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Supported platforms

Our primary supported platform is Ubuntu 14.04 (64-bit). SeqTools is well tested and in daily use on this architecture. It is also tested frequently on Mac OS X. It should also work on several other platforms, as listed below, but is less thoroughly supported.

• Linux – Ubuntu 14.04 (64-bit) – primary supported architecture
• Linux – other
• Mac OS X (Intel)
• Windows (under Cygwin)
• Other platforms (using VirtualBox)
• FreeBSD (in the ports).

Note that the SeqTools package provides some optional tools that can be called from within ZMap to give a more detailed nucleotide-level view of alignments. It is not required to run ZMap, and it can be installed at a later date if you don’t want to install it initially.

Production release

This is the recommended release for most users. It is well-tested, stable and supported code.

The latest versions of seqtools and zmap are available from here.

Development build

Reasonably stable development code, which contains most of the latest features.

The latest development versions are here.

Overnight build

Experimental code; not guaranteed to be stable (or even to compile). Should only be used if you require the very latest changes.

Daily builds are to be found here.

Installation:

Linux:

• Install the following pre-requisites. This is most easily done using your system package manager (e.g. synaptic on Ubuntu, available from the System/Administration menu). Depending on your system, packages may be named differently or additional packages may be required. In this case the ./configure step below will fail and you will need to install the required package before running it again. If you cannot find a package it can be useful to search for just the main part of the name excluding numbers/dashes, e.g. “gtk” or “libgtk” rather than “libgtk2.0-dev”.

libcurl4-gnutls-dev
libgtk-2.0-dev
libglib-2.0-dev
libreadline6-dev
libsqlite3-dev      (optional)

• In the terminal, unpack the downloaded zmap tar file using the following command, where XXX is the version you downloaded:

tar -xf zmap-XXX.tar.gz

• To install in the default location (usually /usr/bin):

cd zmap-XXX
./configure
make
make install

• Optionally, repeat the process for SeqTools if you want the Blixem and Dotter programs to be available from within ZMap (these can be installed at a later date if you are not sure).

To install in a different location, or for help with dependencies, see the “tips” section below. For more detailed instructions, see the INSTALL file in the source code.

MacOSX:

• Install the following pre-requisites. We strongly recommend that you use MacPorts to install these packages as this will also install any dependencies for you.

curl
gtk2
glib2
readline
sqlite3 (optional)

• In the terminal, unpack the downloaded zmap tar file using the following commands, where XXX is the version you downloaded:

tar -xf zmap-XXX.tar.gz

• To install in the default location (usually /opt/local/bin):

cd zmap-XXX
./configure
make
make install

• Optionally, repeat the process for SeqTools if you want the Blixem and Dotter programs to be available from within ZMap (these can be installed at a later date if you are not sure).

To install in a different location, or for help with dependencies, see the “tips” section below. For more detailed instructions, see the INSTALL file in the source code.

Windows / Other platforms:

ZMap cannot currently run natively on Windows. However, it can be installed and run in a virtual machine (VM) using VirtualBox. It should also be possible to install ZMap using Cygwin (which provides a Linux-like environment on Windows). The VM uses more disk space and memory, but is likely to be more robust because it can emulate our primary supported architecture.

VirtualBox (all platforms)

• Download and install VirtualBox.
• Download the 64-bit Ubuntu 14.04 image.
• Open VirtualBox and create a new VM, using the Ubuntu 14.04 image.
• Start the VM and go through the Ubuntu installation procedure.
• Install the guest additions (from the Devices menu, select “Insert Guest Additions CD image…”).
• Restart the VM to apply the changes.
• You should then be able to install ZMap by following the standard Linux instructions above. You can type the following in a Terminal to install the pre-requisites:

More detailed instructions are available here.

Cygwin (Windows only)

• From the Cygwin website, download setup-x86.exe (or setup-x86_64.exe if you have a 64-bit machine).
• Run the setup program, accepting all the default options. You will need to choose a mirror on the Choose Download Site page (e.g. cygwin.mirror.constant.com).
• On the Select Packages page, select these packages:

Devel/gcc-core
Devel/gcc-g++
Devel/libsqlite3-devel  (optional)
Devel/make
Devel/pkg-config
Editors/nano            (optional)
Libs/libcurl-devel
Libs/libglib2.0-devel   **also tick SOURCE checkbox**
Libs/libgtk2.0-devel    **also tick SOURCE checkbox**
Libs/libreadline-devel  (or Libs/readline)
Web/wget                (optional)
X11/xinit

• When installation is complete, open the Cygwin terminal and type the following commands, replacing XXX with the version of ZMap you want to download.

wget ftp://ftp.sanger.ac.uk/pub/resources/software/zmap/PRODUCTION/zmap-XXX.tar.gz
tar -xf zmap-XXX.tar.gz
cd zmap-XXX
./configure
make
make install

• Optionally, repeat the process for SeqTools if you want the Blixem and Dotter programs to be available from within ZMap (these can be installed at a later date if you are not sure).
• You need to start an “xterm” terminal to run the SeqTools programs from. This can be done
  by typing the following in the Cygwin terminal:

export DISPLAY=:0; startxwin -- -emulate3buttons &

• Alternatively, to start the xterm automatically each time you open the Cygwin terminal,
  you can add the above command to your bash profile. To do this, type the following
  in the Cygwin terminal (you only need to do this once):

echo "DISPLAY=:0; startxwin -- -emulate3buttons &" >> ~/.bash_profile

For further help, see the “tips” section below or the INSTALL file in the source code.

Tips:

• You may need to run make install using sudo if you do not have root privileges, i.e.:

sudo make install

• Alternatively, to install to a different location (e.g. one not requiring root privileges), use the –prefix argument when you run ./configure. For example, the following command would set the install location to foo/bar in your home directory:

./configure --prefix=~/foo/bar

• If GTK+ is not in the default location then you may need to pass its location to the configure script. GTK+ is usually installed in /usr/lib, /usr/local/lib, /opt/lib or /opt/local/lib. If GTK+ is in e.g. /opt/local/lib then you would call configure with the following arguments:

./configure PKG_CONFIG_PATH=/opt/local/lib/pkgconfig LDFLAGS="-Xlinker -rpath -Xlinker /opt/local/lib"