Installing Galaxy and Hooking into a SGE Cluster
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
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 On 22 Aug 2012, at 21:20, mailing list <margeemail@gmail.com> 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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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 On Thu, Aug 23, 2012 at 11:27 AM, John Jones <mr.johnjones@gmail.com> 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
On 22 Aug 2012, at 21:20, mailing list <margeemail@gmail.com> 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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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 On 23 Aug 2012, at 19:01, mailing list <margeemail@gmail.com> wrote:
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
On Thu, Aug 23, 2012 at 11:27 AM, John Jones <mr.johnjones@gmail.com> 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
On 22 Aug 2012, at 21:20, mailing list <margeemail@gmail.com> 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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
On 23 August 2012 14:39, John Jones <mr.johnjones@gmail.com> wrote:
[...] 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.
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
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 On Thu, Aug 23, 2012 at 2:59 PM, Joachim Baran <joachim.baran@gmail.com> wrote:
On 23 August 2012 14:39, John Jones <mr.johnjones@gmail.com> wrote:
[...] 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.
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
On Thu, Aug 23, 2012 at 8:44 PM, mailing list <margeemail@gmail.com> wrote:
Anyway, back to my question. Does anyone know? Would I be better off asking on the developer mailing list or perhaps Stack Overflow?
Software licensing is a much broader issue that Galaxy, so yes, perhaps Stack Overflow would be a better place. Peter
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 On 23 Aug 2012, at 21:00, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Thu, Aug 23, 2012 at 8:44 PM, mailing list <margeemail@gmail.com> wrote:
Anyway, back to my question. Does anyone know? Would I be better off asking on the developer mailing list or perhaps Stack Overflow?
Software licensing is a much broader issue that Galaxy, so yes, perhaps Stack Overflow would be a better place.
Peter ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (4)
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Joachim Baran -
John Jones -
mailing list -
Peter Cock