ZMap

Overview

ZMap is a genome browser written in C with the aim of providing fast access to high volume data. Data may be requested from a variety of disparate sources in parallel and cached locally allowing new tracks to be loaded or the view of current data adjusted without delay. Multiple views of the data may be presented and tracks configured for different levels of detail. ZMap interfaces seamlessly to the Seqtools package and forms part of the Otterlace genome annotation system used by the HAVANA group at the Wellcome Trust Sanger Institute.

ZMap may also be used as a standalone browser taking data either from external soruces or from simple GFF files held locally.

Download and Installation

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:
sudo apt-get install libcurl4-gnutls-dev libgtk2.0-dev libglib2.0-dev libreadline6-dev libsqlite3-dev

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"

Learn and Support

Supported platforms:

 

ZMap features

  • zoom
  • genomic and feature data cached locally
  • multiple views of the same or different regions
  • configurable display of tracks (show/hide)
  • compact, information rich display of alignments and other features
  • configurable display styles for different type of features
  • traffic light markers for incomplete homolgies
  • non-concensus splice markers
  • highlight evidence for transcripts
  • masking of EST's to remove duplication
  • automatic point and click interface to Blixem
  • 3-Frame Translation (3FT) of genomic DNA
  • highlight of 3FT showing frame shifts and split codons
  • powerful feature search functions
  • request and display selected sub-sequences ('request from mark')
  • navigator pane showing overall view of loaded sequence, allowing zoom to locus and visual scroll
  • pfetch selected features

Background:

ZMap is derived from FMap which was originally written as part of the AceDB genome database system. Version 0.1 involved an extensive re-write to take advantage of modern GUI toolkits and to separate them from AceDB to form this independent ZMap package. It can be used independently or with any other tool that outputs data in a suitable format - the currently supported file format is GFF v2 (GFF v3 will be supported in the near future).

Getting Started:

Run zmap --help to see usage information. ZMap can be run with a GFF file on the command-line or with a configuration file that sets up the data sources. A sample GFF file is provided in the examples directory; to try it, run ZMap like this:

zmap examples/features.gff

User manuals:

There is a user manual (thanks to Charles Steward) available here.

Help pages

Help pages are installed along with ZMap and can be accessed from the Help menu. There will be a link to the user manual from the help pages, if one is available.

 

http://www

License and Citation

ZMap is free software and is distributed under the terms of the GNU General Public License.

Please cite zmap by referring to the ZMap website

Contact

ZMap is maintained by the Annosoft team at the Sanger Institute.

If you have a bug or feature request please raise a ticket by emailing zmap@sanger.ac.uk

For any other enquires please email the Annosoft team

Authors

Sanger Contributors
Tool type
Screenshots
  • Whole Clone display
  • ZMap - split screen
  • ZMap - navigator overview
  • ZMap- track chooser
  • ZMap - marking a region
  • ZMap - context sensitive menus
  • ZMap - search facility
  • ZMap - alignment display
  • ZMap - 3 frame display

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