Question about long term goal of Tool Shed usage
Hello, I've been learning about the tool shed, as precipitated by the decision to move the blast tool out of the standard distribution. (I'm having a problem doing so as documented here: http://dev.list.galaxyproject.org/Cannot-install-ncbi-blast-plus-or-other-to... , but that's not the point of this email) Is there a goal to move every tool that's currently included in the EC2 tools snapshot to the public tool shed to keep the standard galaxy distribution leaner? If so, I have two questions/concerns: 1) How will this work with the concept of a tool volume snapshot? I'd have to make a snapshot of my partition every time I installed/removed a tool from a tool shed. Would it make sense to re-characterize the tools volume as a persistent volume (a la the user data volume) instead of it being snapshot driven like it is now? Is it currently possible for me to point to a persistent EC2 tools volume and not a snapshot in my persistent S3 information in order to make the cluster stop/start process simpler? 2) Are there plans to provide ranking or popularity ratings to the public tool shed so I know which tools are the most stable, popular, or perhaps used to be included in the standard distribution? Thanks again for your work, apologies for the verbosity, I'm just getting to know galaxy. -Joel
Hi Joel, I can provide a couple of comments, or better yet start a discussion, but others please feel free to chime in.
1) How will this work with the concept of a tool volume snapshot? I'd have to make a snapshot of my partition every time I installed/removed a tool from a tool shed. Would it make sense to re-characterize the tools volume as a persistent volume (a la the user data volume) instead of it being snapshot driven like it is now? Is it currently possible for me to point to a persistent EC2 tools volume and not a snapshot in my persistent S3 information in order to make the cluster stop/start process simpler?
Currently, we're working on a new file system management component within cloudman, which will allow for a much greater flexibility in terms of how file systems are managed and maintained in the cloud context. Technically, this should help in getting over the issue that's emerging. We haven't yet made any decisions on how the tool upgrades will be handled across the board in this context but the approach you mention is a very likely one, especially as a first step in this direction.
2) Are there plans to provide ranking or popularity ratings to the public tool shed so I know which tools are the most stable, popular, or perhaps used to be included in the standard distribution?
There are ongoing efforts to address this exact topic. I'm not aware of a the timeline but if someone else is, jump in... Thanks for raising these questions, Enis
Thanks again for your work, apologies for the verbosity, I'm just getting to know galaxy.
-Joel ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (2)
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Enis Afgan -
Joel Rosenberg