Last modified 7 years ago Last modified on 08/13/13 14:25:25

DevOps Weekly Meeting | August 13, 2013

Time & Location: 10am-1:00pm in LHL164


tanthony, jpr, pavgi, mhanby

2013-08-13 Agenda


  • Crashplan updates
    • Netplus for public clouds only
    • Explore private cloud with Code42 directly
  • NGS/Galaxy
    • Galaxy upgrade
      • code merged and ready for deploy.
      • touch base with galaxy devs
      • target this week for deploy
      • open issue with VCF files. Can't display in browser.
    • Toolshed integration
      • worked through example of a toolshed tool fork for local wrapper mods
  • Lustre Cleanup
    • Still working to identify why the deletes aren't freeing the space we anticipate
    • will check our tree navigation code
  • Hardware upgrades
    • RAM upgrade on Sipsey - pending decision
    • Disk upgrade on DDN
  • OpenStackPlusCeph
    • will work on nas-01 connection to admin network so it can be a storage gateway to public and cluster nets, use additional 10G card to connect directly, upgrade to centos6
    • will work on admin node to connect to public network for dns and ntp connectivity
    • need to kick off request for grizzly install before going live with storage
    • old pending issues
      • Fix rcs-srv-02 NAT rules
      • ai: need to create a uab public to floating-public translation table
      • ai: need to embed table in DNS
      • ai: need an ubuntu desktop image in glance. may require contortion of launching vm with iso or getting iso in glance and then installing into a volume and then launch a subsequent instance from that volume
      • ai: jpr: apply changes to ceph read caching, requires nova-compute restart. pending understanding crowbar and chef
      • todo: we need access to the admin node interface via the controller
      • todo: we need to engage with dell on crowbar limitation on storage use, don't know if we get improvements from storage.
    • wiki updated to announce the seminars using div/css code from wikipedia
    • created matlab-annc list for sharing announcements and updates to advertise matlab seminar
  • dspace report.
    • ai: jpr: need to complete draft


Reviewed the Galaxy toolshed in the context of the sam_merge2 tool (UI merge bam files) in Galaxy. It is a tool that uses picard on the backend via it's wrapper. We've had to modify that wrapper in the past to tune the Java environment parameters for the number of open files and such. When the toolshed is used we won't have a ready mechanism (our local galaxy repo) available to maintain such modifications at our downstream site. Instead, we need to work through the toolshed model to fork the tool and then install our forked version.

This will work very similar to the experience on GitHub where one forks a tool and then makes the modifications to the fork and installs the fork in our local galaxy instance. All the regular caveats of forking hold, ie. by forking you take ownership of the code base and will need to maintain your forked codebase with the upstream (original tool) modifications. Nonetheless, this provides a clean method for adapting code to local needs and continuing to use the toolshed for tool installs.