Creating a shared system-wide PhyloSift installation

If you are using a Mac or Linux system shared among many users, each of whom will be running phylosift, it is possible to install a single copy of the software and the database to be shared by all users.

Perhaps the easiest way to do this would be to download and unpack phylosift to a shared storage directory such as /usr/local or /opt. This will need to be done by someone with administrator privileges, possibly via sudo or su. For example:

cd /usr/local
sudo tar xjf phylosift_v1.0.2.tar.bz2

It is then necessary to edit the phylosiftrc file to specify that the phylosift databases should be stored in a shared location. This can be done with your favorite editor, e.g. vim or emacs or gedit or TextEdit or TextWrangler:

vim /usr/local/phylosift_v1.0.2/phylosiftrc

The following two lines should be uncommented:

# $marker_path=””;
# $ncbi_path=””;

and changed to:

$marker_path=”/usr/local/share/phylosift”;
$ncbi_path=”/usr/local/share/phylosift”;

Finally, to finish the setup on a shared system, run phylosift once with administrator privileges so it can download and index the database:

sudo /usr/local/phylosift_v1.0.2/bin/phylosift \ all /usr/local/phylosift_v1.0.2/tutorial_data/HMP_1.fastq.gz

Now when other users of the system want to run phylosift, they can do so from the shared path:

/usr/local/phylosift_v1.0.2/bin/phylosift all my_data.fastq.gz

When set up in this manner, the administrator takes sole responsibility for managing the phylosift installation, including the installation of any database updates or new phylosift releases. Users will not have write access to the database.