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Install Array Studio on Windows
Windows prerequisites: Microsoft .NET 3.5
From Internet Explorer (IE) browser, open the following link:
For Firefox or Chrome user, one needs to first install ClickOnce plugins.
- Plugin for FireFox:
- Plugin for Chrome Plugin:
For first time users, see How to activate your Array Studio.
Install Array Server On Linux
- 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
- 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
Also, 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
- Download Mono 2.10.9
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 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
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://omicsoft.com/software_update/OmicsoftUpdater.exe
- Next, create an empty file named ArrayServerLinuxBeta.exe by typing
- Then, type
Download configuration template
cd /opt/arrayserver wget http://omicsoft.com/software/ArrayServer/ArrayServerConfigTemplate.zip unzip ArrayServerConfigTemplate.zip
- 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 :
- 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.
- 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).
- 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.
- 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.
A sample sample.template file.
A sample default.template file.
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-2.10.9/bin:$PATH cd /opt/array-server mono-sgen ArrayServerLinuxBeta.exe > log &
- For master-analytic server setup, start the master server first and then the analytic server by running the same command above (See also Master and Analytic Servers).
- Connect the server (through Array Studio or Array Viewer) by typing in the server (or master server) address (e.g., tcp://192.168.1.103:8065). In some cases, if you have problems in connecting to the server, please check the firewall settings on your computer.
NOTE: For additional information on server administration, such as stopping or updating array server, see Running Array Server in Linux
Install Array Server On Windows
Test Your Installation
Install OShell on Linux
- Assume mono (version 2.10.9 preferred) has been installed in /opt/mono-2.10.9/ (see mono installation help). Here we install oshell in the home directory.
mkdir ~/oshell cd ~/oshell wget -c http://omicsoft.com/software_update/OmicsoftUpdater.exe touch oshell.exe /opt/mono-2.10.9/bin/mono OmicsoftUpdater.exe
- One way to run oshell is as this (Usually you would wrap the commands below in a bash script).
export PATH=/opt/mono-2.10.9/bin:$PATH export LD_LIBRARY_PATH=/opt/mono-2.10.9/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.
Note that one has to modify this file by setting 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
For details about OShell, see OShell User Guide.
Tips: OShell scripts can be obtained by clicking "Show Script" button in Array Studio (right after the parameter specification).