Installation

PANDAseq binaries can be installed on some platforms and the source should compile on any sufficiently POSIX-ish system.

#Ubuntu Linux Ubuntu users, in the terminal, can install PANDAseq with the command:

sudo apt-add-repository ppa:neufeldlab/ppa && sudo apt-get update && sudo apt-get install pandaseq

It will be automatically updated as new versions are released. After an operating system upgrade, this repository, ppa:neufeldlab must be re-enabled using Synaptic, Muon, or by editing /etc/apt/sources.list.d/neufeldlab-ppa-*.list

#Fedora Linux Fedora users, in the terminal, can install PANDAseq with the command:

yum-config-manager --add-repo http://neufeldserver.uwaterloo.ca/~apmasell/pandaseq-rpms && yum install pandaseq

It will be automatically updated as new versions are released. #Windows Windows users can download the PANDAseq Windows binary (ZIP) and decompress it into a location of their choice. This version does not include the ability to create validation modules. Simply decompress the archive to an appropriate folder and invoke pandaseq.exe from the command prompt.

#MacOS Packages are available for 64-bit Intel MacOS X (PKG). For older systems, packages can be built from source.

#From Source To build the source, zlib, bzip2, and libtool (include libltdl) are required.

• Debian/Ubuntu: Install the dependencies using apt-get install zlib1g-dev libbz2-dev libltdl-dev libtool. It is worth noting that all the packing instructions are available to use debuild to build a binary package for your platform.
• RedHat/Fedora: Install the dependencies using yum install zlib-devel bzip2-devel libtool-ltdl-devel libtool. It is worth noting that all the packing instructions are available to use rpmbuild to build a binary package for your platform.
• MacOS+Fink: Install dependencies using fink install libtool bzip2
• MacOS+MacPort: Install dependencies using sudo port install libtool bzip2
• Windows+Cygwin: Install the packages libbz2-devel, zlib-devel, and libtool in addition to the standard development packages.
• Windows+MinGW: Prepare the dependencies appropriately for your MinGW installation. When building on MinGW, the configure script will attempt to link statically to create a more portable executable.

Building the source should be a matter of:

git clone http://github.com/neufeld/pandaseq.git/
cd pandaseq
./autogen.sh && ./configure && make && sudo make install

as is appropriate for your platform.

Building Modules

PANDAseq can build modules to help validate sequences. The tool pandaxs is provided to help build them. It assumes that the current platform would be capable of building the package. For the Debian/Ubuntu package, pandaxs is in a separate development package, pandaseq-dev. If run as root, pandaxs will install the module.