Installing eagle-i Repository on orchestra:

  1. ssh into orchestra

    ssh ecommonsId@orchestra.med.harvard.edu

  2. navigate to the working directory and make a project folder in tomcat . 

    cd /www/dev.some.website.hms.harvard.edu/tomcat
mkdir blink

  3. get the latest distribution of the repository software

    cd blink/
wget http://infra.search.eagle-i.net:8081/nexus/content/repositories/releases/org/eagle-i/eagle-i-repository-dist/1.7-MS1.02/eagle-i-repository-dist-1.7-MS1.02-dist.zip

  4. unzip the folder

    unzip eagle-i-repository-dist-1.7-MS1.02-dist.zip

  5. create additional folders in the project folder that are needed to install the repository

    mkdir datarepo
cd datarepo
mkdir lib

  6. now copy the required derby jars from the unzipped repository folder to the newly created lib folder

    cd lib
cp ../../repository-1.7-MS1.02/lib/* .

  7. also place a copy of the derby jars in tomcat's lib folder

    ../../repository-1.7-MS1.02/lib/* ../../../lib/

  8. create a symbolic link in the tomcat folder to the docroot folder

    cd ../../../
ln -s ../docroot/ webapps

  9. copy the ROOT.war from the unzipped repository folder into the docroot folder

    cd /www/dev.some.website.hms.harvard.edu/docroot
cp ../tomcat/blink/repository-1.7-MS1.02/webapps/ROOT.war .

Additional configurations needed to continue installation:

  1. Edit the .jkmounts file (https://wiki.med.harvard.edu/Orchestra/TomcatHosting#Content_Placement_and_Tomcat_Con) because we need to serve the repository at the root.  The .jkmounts file should only have the following line in it.

    /* = devalaskau24

  2. Add a catalina.properties file in tomcat's conf folder with the following content, making sure to update the locations:

    org.eaglei.repository.home=/www/dev.some.website.hms.harvard.edu/tomcat/blink/datarepo
derby.system.home=/www/dev.some.website.hms.harvard.edu/tomcat/blink/datarepo
common.loader=${catalina.base}/blink/.config,${catalina.base}/blink/conf,${catalina.base}/lib,/www/dev.some.website.hms.harvard.edu/tomcat/lib/*.jar,${catalina.home}/lib,${catalina.home}/lib/*.jar
org.eaglei.home=/www/dev.some.website.hms.harvard.edu/tomcat/blink

The folder structure in the website directory should now look like this:

  • dev.some.website.hms.harvard.edu
    • docroot
      • ROOT.war
      • (additional files that were set up by RITG)
    • support
    • tomcat
      • blink
        • datarepo
          • lib
            • 2 derby jars
        • repository-1.7.-MS1.02
      • conf
        • catalina.properties
      • lib
        • 2 derby jars
        • (additional folders that were set up by RITG)
      • webapps -> ../docroot/

In order to perform the rest of the installation of the repository, we now need to enter orchestra's interactive LSF (https://wiki.med.harvard.edu/Orchestra/IntroductionToLSF#Interactive_Jobs)

bsub -Is -q shared_int_2h bash

  1. Navigate to the unzipped repository distribution /etc/ folder and run the prepare-install script

    cd blink/repository-1.7-MS1.02/
./etc/prepare-install.sh USERNAME PASSWORD ../datarepo/

    Where USERNAME and PASSWORD are the initial admin creds for the repository.

  2. Now exit out of the interactive shell and start tomcat

    exit
tomcatctl start dev.some.website.hms.harvard.edu

  3. Re-enter the interactive LSF to complete the installation

    bsub -Is -q shared_int_2h bash
./etc/finish-install.sh USERNAME PASSWORD https://dev.some.website.hms.harvard.edu

  4. Finally, edit the configuration file in the datarepo folder to have the sesame property point to the correct place.

    eaglei.repository.sesame.dir = /www/dev.some.website.hms.harvard.edu/tomcat/blink/datarepo/sesame
Additional references:
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