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[[Category: Published in 2016]]
[[Category: ArrayServer Installation]]
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{{Install Array Studio}}
==Array Studio Firewall Permissions==
In order for Array Studio to function properly, certain connections must be allowed:

* http://www.arrayserver.com:443 (primary license activation server)
* http://omicsoft.com:443
** Note: port 443 is normally HTTPS, so IT departments may need to compensate for our HTTP traffic on this port

* http://onlinebas.omicsoft.com:80 (streaming data from Omicsoft, for legacy clients)
* http://onlinebas.qiagenbioinformatics.com:80 (streaming data from OmicSoft for modern clients)
* http://omicsoft.com/* (downloading software and other datasets from OmicSoft)
* http://www.omicsoft.net:80 (downloads land data from OmicSoft via HTTP streaming)

In addition, the following ftp URLs should be open (if possible):
* ftp://ftp.omicsoft.com
* ftp://ftp.arrayserver.com

Finally, the following external resource URLs should be open (hopefully these are already opened)
* https://www.ncbi.nlm.nih.gov/*
* http://www.ncbi.nlm.nih.gov/*
* http://eutils.ncbi.nlm.nih.gov/*
* https://eutils.ncbi.nlm.nih.gov/*
* ftp://ftp-trace.ncbi.nih.gov/*
* ftp://ftp.ncbi.nih.gov/*
* ftp://ftp.sra.ebi.ac.uk/*
* ftp://ftp.ebi.ac.uk
* http://www.ebi.ac.uk/*

== Install Array Server On Linux ==
{{Tips|Most of our clients run ArrayServer on a Linux machine, which can enable [[Setup ArrayServer in Cluster|HPC cluster]] and [[External Script Integration|external tool integration]].}}
===Prerequisites===
==== Required Linux packages ====
{{LinuxLibraryRequirement}}
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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. 

{{InstallSqlite}}

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

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==== Setting ulimit ====
{{SetUpUlimit}}

{{Tips|Also read [[Setting up ulimit for ArrayServer]]}}
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====Mono====
{{InstallMono}}
{{InstallMono404}}
{{InstallMono481}}
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==== Libgdiplus ====
{{InstallLibgdiplus}}

=====Troubleshooting Libgdiplus errors:=====

[[Libgdiplus complie error|Libgdiplus compile error]]

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=== Installing and Configuring 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  http://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 http://omicsoft.com/software/ArrayServer/ArrayServerConfigTemplate.zip
 unzip ArrayServerConfigTemplate.zip

{{ConfigArrayServer}}

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==== Start Running ArrayServer ====
* For first time admin, you can use [[Typical way to update/restart ArrayServer]]. Basically, it uses mono-sgen to run 
* For advanced admin, server can be maintained using crontab and shell script such as [[Run-omicsoft.sh]]

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

[[image:ConnectServer.png]]

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== Install Array Server On Windows ==
[[Running Array Server in Windows]]

== Test Your Installation ==
Please watch the [[Getting Started With Server Analysis|video tutorial for server analysis basics]] and test the ArrayServer connectivity.
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== Related Articles ==
*[[Getting Started With Server Analysis]]
*[[Running Array Server in Windows]]
*[[Master Server and Analytic Server]]
*[[Oshell|Get started with Oshell]]
*[[Hardware_/_Software_requirements_for_Array_Server|Hardware and Software Requirements for ArrayServer]]
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