Installation of Collector version 1.5.0
July 2017


Before you start
----------------
You need to have installed in your system

- Java Development Kit 8 (Oracle JDK7)

   If you don't have this software installed you can download the latest version from here:

      http://www.oracle.com/technetwork/java/javase/downloads/index.html

   The easiest way to install is to download the tgz file and extract it to a suitable place (for example /opt).

   Alternatively, you can download a version of Collector with a bundled 64bit JDK distribution

- PostgreSQL 8.4 or higher

   If you don't have this version installed you can download it from here:

      http://www.enterprisedb.com/products-services-training/pgdownload

   The easiest way is to use the graphical installer. It installs postgresql, configures it to start with the system and creates a postgres user.
   We will assume that you have PostgresSQL installed at "/opt/PostgreSQL/9.2", and a user "postgres" with a password "postgres". If you have changed any of these settings please introduce the correct settings in the step 2 below.


Installation procedure
----------------------

1. Extract the contents of collector_bin.tgz to a suitable place. For example /opt/collector

2. Define the correct settings in the file environment. In particular:

        COLLECTOR_HOME=/opt/collector # the location of collector

        JAVA_HOME=$COLLECTOR_HOME/jdk # the location of JDK. We assume we will use the bundled JDK. If not modify accordingly.
	JDK_KEYSTORE_PWD=changeit # JDK default keystore value
   
        PGPASSWORD=postgres # the password of the user postgresexport
	PG_HOME=/opt/PostgreSQL/9.2 # Location of Postgres installation

4. Execute the install script

      ./install

   That's all!

If the installation completed successfully you can test it executing directly collector

      ./collector

You must see the following text appear in the screen:


Collector v1.4.6
Usage: collector [newjobuniprotid|executejob|listfilters|listprotocols|listjobs|listjobexecutions|export|deletejob|deletejobexecution|deletejobexecutionsforjobid] [options]

Command: newjobuniprotid [options]
newjobuniprotid is a command.
  --protocolid <value>
        protocolid is Int property.

  --uniprotid <value>
        uniprotid is string property.

  --jobdescription <value>
        jobdescription is String property.

Command: executejob [options]
executejob is a command.
  --jobdescription <value>
        jobdescription is a string property.

Command: listfilters
listfilters is a command.

Command: listprotocols
listprotocols is a command.

Command: listjobs
listjobs is a command.

Command: listjobexecutions [options]
listjobexecutions is a command.
  --jobid <value>
        jobid is a integer property

Command: export [options]
export data to file
  --raw
        raw is a flag
  --jobexecutionid <value>
        jobexecutionid is a integer property
  --datatoexport <value>
        datatoexport must be "activities" or "compounds"
  --exportformat <value>
        exportformat must be "sdf" or "csv"

  --filename <value>
        filename is a string
Command: deletejob [options]
deletejob is a command.
  --jobid <value>
        jobid is a integer property.

Command: deletejobexecution [options]
deletejobexecution is a command.
  --jobexecutionid <value>
        jobexecutionid is a integer property.

Command: deletejobexecutionsforjobid [options]
deletejobexecutionsforjobid is a command.
  --jobid <value>
        jobid is a integer property.


If you have any problem with the installation, contact us at the following e-mail addresses:

   Manuel Pastor  	manuel.pastor@upf.edu
   Oriol L. Masasaguer 	oriol.lopez@upf.edu