Thanks Assaf.

Would anyone know about my question 1?  If I install a local version
of Galaxy and connect it to our cluster, where is each user's
(uploaded?) data stored?  How will the cluster jobs be able to access
the data?

If anyone has installed galaxy and hooked it up to Sun Grid engine,
I'd love to hear from you.



On Thu, Aug 23, 2012 at 6:29 PM, Assaf Gordon <> wrote:
> (Moving to Galaxy-dev, seems more appropriate).
> John Jones wrote, On 08/23/2012 05:29 PM:
>> 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.
> 1. Technically (billing on an SGE cluster):
> There's a script in "./contrib" called "" .
> details are here:
> Assuming you're using PostgreSQL + SGE, it will give you what you want 
> (break-down of SGE jobs timings and Galaxy users).
> With little adaptation, you can use it to exact SGE JobID and Galaxy Tool-ID 
> / user ID.
> If you want to extract it directly from the galaxy database, then the 
> following SQL will get you started:
> ===
> select
>  email as "user",
>  tool_id as "tool",
>  job_runner_external_id as "SGE_ID"
> from
>  job, galaxy_user
> where
>  job.user_id =
>  and
>  job_runner_name like 'drmaa%'
>  ;
> ===
> "job_runner_external_ID" will be the SGE-ID, and once you have the list (per 
> each galaxy user), you can use "qacct" to get the information for the job, 
> then calculate the charges.
> 2. Legally:
> IANAL, but to the best of my (limited) understanding:
> 1. Galaxy itself (server code, etc.) - completely legal to run it 
> commercially, even charge money for it - it is licensed as a BSD/MIT style 
> license.
> 2. Individual tools:
> if the tools are GPL'd (e.g. bowtie, tophat, bwa, cufflinks) or BSD/MIT - 
> completely legal to run them commercially, and even charge money for them.
> if the tools use any special license that restrict commercial use (commonly 
> stated as "free for personal, academic, non-commercial use", e.g. Jim Kent's 
> UCSC Genome Browser tools) - then you can't use them in your commercial 
> company without buying a special license (not even internally).
> It's really not complicated at all, and most (if not all) tools that you 
> compile from source to install them will have a file called "license" or 
> "copying" that will tell you what is the license.
> If the tools didn't come with a source code, they are probably not 
> free/open-source for commercial use (e.g. - novoalign).
> 3. Morally:
> Anyone who thinks of free/open-source as "charity" is missing the point.
> There is no "charity", and it's perfectly legal, moral, and even recommended 
> to charge money when offering services that are based on free/open-source 
> tools - the requirement (when using GPL) is to give the source code to users 
> when they ask for it (and some other complications, don't want to start a 
> flame war here) - so if they don't want to pay $1,000 for your service - the 
> are more than welcomed to buy their own cluster and storage and servers and 
> run the program themselves - that is the whole point of free/open source. 
> There is not charity.
> When people write (and publish) software - they explicitly decide upon the 
> license they prefer, and they should know what are the affects of the license.
> For example, the Galaxy team released Galaxy under a permissive BSD/MIT style 
> license, so they were completely aware of the fact that not only Galaxy can 
> be incorporated into a commercial product, the license doesn't even require 
> the commercial company to release any code changes they make to Galaxy. It's 
> a conscious decision, not an after-thought, and not charity.
> (end of my rambling...)
> -gordon

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