Our lab is in the process of installing a local version of Galaxy on a
computer with the following specs:

- Mac Pro mid-2012
- OS X 10.8.3
- 2 2.4 GHz Intel Xeon Processors
- 6 cores per processor, 12 cores total
- 64 GB RAM

This installation is meant to be used by a single user. We followed
the instructions at http://wiki.galaxyproject.org/Admin/Get%20Galaxy
and now have a working version of Galaxy available at localhost:8080,
but we have a few questions before using it:

1. We want to use the NGS:Mapping tool 'Map with Bowtie for Illumina'
which requires 'bowtie (0.12.7) with bowtie indexes'. Do we simply
download the bowtie software, place it into
/Users/administrator/galaxy-dist/tools, restart Galaxy, and the tool
is available under NGS:Mapping ?

2. Continuing from question #1, does a type of 'package manager' exist
for automating the installation of tools and dependencies? Can
mercurial accomplish this or is this the purpose of the Tool Shed?

3. What is the purpose of the Galaxy-specific environment file and how
is it used?

4. We have two hard drives: drive1 and drive2. Galaxy is installed on
drive1 and our data files are on drive2. Will Galaxy know how to find
the location of our data files on drive2? Also, will Galaxy know how
to write the result of a job to drive2?

5. Does Galaxy come configured with an admin account and, if so, how
is it accessed?

6. Does Galaxy use as many hardware resources as possible to execute
each job (for example, all 12 cores)? If not, can it be configured to
do so?

Thank you for your help!
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