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Installation of iRODS 4.1

This document describes how to install iRODS4.1 on a Ubuntu machine with a postgresql 9.3 database as iCAT.

Environment

Ubuntu 14.04 server

##Prerequisites

1. Update and upgrade if necessary

apt-get update
apt-get upgrade

2. Set firewall

sudo apt-get install iptables-persistent
  • edit /etc/iptables/rules.v4
*filter
:INPUT ACCEPT [0:0]
:FORWARD ACCEPT [0:0]
:OUTPUT ACCEPT [4538:480396]
-A INPUT -m state --state INVALID -j DROP
-A INPUT -p tcp -m tcp ! --tcp-flags FIN,SYN,RST,ACK SYN -m state --state NEW -j DROP
-A INPUT -f -j DROP
-A INPUT -p tcp -m tcp --tcp-flags FIN,SYN,RST,PSH,ACK,URG NONE -j DROP
-A INPUT -p tcp -m tcp --tcp-flags FIN,SYN,RST,PSH,ACK,URG FIN,SYN,RST,PSH,ACK,URG -j DROP
-A INPUT -p icmp -m limit --limit 5/sec -j ACCEPT
-A INPUT -m state --state RELATED,ESTABLISHED -j ACCEPT
-A INPUT -p tcp -m tcp --dport 22 -j ACCEPT
-A INPUT -p tcp -m tcp --dport 80 -j ACCEPT
-A INPUT -p tcp -m tcp --dport 1248 -j ACCEPT
-A INPUT -p tcp -m tcp --dport 1247 -j ACCEPT
-A INPUT -p tcp -m tcp --dport 20000:20199 -j ACCEPT
-A INPUT -p tcp -m tcp --dport 4443 -j ACCEPT
-A INPUT -p tcp -m tcp --dport 443 -j ACCEPT
-A INPUT -p tcp -m tcp --dport 5432 -j ACCEPT
-A INPUT -j LOG
-A INPUT -j DROP
COMMIT
  • edit /etc/iptables/rules.v4
*filter
:INPUT ACCEPT [0:0]
:FORWARD ACCEPT [0:0]
:OUTPUT ACCEPT [0:0]
-A INPUT -j DROP
COMMIT 
/etc/init.d/iptables-persistent start

3. Create admin user for machine and irods

adduser irodsadmin

(Optional)

To change the user name (useful when working with VM templates)

usermod -l alice irodsadmin 
groupmod -n alice irodsadmin
usermod -d /home/alice -m alice
usermod -c alice alice

Add newuser to sudoers

4. Install postgresql

sudo apt-get install postgresql

5. Set localhost name

hostnamectl set-hostname new-hostname
echo "IPa.ddr.ess new-hostname" >> /etc/hosts

Installing iRODS

6. Configure and create porstgresql database

sudo su - postgres
psql
CREATE DATABASE "ICAT";
CREATE USER irods WITH PASSWORD 'irods';
GRANT ALL PRIVILEGES ON DATABASE "ICAT" to irods;
\q
exit

7. Download iand install iRODS packages

wget ftp://ftp.renci.org/pub/irods/releases/4.1.6/ubuntu14/irods-icat-4.1.6-ubuntu14-x86_64.deb
wget ftp://ftp.renci.org/pub/irods/releases/4.1.6/ubuntu14/irods-database-plugin-postgres-1.6-ubuntu14-x86_64.deb
sudo dpkg -i irods-icat-4.1.6-ubuntu14-x86_64.deb irods-database-plugin-postgres-1.6-ubuntu14-x86_64.deb

This will exit with the following error message:

dpkg: dependency problems prevent configuration of irods-icat:
...
Errors were encountered while processing:
 irods-icat
 irods-database-plugin-postgres

The dependencies will be fixed by executing:

sudo apt-get -f install

8. Configuring iRODS

  • First we create the irods vault (where data put into iRODS will be physically stored).
sudo mkdir /irodsVault

sudo chmod 777 /irodsVault
  • Configure iRODS
sudo /var/lib/irods/packaging/setup_irods.sh
iRODS servers zone name [tempZone]: alicetestZone
iRODS Vault directory [/var/lib/irods/iRODS/Vault]: /irodsVault
iRODS servers zone_key [TEMPORARY_zone_key]: alicetest_zone_key
iRODS servers administrator username [rods]: alice
Database servers hostname or IP address: localhost

9. Login to iRODS

iinit
Enter the host name (DNS) of the server to connect to: localhost
Enter the port number: 1247
Enter your irods user name: alice
Enter your irods zone: alicetestZone
  • Test whether you can list your iRODS directory
ils