Getting Started

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Install OmicSoft Studio on Windows

Windows prerequisites: Microsoft .NET 4.5

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

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Most users find that Internet Explorer is the best browser to launch OmicSoft Studio Launcher the first time.

However, some have found that Internet Explorer does not work, but Google Chrome successfully runs.


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

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Install OmicSoft Studio on Mac

Please follow these instructions to install Array Studio on Mac.

OmicSoft Studio Firewall Permissions

In order for OmicSoft Studio to function properly, certain connections must be allowed:

In addition, the following ftp URLs should be open (if possible):

Finally, the following external resource URLs should be open (hopefully these are already opened)

Install Array Server On Linux

Tips.pngMost of our clients run ArrayServer on a Linux machine, which can enable HPC cluster and external tool integration.

Prerequisites

For hardware requirements and storage needs, please see Hardware_/_Software_requirements_for_Array_Server

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

The user can either use an sqlite-based database for Array Server, or Oracle. If using Sqlite, version 3.6.4 or higher is required. It's recommended to install Sqlite with the same prefix as that used to install mono.

Sqlite can be downloaded from: sqlite download. The tar.gz file is recommended for installation. 

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

sqlite3  --version

After installation, specify SqlitePath in either ArrayServer.cfg or AnalyticServer.cfg

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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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Mono

Install Mono 4.0.4
  • Download Mono 4.0.4 
    wget -c http://download.mono-project.com/sources/mono/mono-4.0.4.1.tar.bz2

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

  • Compile and install. On the command line, type 
    tar jxvf mono-4.0.4.1.tar.bz2
    cd  mono-4.0.4
    ./configure  --prefix=/opt/mono-4.0.4 --with-large-heap=yes
    make
    make  install

Note:

  • 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-4.0.4/bin/mono* -all
/opt/mono-4.0.4/bin/mono --version
/opt/mono-4.0.4/bin/mono-sgen --version


Add appropriate SSL certificates

Mono does not store any valid SSL certificates by default for HTTPS web sites, so you must manually accept the certificate for https://*.omicsoft.com

Run 

certmgr --ssl https://resources.omicsoft.com

and accept the certificates as you are prompted.

Learn more on this page.

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Libgdiplus

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 libgdiplus.so. 

cd /opt
wget http://download.mono-project.com/sources/libgdiplus/libgdiplus-2.10.tar.bz2
tar  jxvf   libgdiplus-2.10.tar.bz2
cd  /opt/libgdiplus-2.10
./configure  --prefix=/opt/libgdiplus-2.10
make
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
     libgdiplus.so (libc6,x86-64) => /opt/libgdiplus-2.10/lib/libgdiplus.so

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/ld.so.conf.d/libgdiplus.conf
 ldconfig

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/libgdiplus.so"/>

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

Troubleshooting Libgdiplus errors:

Libgdiplus compile error

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Installing and Configuring Array Server

For hardware requirements and storage needs, please see Hardware_/_Software_requirements_for_Array_Server

Configure your Linux environment

Open Firewall Ports

The ArrayServer machine will need to allow certain connections to occur from Array Studio.

For example, if the ArrayServer.cfg file is configured to allow connections to 

(ArrayServer.cfg)
...
port=8064
port2=8065
port3=8066
DataPortBegin=50801
DataPortEnd=50900
...

(see below for details),

Then firewalld would need to be changed as follows: 

firewall-cmd --permanent --add-port=8064-8066/tcp
firewall-cmd --permanent --add-port=50801-50900/tcp
firewall-cmd --reload

Download Array Server

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

On command line, type 
     mkdir /opt/arrayserver
     cd    /opt/arrayserver
     wget -c  https://resources.omicsoft.com/software_update/OmicsoftUpdater.exe
Next, create an empty file named ArrayServerLinuxBeta.exe by typing 
     touch ArrayServerLinuxBeta.exe
Then, type 
     cd /opt/arrayserver
     /opt/mono/bin/mono  ./OmicsoftUpdater.exe
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Download and Update Configuration Files

Download configuration template 

cd /opt/arrayserver
wget https://resources.omicsoft.com/software/ArrayServer/ArrayServerConfigTemplate.zip
unzip ArrayServerConfigTemplate.zip


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. Make sure to open these ports on firewall.
    • DataPortBegin and DataPortEnd define the port range for Threaded Ftp data transfer. Make sure to open the port range on firewall.
    • 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 customize the project meta data 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 customize 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 customize 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:

ConnectServer.png

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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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