Revision as of 12:05, 6 November 2012

Install Array Studio on Windows

Windows prerequisites: Microsoft .NET 2.0

From Internet Explorer (IE) browser, select (or copy) one of the two URLs (depending on the version chosen)

• Release version: http://www.omicsoft.com/software/ArrayStudio/ArrayStudio.application
• Beta version: http://www.omicsoft.com/software/ArrayStudioBeta/ArrayStudio.application

For Firefox or Chrome user, one needs to first install ClickOnce plugins.

• Plugin for FireFox:

https://addons.mozilla.org/en-US/firefox/addon/microsoft-net-framework-assist/

• Plugin for Chrome Plugin:

https://chrome.google.com/webstore/detail/eeifaoomkminpbeebjdmdojbhmagnncl

Install Array Server On Linux

Before Installation

• 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

• Install sqlite3, version 3.6.4 or higher is required.

• Install libgdiplus. 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/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

Install mono

We need to compile and install two versions of mono (both are required).

• mono-2.8.2 : for running the server
• mono-2.10.8 : for performing sequence alignment and other tasks

Note: The example given below is based on CentOS 6.

Installing mono-2.8.2

1. Remove old or existing version of mono (mono-runtime)

2. Download Mono 2.8.2

    wget -c  http://origin-download.mono-project.com/sources/mono/mono-2.8.2.tar.bz2

Note: For obtaining version 2.10.8, change the version number in the URL above. The bz2 file can be saved to a temporary location, e.g. ~/temp/

3. Compile and install. On the command line, type

    export PATH=/opt/mono-2.8.2/bin:$PATH
    export LD_LIBRARY_PATH=/opt/mono-2.8.2/lib:$LD_LIBRARY_PATH
    export PKG_CONFIG_PATH=/opt/mono-2.8.2/lib/pkgconfig:$PKG_CONFIG_PATH
    tar  jxvf   mono-2.8.2.tar.bz2
    cd  mono-2.8.2
    ./configure  --prefix=/opt/mono-2.8.2 --with-large-heap=yes  CXXFLAGS=-Wno-unused-but-set-variable CFLAGS=-Wno-unused-but-set-variable
    make
    make  install

Note:
(1) The location of mono installed is set by the option "--prefix" in the configure step, which can be changed to another location.
(2) When installing mono-2.10.8, replace "mono-2.8.2" with "mono-2.10.8" in commands above.

4. Test mono installation

     mono-test-install

5. Follow the similar steps to install the mono-2.10.8

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  http://www.omicsoft.com/software_update/OmicsoftUpdater.exe

Next, create an empty file named ArrayServerLinuxBeta.exe by typing

     touch ArrayServerLinuxBeta.exe

Then, type

     mono  OmicsoftUpdater.exe

Configuration Files

• ArrayServer.cfg

This file is required if this is a single server setup (i.e. no analytic server attached to this server), or the current server is used as a master server.

A sample ArrayServer.cfg for a single server setup.

A sample ArrayServer.cfg for a master server setup. In this example, a network drive folder has been mounted at the same path "/media/IData" on both the master and analytic servers.

Note: If you right click to download the sample files, it should be named as ArrayServer.cfg (not .txt).

A few key options are :

BaseDirectory

This will be the working directory of the array server, storing all the raw and prossessed data. Depending on the projects, it can take huge amount of disk space.

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).

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.

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.

• AnalyticServer.cfg

This file is required if the current server is an analytic server. Note that if you right click to download the sample files, it should be named as AnalyticServer.cfg.

A sample AnalyticServer.cfg for an analytic server setup.

Please follow the similar guideline above in setting the BaseDirectory and other related directory options.

Start Running Array Server

One can start the server by using the run-omicsoft.sh script (recommended), or start it directly as this.

For single server setup, run

     export PATH=/opt/mono-2.8.2/bin:$PATH
     cd /opt/array-server
     mono-sgen  ArrayServerLinuxBeta.exe > log &

For master-analytic server setup, start the master server first and then the analytic server by running the same command above (See also Master and Analytic Servers). The mono-sgen version 2.8.2 is required for running the servers. For other tasks, such as alignment and oshell, mono 2.10.8 is recommended.

Connect the server (through Array Studio or Array Viewer) by typing in the server (or master server) address (e.g., tcp://192.168.1.103:8065). In some cases, if you have problems in connecting to the server, please check the firewall settings on your computer.

NOTE: For additional information on server administration, such as stopping or updating array server, see Running Array Server in Linux

Install Array Server On Windows

Running Array Server in Windows

Test Your Installation

Add this small test bam file: Illumina.Paired.bam to genome browser Human37.3 (for instructions to create new genome browser, see New Browser).

Install Oshell

Install Oshell on Linux

Assume mono (version 2.10.8 preferred) has been installed. Here we install oshell in the home directory.

      mkdir ~/oshell
      cd ~/oshell
      wget -c  http://www.omicsoft.com/software_update/OmicsoftUpdater.exe
      touch oshell.exe
      mono OmicsoftUpdater.exe

One way to run oshell is as this (Usually you can wrap the commands below in a bash script).

      export PATH=/opt/mono-2.10.8/bin:$PATH
      export LD_LIBRARY_PATH=/opt/mono-2.10.8/lib:$LD_LIBRARY_PATH
      mono ~/oshell/oshell.exe --runscript   OmicSoftBaseDir  MyOShellScript  MyTempDir

Oshell script example

example.rna.pe.oscript: Oshell script for Paired end RNASeq alignment (attached).

Note that one has to modify this file to set the correct input and output file locations.

One can run the script as this,

     mono ~/oshell/oshell.exe  --runscript  ~/OmicsoftHome  example.rna.pe.oscript   ~/temp

Tips: oshell scripts can be obtained by clicking 'Show Script' button in Array Studio (right after the parameter specification).