GenePattern Team Blog

The GenomeSpace servers are shutting down on November 15, 2019

Posted on Tuesday, October 01, 2019 at 05:40PM by GenePattern Team

As many of you may have heard, and those of you who are registered GenomeSpace should have read in an email, the GenomeSpace servers are shutting down permanently on November 15, 2019.

The email sent to the GenomeSpace users list is as follows:

Dear GenomeSpace user,

The GenomeSpace servers are shutting down on November 15, 2019 due to expiration of its NHGRI funding. We would like to thank all GenomeSpace users for their support and for all the important science they have done on the platform over the last nine years.

GenomeSpace-enabled tools are separately funded and will continue to be available subject to their own lifecycles, but any connection to GenomeSpace or GenomeSpace-hosted files will cease with the termination of the servers. If you do not remember your login credentials for any individual tools that you rely on, you should use the ‘forgot password’ links on their websites to reset your login credentials.

NOTE: We are unable to archive...

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Cloud GenePattern Job purge interval changing to 14 days on Tuesday, October 1, 2019

Posted on Tuesday, September 24, 2019 at 10:20AM by Barbara Hill

Since officially switching to cloud.genepattern.org as our official production GenePattern server in January of this year, we have seen a steady increase in the number and size of jobs being run on the server, which is fantastic! We love that we have been able to provide a platform for so much great science, and we want to continue to do so. So, to limit our storage costs, and make sure that we can sustain this free service, we will be shortening our job purge interval from 30 days to 14 days as of Tuesday, October 1, 2019.

What this means is that any jobs older than 14 days as of Oct 1 will be purged from the server, and any jobs run on Oct 1 and beyond will be retained on the server for 14 days. This does not impact data you have uploaded to the Files tab.

If you have jobs you wish to retain for longer than 14 days, you have a few options:

  1. Reload the job - this creates a new job with the same parameters and outputs which now has another 14-day lease...

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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://...

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