Hello Jubao, In the future, please direct questions like this to galaxy-dev@bx.psu.edu. Some Galaxy tools use 3rd party components. See our Tool Dependencies page at http://bitbucket.org/galaxy/galaxy-central/wiki/ToolDependencies for a list. This page is being updated with new tool dependencies which include: bowtie http://sourceforge.net/projects/bowtie-bio/files/bowtie/ bwa http://sourceforge.net/projects/bio-bwa/files/bwa-0.5.3.tar.bz2/download fastx_toolkit http://hannonlab.cshl.edu/fastx_toolkit/ samtools http://sourceforge.net/projects/samtools/files/ Greg Von Kuster Galaxy Development Team Jubao Duan wrote:

Greg,

I installed Galaxy locally, everything seemed OK, but some tools are not there when I run the galaxy, e.g., bowtie mapping. Here was how I installed it:

1. Get the latest copy from the repository:

The latest source code can be downloaded from the anonymous†Mercurial <http://www.selenic.com/mercurial/wiki/>†repository with this command:

1 <http://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy#cl-1>

% hg clone http://www.bx.psu.edu/hg/galaxy galaxy_dist

Any comments?

Jubao Duan