Re: [galaxy-dev] trying to get a Galaxy instance working w/ SGE cluster.
Hi Nate, Thanks for this! It has saved me wasting time barking up an inappropriate tree, and we'll rethink the plans. Regards, Mike. -- Mike Wallis +44(0)113 343 1880 ARC/HPC Systems Support ISS, University of Leeds, Leeds, LS2 9JT, UK -Original Message- From: Nate Coraor [mailto:n...@bx.psu.edu] Sent: 03 October 2011 19:12 To: Mike Wallis Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] trying to get a Galaxy instance working w/ SGE cluster. Mike Wallis wrote: Hello, I'm trying to get an instance of Galaxy working where the application server - the web front end, as I understand it - is on a completely separate host to the SGE cluster the back end runs on. Is there any way of setting up galaxy that it uses ssh instead of having to have the application server/SGE have a shared NFS filesystem? Is having a shared filesystem the only way I can get Galaxy to work in this kind of scenario? We have a general-purpose cluster which doesn't export filesystems for security reasons, and doesn't run shared web applications. Thanks for any help you could offer. Hi Mike, Unless you can add file-staging support to the DRMAA job runner, you need a shared filesystem. I had been under the impression that staging was not supported in the DRMAA 1.0, although it might be possible with the native spec field. That said, there are some tools which write files to the working directory and those outputs are collected by the job runner, so if the working directory is not in a shared filesystem, these tools won't work properly. Unfortunately, I don't have a list of such tools, but there are quite a few. --nate Mike. -- Mike Wallis +44(0)113 343 1880 ARC/HPC Systems Support ISS, University of Leeds, Leeds, LS2 9JT, UK ___ 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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] trying to get a Galaxy instance working w/ SGE cluster.
Mike Wallis wrote: Hello, I'm trying to get an instance of Galaxy working where the application server - the web front end, as I understand it - is on a completely separate host to the SGE cluster the back end runs on. Is there any way of setting up galaxy that it uses ssh instead of having to have the application server/SGE have a shared NFS filesystem? Is having a shared filesystem the only way I can get Galaxy to work in this kind of scenario? We have a general-purpose cluster which doesn't export filesystems for security reasons, and doesn't run shared web applications. Thanks for any help you could offer. Hi Mike, Unless you can add file-staging support to the DRMAA job runner, you need a shared filesystem. I had been under the impression that staging was not supported in the DRMAA 1.0, although it might be possible with the native spec field. That said, there are some tools which write files to the working directory and those outputs are collected by the job runner, so if the working directory is not in a shared filesystem, these tools won't work properly. Unfortunately, I don't have a list of such tools, but there are quite a few. --nate Mike. -- Mike Wallis +44(0)113 343 1880 ARC/HPC Systems Support ISS, University of Leeds, Leeds, LS2 9JT, UK ___ 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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] trying to get a Galaxy instance working w/ SGE cluster.
Hello, I'm trying to get an instance of Galaxy working where the application server - the web front end, as I understand it - is on a completely separate host to the SGE cluster the back end runs on. Is there any way of setting up galaxy that it uses ssh instead of having to have the application server/SGE have a shared NFS filesystem? Is having a shared filesystem the only way I can get Galaxy to work in this kind of scenario? We have a general-purpose cluster which doesn't export filesystems for security reasons, and doesn't run shared web applications. Thanks for any help you could offer. Mike. -- Mike Wallis +44(0)113 343 1880 ARC/HPC Systems Support ISS, University of Leeds, Leeds, LS2 9JT, UK ___ 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: http://lists.bx.psu.edu/
