The following tools have been eliminated from the distribution:
Map with Bowtie for Illumina, Map with Bowtie for SOLiD, Lastz,
and Lastz paired reads. The tools are now available in the
repositories named bowtie_wrappers, bowtie_color_wrappers, lastz,
and lastz_paired_reads from the main Galaxy tool shed at
http://toolshed.g2.bx.psu.edu, and will be installed into your
local Galaxy instance at the location discussed above by running
the following command.