Downloading PhyloSift

SOFTWARE REQUIREMENTS:

PhyloSift runs on Unix-based operating systems (Linux distributions, Mac OS X).

A 64-bit operating system is required (PhyloSift will NOT work on a 32-bit operating system), since the binaries packaged with the pipeline scripts were compiled using a 64-bit system. PhyloSift relies on a number of other open source software packages (see About for citations). The precompiled version linked below (tarball archive) bundles most of these dependencies into a single downloadable package.

Although BioPerl and other packages come wrapped into the tarball archive, it may also be necessary to install several support packages on your local machine, including BioPerl, Bio::Phylo, and others.

INSTALLATION

Easy way (for most users):

Download the tar ball archive from:

http://edhar.genomecenter.ucdavis.edu/~koadman/phylosift/releases/phylosift_v1.0.1.tar.bz2

This compressed archive is the latest stable release of PhyloSift (currently v1.0.1, released 4/8/14).

Unzip this file within a Finder/Explorer window, or alternatively navigate to the directory where you downloaded the software and run the command:

tar -xvf phylosift_vX.X.X.tar.bz2

All pipeline files come prepacked in the tarball archive, and PhyloSift is ready to use once unzipped. The unzipped directory name will be appended with the date that the PhyloSift was originally compressed and packaged on our UC Davis servers.

**Note that PhyloSift is currently in active development at UC Davis, and we are improving the software functionality every day. The development branch (devel) on GitHub may contain additional features, but it may also contain bugs. If you are interested in using the devel version of PhyloSift, we package this code into an archive on a daily basis (installation procedure is the same as above): http://edhar.genomecenter.ucdavis.edu/~koadman/phylosift/devel/phylosift_latest.tar.bz2

The hard way (installing from the development repository–for power users):

Download and install Git from http://github.com/   OR if on debian/ubuntu run the following unix command :

sudo apt-get install git

To download PhyloSift, run the following command:

git clone git://github.com/gjospin/PhyloSift.git

UPDATING PHYLOSIFT

If running PhyloSift from a packaged release (i.e., you chose the “easy way”), simply download the newest tarball archive from the UC Davis Genome Center server.
If running PhyloSift from the development repository, run the following command :
   git update


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