Re: [galaxy-dev] Access control for galaxy
Hi Raghu, On Apr 21, 2011, at 4:44 AM, Raghuraman Ramamurthy wrote: Hello, I would first like to thank and appreciate the Galaxy team for their efforts. I want to clone galaxy and host it in my website. In doing so, I want to restrict the users who use galaxy on my website. So, is there any access control module which could be integrated with galaxy, to make it secure and grant access to only a set number of people. Have a look at External Authentication as described here: https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy Cheers, Pi Thanks, Raghu ___ 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/ - mobile: +31 6 143 66 783 e-mail: pieter.neeri...@gmail.com skype: pieter.online - ___ 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] Plotting tools - best output format? PDF, PNG, ... SVG!
On Thu, Apr 21, 2011 at 10:50 AM, Pieter Neerincx pieter.neeri...@gmail.com wrote: Hi Peter, On Apr 20, 2011, at 5:47 PM, Peter Cock wrote: On Wed, Apr 20, 2011 at 4:30 PM, Pieter Neerincx pieter.neeri...@gmail.com wrote: Hi Peter, On Apr 20, 2011, at 11:07 AM, Peter Cock wrote: Hi all, ...cut... How about SVG? Don't most of the mainline browsers have reasonably good SVG support built in (possibly via a plugin)? Yep, SVG support is pretty good nowadays especially in FireFox and Opera. Safari, IE and Chrome have only partial support, but for simple charts without 3D filters it works fine. I've added SVG as a datatype to my Galaxy and this works great. You won't need a plugin; in fact the old Adobe SVG plugin is depreciated already for a few years now and no longer compatible with recent browser versions. I looked at SVG about a year ago, and was pretty impressed. I did run into some issues, particularly with links, and opted to use PNG files in the end. Since then we've finally dropped IE6, so hopefully SVG would be safe now. Are your changes to add SVG as a datatype to Galaxy public? I'd like to suggest that be merged to the trunk. I simply added this line to my datatypes_conf.xml: datatype extension=svg type=galaxy.datatypes.images:Image mimetype=image/svg+xml/ I didn't make a sniffer as I don't have a use case for users uploading SVGs, so I didn't have to create a Python class and SVG is just another instance of galaxy.datatypes.images:Image from a plain vanilla Galaxy. That makes sense if the sniffer is only used on upload. To make sure the client displays the SVG you may have to add the SVG mimetype to your web server's config too. Where this is defined may differ per linux distro. I use apache as a proxy and had to add image/svg+xml svg svgz to /etc/mime.types. Thanks for the details - it looks simple enough to add here too. If/when any SVG producing tools are added to Galaxy or the Galaxy Tool Shed, then it would be nice to have this done in the main repository. The nice benefit of SVG in addition to not needing a plugin is that the image can scale with the surrounding text if you zoom in your browser (without loosing resolution). The disadvantage is that although my users know what a PDF file is and can process them for posters/manuscripts, most of them never heard of SVG and get stuck when it doesn't import into PowerPoint et al. :( Do they cope with PDF? Well, they know how to view and print one :). Importing them directly into PowerPoint and Word is just as problematic though, so that usually involves opening the PDF in a different program and copy/paste or exporting to another format. Still a hassle, but they manage... Getting a PDF into PowerPoint or Word is easy on a Mac ;) But yes, point taken - even though a PDF is easier to work with than an SVG (or a postscript file), it can still be a hassle. 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] Launching multiple jobs using one tool form with multiple selected datasets
Hi again, Sorry to maybe not understand how to get started, but I'm trying for something even without the added complexity of a workflow. If you could point me into the right direction: how would I have a single tool where on the tool form there is a multi-select of certain datasets in the user's history. The user multi selects X datasets in the form and hits submit and Galaxy will launch X tool jobs (on for each of the datasets) at the same time in the history. How do I go about doing this? Sorry for being daft, Leandro On Tue, Apr 19, 2011 at 4:34 PM, Dave Walton dave.wal...@jax.org wrote: Is the server below down? I'm trying to get there this morning and having no luck... https://wiki.nbic.nl/index.php/NBIC_Galaxy_Hackathon_project#Loop_over_files _in_a_directory Dave On 4/15/11 12:16 PM, Pieter Neerincx pieter.neeri...@gmail.com wrote: Hi, You're not alone with this request! Unfortunately I wasn't able to join the 2-day Galaxy Hackathon, but I heard from a colleague who just came back that this was one of the topics they worked on. At the end of the hackathon they had a working prototype: https://wiki.nbic.nl/index.php/NBIC_Galaxy_Hackathon_project#Loop_over_files_i n_a_directory Since they had only 2 days, it will need some polish, but I heard this hack already made it into the development branch of Galaxy, so we may see something like this in the near future :) Cheers, Pi On Apr 15, 2011, at 4:28 PM, Dave Walton wrote: I've essentially asked the same question of the list in the past and gotten no real response. I have the same interest, but from a workflow perspective. * A module that allows me to select multiple datafiles (say fastq files) * Then pass each data file to a separate instance of a workflow that runs tophat and cufflinks * then another module that takes the final outputs of each of the workflow runs and sends them to a final module that merges results. I am attempting to implement something like this using the API, though the API is still pretty green from my perspective. I think functionality like this built into the workflow editor would be a great addition. Dave On Apr 15, 2011, at 8:14 AM, Leandro Hermida wrote: Hi everyone, I was wondering what would be the way in Galaxy to program the following: - User clicks on a tool and form is displayed - They use a select multi menu in the form to pick lets say X multiple datasets from their history - When they click submit the tool launches X number of jobs in the history, on for each of the datasets selected. I have a common use case where users have to manually run the same tool over and over again with the same parameters for each dataset of interest in their history. I would be great to be able programmatically or otherwise with Galaxy to be able to use one form and multi select the datasets and then launch the parallel jobs in one go. regards, Leandro ATT1..txt ___ 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/ - mobile: +31 6 143 66 783 e-mail: pieter.neeri...@gmail.com skype: pieter.online - ___ 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] Launching multiple jobs using one tool form with multiple selected datasets
Leandro, I see what you mean, I misunderstood your original goal. There currently isn't a way to execute single tools in this fashion. It isn't exactly straightforward, but you could construct a workflow that consisted of two steps-- an Input Dataset step, and whatever tool you wanted to use, and then you'd be able to use the functionality described in this thread as long as your instance is at 5386:67a19816034b or higher. -Dannon On Apr 21, 2011, at 7:49 AM, Leandro Hermida wrote: Hi again, Sorry to maybe not understand how to get started, but I'm trying for something even without the added complexity of a workflow. If you could point me into the right direction: how would I have a single tool where on the tool form there is a multi-select of certain datasets in the user's history. The user multi selects X datasets in the form and hits submit and Galaxy will launch X tool jobs (on for each of the datasets) at the same time in the history. How do I go about doing this? Sorry for being daft, Leandro On Tue, Apr 19, 2011 at 4:34 PM, Dave Walton dave.wal...@jax.org wrote: Is the server below down? I'm trying to get there this morning and having no luck... https://wiki.nbic.nl/index.php/NBIC_Galaxy_Hackathon_project#Loop_over_files _in_a_directory Dave On 4/15/11 12:16 PM, Pieter Neerincx pieter.neeri...@gmail.com wrote: Hi, You're not alone with this request! Unfortunately I wasn't able to join the 2-day Galaxy Hackathon, but I heard from a colleague who just came back that this was one of the topics they worked on. At the end of the hackathon they had a working prototype: https://wiki.nbic.nl/index.php/NBIC_Galaxy_Hackathon_project#Loop_over_files_i n_a_directory Since they had only 2 days, it will need some polish, but I heard this hack already made it into the development branch of Galaxy, so we may see something like this in the near future :) Cheers, Pi On Apr 15, 2011, at 4:28 PM, Dave Walton wrote: I've essentially asked the same question of the list in the past and gotten no real response. I have the same interest, but from a workflow perspective. * A module that allows me to select multiple datafiles (say fastq files) * Then pass each data file to a separate instance of a workflow that runs tophat and cufflinks * then another module that takes the final outputs of each of the workflow runs and sends them to a final module that merges results. I am attempting to implement something like this using the API, though the API is still pretty green from my perspective. I think functionality like this built into the workflow editor would be a great addition. Dave On Apr 15, 2011, at 8:14 AM, Leandro Hermida wrote: Hi everyone, I was wondering what would be the way in Galaxy to program the following: - User clicks on a tool and form is displayed - They use a select multi menu in the form to pick lets say X multiple datasets from their history - When they click submit the tool launches X number of jobs in the history, on for each of the datasets selected. I have a common use case where users have to manually run the same tool over and over again with the same parameters for each dataset of interest in their history. I would be great to be able programmatically or otherwise with Galaxy to be able to use one form and multi select the datasets and then launch the parallel jobs in one go. regards, Leandro ATT1..txt ___ 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/ - mobile: +31 6 143 66 783 e-mail: pieter.neeri...@gmail.com skype: pieter.online - ___ 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] Galaxy tools' priority level (nice)
Hi all, Our Galaxy is running on a shared server which will sometimes be running other computationally demanding jobs (outside of Galaxy). In some cases I'd like these to have priority, perhaps by having Galaxy run the tool child processes at a nice level of 10 (say). Is there any built in way to control the Unix priority level (e.g. nice or ionice) used to run tasks? I don't see anything on here, but perhaps I'm looking in the wrong place: https://bitbucket.org/galaxy/galaxy-central/wiki/Config/WebApplicationScaling Thanks, 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 tools' priority level (nice)
Hi Peter, Peter Cock wrote, On 04/21/2011 11:00 AM: Is there any built in way to control the Unix priority level (e.g. nice or ionice) used to run tasks? I don't see anything on here, but perhaps I'm looking in the wrong place: https://bitbucket.org/galaxy/galaxy-central/wiki/Config/WebApplicationScaling I've been experimenting with 'nice' as well (for other servers), and it seems the consensus is that 'nice' is broken. Linus puts it in a colorful way here: https://lwn.net/Articles/418739/ [...] Seriously. Nobody _ever_ does nice make, unless they are seriously repressed beta-males (eg MIS people who get shouted at when they do system maintenance unless they hide in dark corners and don't get discovered). It just doesn't happen. One recommended solution is to use cgroups, which can control CPU, Disk I/O, Memory usage and network load, as explained here: http://broadcast.oreilly.com/2009/06/manage-your-performance-with-cgroups-and-projects.html With cgroups there will be no need to change anything in galaxy (just apply a cgroup to the galaxy user, or something similar). Unfortunately, cgroups requires a recent kernel, so it might not be applicable in your case. -gordon ___ 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 tools' priority level (nice)
On Thu, Apr 21, 2011 at 5:43 PM, Assaf Gordon gor...@cshl.edu wrote: Hi Peter, Peter Cock wrote, On 04/21/2011 11:00 AM: Is there any built in way to control the Unix priority level (e.g. nice or ionice) used to run tasks? I don't see anything on here, but perhaps I'm looking in the wrong place: https://bitbucket.org/galaxy/galaxy-central/wiki/Config/WebApplicationScaling I've been experimenting with 'nice' as well (for other servers), and it seems the consensus is that 'nice' is broken. Linus puts it in a colorful way here: https://lwn.net/Articles/418739/ [...] Seriously. Nobody _ever_ does nice make, unless they are seriously repressed beta-males (eg MIS people who get shouted at when they do system maintenance unless they hide in dark corners and don't get discovered). It just doesn't happen. I know nice isn't perfect, but in the case of the sys admin setting up Galaxy, we don't have the human laziness problem to overcome: We could ensure all job tasks get run with nice 10 automatically, without the Galaxy users having to do anything special. One recommended solution is to use cgroups, which can control CPU, Disk I/O, Memory usage and network load, as explained here: http://broadcast.oreilly.com/2009/06/manage-your-performance-with-cgroups-and-projects.html With cgroups there will be no need to change anything in galaxy (just apply a cgroup to the galaxy user, or something similar). Yes, but I want to treat the Galaxy webserver differently from the compute jobs it launches. Unfortunately, cgroups requires a recent kernel, so it might not be applicable in your case. -gordon Are you using cgroups on your Galaxy? 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 tools' priority level (nice)
Peter Cock wrote, On 04/21/2011 12:59 PM: On Thu, Apr 21, 2011 at 5:43 PM, Assaf Gordon gor...@cshl.edu wrote: Hi Peter, Peter Cock wrote, On 04/21/2011 11:00 AM: Is there any built in way to control the Unix priority level (e.g. nice or ionice) used to run tasks? I don't see anything on here, but perhaps I'm looking in the wrong place: https://bitbucket.org/galaxy/galaxy-central/wiki/Config/WebApplicationScaling I've been experimenting with 'nice' as well (for other servers), and it seems the consensus is that 'nice' is broken. Linus puts it in a colorful way here: https://lwn.net/Articles/418739/ [...] Seriously. Nobody _ever_ does nice make, unless they are seriously repressed beta-males (eg MIS people who get shouted at when they do system maintenance unless they hide in dark corners and don't get discovered). It just doesn't happen. I know nice isn't perfect, but in the case of the sys admin setting up Galaxy, we don't have the human laziness problem to overcome: We could ensure all job tasks get run with nice 10 automatically, without the Galaxy users having to do anything special. The article goes to explain further why nice is not the best option, the above quote was just a jest. But you are right that it's better than nothing. One recommended solution is to use cgroups, which can control CPU, Disk I/O, Memory usage and network load, as explained here: http://broadcast.oreilly.com/2009/06/manage-your-performance-with-cgroups-and-projects.html With cgroups there will be no need to change anything in galaxy (just apply a cgroup to the galaxy user, or something similar). Yes, but I want to treat the Galaxy webserver differently from the compute jobs it launches. I'm certain there's a way to set limits per processes, not just per users - but I haven't experimented with it. Unfortunately, cgroups requires a recent kernel, so it might not be applicable in your case. Are you using cgroups on your Galaxy? Only on my development system - unfortunately my production serve uses CentOS 5 with an old kernel and no cgroup support. -gordon ___ 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/
