Installing Galaxy And Hooking Into A Sge Cluster

Question: Installing Galaxy And Hooking Into A Sge Cluster

6.3 years ago by

mailing list • 840 wrote:

Hi guys, I want to install Galaxy on a local server and hook it into our SGE cluster. This excellent document seems to provide a lot of the steps http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster however I have two questions I'm not sure about. 1. Right now users keep their data in their home directories. The jobs they run on the cluster have access to the user's home directory and use that data. How would this work with Galaxy? Can the Galaxy interface and jobs reference data in the users' home directories? Or I guess how does this work? 2. Also can I integrate the Galaxy user system with LDAP? And can that user information be passed to the cluster to run the jobs under that user? We need this for cluster billing purposes. Thanks in advance for any help. Everyone is our company is really pining for a Galaxy install and I'm really hoping I can set it up for them. -Greg

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modified 6.3 years ago by John Jones • 40 • written 6.3 years ago by mailing list • 840

6.3 years ago by

John Jones • 40

John Jones • 40 wrote:

Is it acceptable/legal to bill people for using the opensource tools in Galaxy? I can understand billing for server/cluster usage, perhaps even for a profit, but when I write a tool in my own time for free and then specify that people who distribute my tool may only do so non- commercially, it would make me very sad to think that people are getting around this buy charging excessive amounts in "sever-usage- fees", and thus making a business out of my free work. I'm not saying that this is what you are doing Greg, and I'm sure you have your reasons, but I'm really just wondering what sort of copyright protection i would need as a bioinformatics software developer to prevent such abuse of charity. All the best, - John

ADD COMMENT • link written 6.3 years ago by John Jones • 40

No, no it's just internal billing within our organization. We're charging for compute time on the cluster, not for any particular software. No one is making any money off of Galaxy, it's just a way to fairly divide up the compute time available to the organization. -Greg

ADD REPLY • link written 6.3 years ago by mailing list • 840

I completely understand what you're saying Greg and I have no doubt that your billing only covers the maintainence costs of your cluster - and I don't want to derail your thread because you ask a very legitimate question (to which im afraid I dont know the answer to, and would also be interested to hear the outcome of!); but I was just curious to hear if anyone in the community knew what protection there is for the developers of software if anyone can charge, say, $1000 for an alignment using free tools that takes only an hour to run. In retrospect I should never have brought this up within your thread, and should have asked the question in it's own right (perhaps in a mailing-list directed at developers rather than users). Anyway, all the best with your question :-) - John

ADD REPLY • link written 6.3 years ago by John Jones • 40

Many open source licenses will permit anyone to charge for redistributing the software and/or reselling services regarding the software. It is up to the users of the software to realize that they do not need to pay fees, which I think makes a lot of sense because the only other option would be to sue license violators. At least I cannot afford such a thing. Making money out of open source software is also not a bad thing. You can get Linux for free, or you can pay RedHat many monies for also receiving additional services. You can install Darwin for free, or you pay and get Apple's extensions on top of it. Best, Joachim

ADD REPLY • link written 6.3 years ago by Joachim Baran • 50

Anyway, back to my question. Does anyone know? Would I be better off asking on the developer mailing list or perhaps Stack Overflow? Thanks again, Greg

ADD REPLY • link written 6.3 years ago by mailing list • 840

Software licensing is a much broader issue that Galaxy, so yes, perhaps Stack Overflow would be a better place. Peter

ADD REPLY • link written 6.3 years ago by Peter Cock • 1.4k

Haha, oh dear - I'm so sorry Greg! His original question was about getting Galaxy to recognise LDAP authentication and personal storage space rather than shared storage space as is usual with Galaxy. Licensing only came into it because Greg wanted LDAP authentication to track individual user usage (for billing) and I questioned the legality of billing for the software used by Galaxy, as I'm sure some components have a non-commercial usage licence clause. Again, sorry Greg for the hijack! Hope you get an answer soon :-) - John

ADD REPLY • link written 6.3 years ago by John Jones • 40

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