Re: [galaxy-dev] [galaxy-user] Installing Galaxy and Hooking into a SGE Cluster
On Mon, Aug 27, 2012 at 2:25 PM, greg wrote: >>> >>> How do users get data into Galaxy in your system? >>> >> >> Mostly via the "upload" tool, or sometimes the remote >> data tools (eg from UCSC). Some commonly used >> files are also setup on our system as shared libraries >> within Galaxy. > > It seems weird to ask them to upload something that's > already in their home directory and available to the > cluster jobs otherwise. I was answering about *our* Galaxy, where only a few of the users have a Linux account. In most cases their home directory is on Windows... and not easily accessed from our Linux cluster if at all. > I wonder if there's a way they can copy files to the Galaxy data > directory? I guess they'd have to let Galaxy know about the new data > somehow? This is available to a Galaxy administrator for shared libraries of files made available within Galaxy, see: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files Perhaps something like Alban Lermine's upload_local_file or Edward Kirton's data_nfs tool on the ToolShed would work for you? Peter ___ 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] [galaxy-user] Installing Galaxy and Hooking into a SGE Cluster
On Fri, Aug 24, 2012 at 4:30 PM, Peter Cock wrote: >> >> >> >> 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? >> > >> > By default, all the data is under a single folder, belonging to the >> > galaxy Linux user account. We use /mnt/galaxy/galaxy-dist for >> > this. In order that the cluster jobs can access the data, they must >> > also be able to see this mount. >> >> So can one user see another's files in your setup? I'd prefer if each >> user could only see and use his own files. >> > > No - they only access their data via the website, which has > it's own user controls, and prevents user A seeing the files > of user B (unless explicitly shared). > >> >> How do users get data into Galaxy in your system? >> > > Mostly via the "uplad" tool, or sometimes the remote > data tools (eg from UCSC). Some commonly used > files are also setup on our system as shared libraries > within Galaxy. It seems weird to ask them to upload something that's already in their home directory and available to the cluster jobs otherwise. I wonder if there's a way they can copy files to the Galaxy data directory? I guess they'd have to let Galaxy know about the new data somehow? >> >> Thanks, >> >> Greg >> >> >> > >> > P.S. It is very confusing that your emails give your name >> > as "mailing list" rather than Greg. >> >> I think I fixed this? > > > Yes :) > ___ 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] [galaxy-user] Installing Galaxy and Hooking into a SGE Cluster
On Friday, August 24, 2012, greg wrote: > On Fri, Aug 24, 2012 at 9:56 AM, Peter Cock > > > wrote: > > On Fri, Aug 24, 2012 at 1:25 PM, mailing list > > > > > > aka Greg wrote: > >> 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? > > > > By default, all the data is under a single folder, belonging to the > > galaxy Linux user account. We use /mnt/galaxy/galaxy-dist for > > this. In order that the cluster jobs can access the data, they must > > also be able to see this mount. > > So can one user see another's files in your setup? I'd prefer if each > user could only see and use his own files. > > No - they only access their data via the website, which has it's own user controls, and prevents user A seeing the files of user B (unless explicitly shared). > How do users get data into Galaxy in your system? > > Mostly via the "uplad" tool, or sometimes the remote data tools (eg from UCSC). Some commonly used files are also setup on our system as shared libraries within Galaxy. > Thanks, > > Greg > > > > > P.S. It is very confusing that your emails give your name > > as "mailing list" rather than Greg. > > I think I fixed this? > Yes :) ___ 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/
