/usr/local, followed by sudo ./bjam threading=multi install, then mira needed: ./configure --with-boost-libdir=/usr/local/lib, followed by make/make install.
