How to configure your GenePattern server to connect to the new module repository URLs

Posted on Tuesday, July 30, 2019 at 03:52PM by Barbara Hill

As mentioned in our help forum, our module repositories have been brought back online.

Below are the steps required to get the 'Install from Repository' page to work on your own server ahead of the next release of GenePattern.

step 1: Replace your repo.yaml file with this file

https://github.com/genepattern/genepattern-server/blob/develop/resources/repo.yaml

*note that you will need to reload the job configuration for this to take effect

 

step 2: Edit genepattern.properties file

Set the *RepositoryURL(s) to use the new location. Make the following edits in your 'genepattern.properties' file. As usual, for best results, first shut down the server, then make the edits, then start the server.

# GenePattern Production module repository url
ModuleRepositoryURL=https://modulerepository.genepattern.org/gpModuleRepository/
DefaultModuleRepositoryURL=https://modulerepository.genepattern.org/gpModuleRepository/
ModuleRepositoryURLs=https://modulerepository.genepattern.org/gpModuleRepository/,https://modulerepository.genepattern.org/gparcModuleRepository/,https://modulerepository.genepattern.org/betaModuleRepository/


SuiteRepositoryURL=https://modulerepository.genepattern.org/gpModuleRepository/suite 
DefaultSuiteRepositoryURL=https://modulerepository.genepattern.org/gpModuleRepository/suite 
SuiteRepositoryURLs=https://modulerepository.genepattern.org/gpModuleRepository/suite

Note: The DefaultPatchURL and DefaultPatchRepositoryURL properties are no longer required. Feel free to delete them from the file.

 

step 3: Update TASK_INSTALL.REPO_URL in the database

This step is only needed for the Source label and icon in the user interface, e.g. Production, Gparc, or Beta. Update the TASK_INSTALL.REPO_URL column in the database to match the newer urls. This example update statement was tested on our Amazon hosted servers with a MySQL database. 

UPDATE task_install 
SET repo_url = REPLACE(
                   REPLACE(
                       REPLACE(repo_url, 'http://software.broadinstitute.org/webservices/gpModuleRepository', 'https://modulerepository.genepattern.org/gpModuleRepository/'),
                   'http://software.broadinstitute.org/webservices/gparcModuleRepository', 'https://modulerepository.genepattern.org/gparcModuleRepository/'),
              'http://software.broadinstitute.org/webservices/betaModuleRepository', 'https://modulerepository.genepattern.org/betaModuleRepository/')

Note: If you are using an Oracle database, you will need to commit 

 

step 4: Update GP_USER_PROP['ModuleRepositoryURL'] in the database

As an additional step (not required) change the per-user 'ModuleRepositoryURL' setting. This example update statement was tested on our Amazon hosted servers with a MySQL database. 

UPDATE gp_user_prop
    SET value = 'https://modulerepository.genepattern.org/gpModuleRepository/' 
WHERE `key` = 'ModuleRepositoryURL'

Note: If you are using an Oracle database, you will need to commit , and you do not need the `` around "key"

 

If you run into any issues or have any questions, please feel free to contact us.

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