Getting Started
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Revision as of 11:05, 6 November 2012
Contents |
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:
- Plugin for Chrome Plugin:
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.
- BaseDirectory
- 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).