Getting Started

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{{Tips|Also read [[Setting up ulimit for ArrayServer]]}}
{{Tips|Also read [[Setting up ulimit for ArrayServer]]}}

Revision as of 10:34, 21 January 2016


Install Array Studio on Windows

Windows prerequisites: Microsoft .NET 3.5

From Internet Explorer (IE) browser, open the following link:

For first time users, see How to activate your Array Studio.

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Install Array Server On Linux

Required Linux packages

Make sure you have some basic packages installed:

    yum install gcc gcc-c++ bison pkgconfig libtool libstdc++-devel \
       glib2-devel gettext make freetype-devel fontconfig-devel \
       libXft-devel libpng-devel libjpeg-devel libtiff-devel giflib-devel \
       ghostscript-devel libexif-devel libX11-devel
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Sqlite can be downloaded from: sqlite download. The tar.gz file is recommended for installation.

wget -c
tar zxvf sqlite-autoconf-3071401.tar.gz
sudo mv sqlite-autoconf-3071401 sqlite
cd sqlite
./configure --prefix=/opt/sqlite
make install

sqlite3  --version
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The mono libgdiplus package must be installed (either using yum, apt-get, or installing from source at libgdiplus). In addition, the mono config file must be edited to explicitly specify the location of

cd /opt
tar  jxvf   libgdiplus-2.10.tar.bz2
cd  /opt/libgdiplus-2.10
./configure  --prefix=/opt/libgdiplus-2.10
make  install

If installing from source, you may need to add the "/libgdiplusPrefix/lib" to the shared library search paths, and check to make sure libgdiplus library is on the shared library search paths. To check, type

 $ ldconfig -p | grep libgdiplus (libc6,x86-64) => /opt/libgdiplus-2.10/lib/

Here the libgdiplus is installed at "/opt/libgdiplus" and has been set correctly. If not, one way to add it to the shared library path is by doing this (with root privilege),

 echo "/opt/libgdiplus/lib" > /etc/

If installing from yum, it may be necessary to additionally install the following:

yum install libgdiplus
yum install libungif libungif-devel

Edit mono config to point to libgdiplus

To connect mono and libgdiplus, modify the following config file: /MonoPrefix/etc/mono/config: Add the following line at the end of the file before </configuration>

<dllmap dll="gdiplus.dll" target="/opt/libgdiplus-2.10/lib/"/>

Further details can be found here, including a description of the error message if this is improperly performed.

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Setting ulimit

Make sure the ulimit for "max user processes" and "open files" are set to the max value: 65536. You can check the values by typing: ulimit -a.

$ ulimit -a
core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 0
file size               (blocks, -f) unlimited
pending signals                 (-i) 515184
max locked memory       (kbytes, -l) 64
max memory size         (kbytes, -m) unlimited
open files                      (-n) 65536
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) 10240
cpu time               (seconds, -t) unlimited
max user processes              (-u) 65536
virtual memory          (kbytes, -v) unlimited
file locks                      (-x) unlimited

Modify ulimit in two config files following ulimit setup wiki.

Tips.pngAlso read Setting up ulimit for ArrayServer
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Tips.pngFor Linux kernels prior to 3.10.0-327 we recommended to use mono 2.10.9 in Linux. For newer kernels, mono4.0.4 is required.
Install mono2
  • Download Mono 2.10.9
    cd /opt
    wget -c

The bz2 file can be saved to a temporary location, e.g. ~/temp/

  • Extract and modify certificate if necessary
    tar  jxvf   mono-2.10.9.tar.bz2
    cd  /opt/mono-2.10.9

For mono 2.10.9, it is recommended to modify X509Certificate to the latest standard.

  • Compile and install. On the command line, type
    cd  /opt/mono-2.10.9
    ./configure  --prefix=/opt/mono-2.10.9 --with-large-heap=yes
    make  install


  • The location of mono installed is set by the option "--prefix" in the configure step, which can be changed to another location.
  • The option --with-large-heap=yes is to enable support for GC heaps larger than 3gb, which is required for NGS alignment, as well as some Array Server functions)

Double check mono installation and version

ls /opt/mono-2.10.9/bin/mono* -all
/opt/mono-2.10.9/bin/mono --version
/opt/mono-2.10.9/bin/mono-sgen --version
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Install Array Server

Download Array Server

Assume we would like to install the Array Server under the directory /opt

On command line, type
     mkdir /opt/array-server
     cd    /opt/array-server
     wget -c
Next, create an empty file named ArrayServerLinuxBeta.exe by typing
     touch ArrayServerLinuxBeta.exe
Then, type
     cd /opt/array-server
     /opt/mono/bin/mono  ./OmicsoftUpdater.exe
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Configuration Files

Download configuration template

cd /opt/arrayserver

Admin will have to modify three important configuration files based on downloaded template:

  • ArrayServer.cfg is the key configuration file. A few important options are :
    • Port, Port2 and Port3 define the port number for data communication between ArrayStudio client and ArrayServer
    • BaseDirectory: this will be the working directory of the array server, storing all the raw and possessed data. Depending on the projects, it can take huge amount of disk space.
    • OmicsoftDirectory: This directory can sit locally or on a network drive. All the reference genomes, gene models, Affymetrix CDF files, log files, etc. are stored in this folder.
    • TempDirectory: This should be a local directory (i.e. NOT a network drive) for fast read and write access. It can take twice the size of an unzipped fastq file in some NGS tasks (we would suggest use a drive with at least 100GB storage).
    • The Folder section defines additional local or network folders monitored and available for access by array server users.
    • For a full list of options, see ArrayServer.cfg for more details.
    • For master-analytic server setup, please read Master Server and Analytic Server for more details.
  • default.template: it defines project level meta data, such as requiring project title, and list organism. Admin can customized the project meta based on this template file and even enforce controlled vocabulary. For first time setup, the default values we prepared should be good to go. Admin can further customized based on the understanding of default.template wiki article.
  • sample.template: it defines sample level meta data, such as requiring users to fill organism and tissue for each samples in sample registration. Admin can customized the sample meta based on this template file and even enforce controlled vocabulary. For first time setup, the default values we prepared should be good to go. Admin can further customized based on the understanding of sample.template wiki article.
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Start Running ArrayServer

Once the ArrayServer is ready and running, each user can connect to ArrayServer using the server tab in their ArrayStudio client:


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Install Array Server On Windows

Running Array Server in Windows

Test Your Installation

Please watch the video tutorial for server analysis basics and test the ArrayServer connectivity.

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Related Articles

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