Re: [galaxy-dev] Reloading a tools configuration does not seem to actually work
On Feb 13, 2013, at 5:56 PM, Anthonius deBoer wrote: Interesting! But maybe it is not the manager that is the bottleneck, but which process is the one that takes the inputs from the webpage (or in the API) and prepares all the files that are produced by the workflows? I guess it is the MAIN server? THAT is the one that is the bottleneck I think then... Are there any plans to make that process parallel? Well, you can run as many web servers as you'd like, which should help to alleviate this problem. Whichever server happens to be doing the work will be slow, but the rest should be unaffected. What I am facing, is that I have 100 FASTQ pairs or so, for a single flowcell, I can start the analysis of that set from the UI, but it will just crank through them and takes about 2-4 minutues for each pair to be processed, so with 100 pairs or so, you are looking 3-4 hours of an hourglass before control is given back to the user... Is this in the context of starting a workflow with hundreds of inputs? --nate It would be ideal if we would farm out the parsing of the web input to the cluster, so the creation of the histories and datasets is no longer the bottleneck How do others deal with large sequencing projects on this list? Are there any groups that routinely do 100-200 pairs of FASTQ files from within galaxy? I would like to hear their experience... Thanks Thon On Feb 13, 2013, at 01:44 PM, Nate Coraor n...@bx.psu.edu wrote: On Feb 13, 2013, at 4:12 PM, Anthonius deBoer wrote: Would this problem go away if I only used ONE webserver in my proxy setting and not use a balancer? I may not need it and if it means I could not use the toolshed effectively, it may be worth it not to use balancing.. No, because your manager/handlers will still need to be restarted to pick up the new tools. The only way you can have it work without restarting is to have everything in a single process. What i really need is the manager being balanced, since submitting a workflow with 100's of BAM files can take hours just to get started...ANy change we can run multiple managers? I'm surprised the manager is the holdup here since all it does is assign a handler. Regardless, in the development branch (which will be the next stable/release branch), the manager has been killed, and handlers are assigned directly by the web processes. --nate Thanks On Feb 13, 2013, at 07:59 AM, Nate Coraor n...@bx.psu.edu wrote: On Feb 7, 2013, at 2:43 PM, Anthonius deBoer wrote: That's very unfortunate... I have a ton of tools and I guess now I have to create a package for them in a local toolshed to update them in a running galaxy server? In any case...The toolshed installation also does not work for me...I still have to restart galaxy, even after using the toolshed approach to install a tool...It either does not show up at all or give a bunch of errors, about not being able to find the tool... Is this also related to the fact I have two webservers and am behind a proxy server as well? Hi Thon, Essentially yes, there is no way for one web process to communicate with others that it has installed a tool. We'd like to allow for this sort of notification via a message queue, but we don't have a proper message queue in Galaxy right now. --nate Thon On Feb 07, 2013, at 05:29 AM, Dannon Baker dannonba...@me.com wrote: Unfortunately not, and with the migration of tools to the toolshed installation mechanism I don't imagine this will be addressed (at least by the team) anytime soon. If you wanted you could probably write a script that would reload a specified tool in each of the separate web processes, or just implement a complete rolling restart of your web processes to avoid service disruption while still loading the tool updates. -Dannon On Feb 6, 2013, at 8:40 PM, Anthonius deBoer thondeb...@me.com wrote: I am indeed using multiple web processes and I guess I am talking about the old admine tool reloader... Is there any other way to do this for your own tools that you just manually place in tools etc.? Thon On Feb 05, 2013, at 06:22 PM, Dannon Baker dannonba...@me.com wrote: Are you using multiple web processes, and are you referring to the old admin tool reloader or the toolshed reloading interface? -Dannon On Feb 5, 2013, at 9:13 PM, Anthonius deBoer thondeb...@me.com wrote: Hi, I find that reloading a tool's configuration file does not really work. First, you have to click the reload buttow twice to actually have it update the VERSION number (so it does read something)... But when I try to run my tool, the old bug is still there... I am using proxy server so something may still be
Re: [galaxy-dev] Reloading a tools configuration does not seem to actually work
On Thu, Feb 14, 2013 at 10:40 AM, Nate Coraor n...@bx.psu.edu wrote: What I am facing, is that I have 100 FASTQ pairs or so, for a single flowcell, I can start the analysis of that set from the UI, but it will just crank through them and takes about 2-4 minutues for each pair to be processed, so with 100 pairs or so, you are looking 3-4 hours of an hourglass before control is given back to the user... Is this in the context of starting a workflow with hundreds of inputs? I believe this is entirely in the web process, creating a workflow requires creating tons of datasets, which requires tons of database flushes. I have a patch to fix this from a long time ago but it would need substantial testing. I think we should also background the process, but this depends on having a way to attach the workflow invocation to the history, hence dataset groups. All the pieces are coming together on this. -- James Taylor, Assistant Professor, Biology/CS, Emory University ___ 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] Reloading a tools configuration does not seem to actually work
On Feb 7, 2013, at 2:43 PM, Anthonius deBoer wrote: That's very unfortunate... I have a ton of tools and I guess now I have to create a package for them in a local toolshed to update them in a running galaxy server? In any case...The toolshed installation also does not work for me...I still have to restart galaxy, even after using the toolshed approach to install a tool...It either does not show up at all or give a bunch of errors, about not being able to find the tool... Is this also related to the fact I have two webservers and am behind a proxy server as well? Hi Thon, Essentially yes, there is no way for one web process to communicate with others that it has installed a tool. We'd like to allow for this sort of notification via a message queue, but we don't have a proper message queue in Galaxy right now. --nate Thon On Feb 07, 2013, at 05:29 AM, Dannon Baker dannonba...@me.com wrote: Unfortunately not, and with the migration of tools to the toolshed installation mechanism I don't imagine this will be addressed (at least by the team) anytime soon. If you wanted you could probably write a script that would reload a specified tool in each of the separate web processes, or just implement a complete rolling restart of your web processes to avoid service disruption while still loading the tool updates. -Dannon On Feb 6, 2013, at 8:40 PM, Anthonius deBoer thondeb...@me.com wrote: I am indeed using multiple web processes and I guess I am talking about the old admine tool reloader... Is there any other way to do this for your own tools that you just manually place in tools etc.? Thon On Feb 05, 2013, at 06:22 PM, Dannon Baker dannonba...@me.com wrote: Are you using multiple web processes, and are you referring to the old admin tool reloader or the toolshed reloading interface? -Dannon On Feb 5, 2013, at 9:13 PM, Anthonius deBoer thondeb...@me.com wrote: Hi, I find that reloading a tool's configuration file does not really work. First, you have to click the reload buttow twice to actually have it update the VERSION number (so it does read something)... But when I try to run my tool, the old bug is still there... I am using proxy server so something may still be cached, but I have to restart my server for it actually to pick up the changes... Any ideas? Thon ___ 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/ ___ 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] Reloading a tools configuration does not seem to actually work
Would this problem go away if I only used ONE webserver in my proxy setting and not use a balancer?I may not need it and if it means I could not use the toolshed effectively, it may be worth it not to use balancing..What i really need is the manager being balanced, since submitting a workflow with 100's of BAM files can take hours just to get started...ANy change we can run multiple managers?ThanksOn Feb 13, 2013, at 07:59 AM, Nate Coraor n...@bx.psu.edu wrote:On Feb 7, 2013, at 2:43 PM, Anthonius deBoer wrote: That's very unfortunate... I have a ton of tools and I guess now I have to create a package for them in a local toolshed to update them in a running galaxy server?In any case...The toolshed installation also does not work for me...I still have to restart galaxy, even after using the toolshed approach to install a tool...It either does not show up at all or give a bunch of errors, about not being able to find the tool...Is this also related to the fact I have two webservers and am behind a proxy server as well? Hi Thon, Essentially yes, there is no way for one web process to communicate with others that it has installed a tool. We'd like to allow for this sort of notification via a message queue, but we don't have a proper message queue in Galaxy right now. --nate ThonOn Feb 07, 2013, at 05:29 AM, Dannon Baker dannonba...@me.com wrote:Unfortunately not, and with the migration of tools to the toolshed installation mechanism I don't imagine this will be addressed (at least by the team) anytime soon. If you wanted you could probably write a script that would reload a specified tool in each of the separate web processes, or just implement a complete rolling restart of your web processes to avoid service disruption while still loading the tool updates.-Dannon On Feb 6, 2013, at 8:40 PM, Anthonius deBoer thondeb...@me.com wrote: I am indeed using multiple web processes and I guess I am talking about the "old" admine tool reloader... Is there any other way to do this for your own tools that you just manually place in tools etc.? Thon On Feb 05, 2013, at 06:22 PM, Dannon Baker dannonba...@me.com wrote: Are you using multiple web processes, and are you referring to the old admin tool reloader or the toolshed reloading interface? -Dannon On Feb 5, 2013, at 9:13 PM, Anthonius deBoer thondeb...@me.com wrote: Hi,I find that reloading a tool's configuration file does not really work.First, you have to click the reload buttow twice to actually have it update the VERSION number (so it does read something)...But when I try to run my tool, the old bug is still there...I am using proxy server so something may still be cached, but I have to restart my server for it actually to pick up the changes...Any ideas?Thon___Please keep all replies on the list by using "reply all"in your mail client. To manage your subscriptions to thisand 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/ ___ 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] Reloading a tools configuration does not seem to actually work
On Feb 13, 2013, at 4:12 PM, Anthonius deBoer wrote: Would this problem go away if I only used ONE webserver in my proxy setting and not use a balancer? I may not need it and if it means I could not use the toolshed effectively, it may be worth it not to use balancing.. No, because your manager/handlers will still need to be restarted to pick up the new tools. The only way you can have it work without restarting is to have everything in a single process. What i really need is the manager being balanced, since submitting a workflow with 100's of BAM files can take hours just to get started...ANy change we can run multiple managers? I'm surprised the manager is the holdup here since all it does is assign a handler. Regardless, in the development branch (which will be the next stable/release branch), the manager has been killed, and handlers are assigned directly by the web processes. --nate Thanks On Feb 13, 2013, at 07:59 AM, Nate Coraor n...@bx.psu.edu wrote: On Feb 7, 2013, at 2:43 PM, Anthonius deBoer wrote: That's very unfortunate... I have a ton of tools and I guess now I have to create a package for them in a local toolshed to update them in a running galaxy server? In any case...The toolshed installation also does not work for me...I still have to restart galaxy, even after using the toolshed approach to install a tool...It either does not show up at all or give a bunch of errors, about not being able to find the tool... Is this also related to the fact I have two webservers and am behind a proxy server as well? Hi Thon, Essentially yes, there is no way for one web process to communicate with others that it has installed a tool. We'd like to allow for this sort of notification via a message queue, but we don't have a proper message queue in Galaxy right now. --nate Thon On Feb 07, 2013, at 05:29 AM, Dannon Baker dannonba...@me.com wrote: Unfortunately not, and with the migration of tools to the toolshed installation mechanism I don't imagine this will be addressed (at least by the team) anytime soon. If you wanted you could probably write a script that would reload a specified tool in each of the separate web processes, or just implement a complete rolling restart of your web processes to avoid service disruption while still loading the tool updates. -Dannon On Feb 6, 2013, at 8:40 PM, Anthonius deBoer thondeb...@me.com wrote: I am indeed using multiple web processes and I guess I am talking about the old admine tool reloader... Is there any other way to do this for your own tools that you just manually place in tools etc.? Thon On Feb 05, 2013, at 06:22 PM, Dannon Baker dannonba...@me.com wrote: Are you using multiple web processes, and are you referring to the old admin tool reloader or the toolshed reloading interface? -Dannon On Feb 5, 2013, at 9:13 PM, Anthonius deBoer thondeb...@me.com wrote: Hi, I find that reloading a tool's configuration file does not really work. First, you have to click the reload buttow twice to actually have it update the VERSION number (so it does read something)... But when I try to run my tool, the old bug is still there... I am using proxy server so something may still be cached, but I have to restart my server for it actually to pick up the changes... Any ideas? Thon ___ 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/ ___ 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] Reloading a tools configuration does not seem to actually work
Interesting!But maybe it is not the manager that is the bottleneck, but which process is the one that takes the inputs from the webpage (or in the API) and prepares all the files that are produced by the workflows?I guess it is the MAIN server?THAT is the one that is the bottleneck I think then...Are there any plans to make that process parallel?What I am facing, is that I have 100 FASTQ pairs or so, for a single flowcell, I can start the analysis of that set from the UI, but it will just crank through them and takes about 2-4 minutues for each pair to be processed, so with 100 pairs or so, you are looking 3-4 hours of an hourglass before control is given back to the user...It would be ideal if we would farm out the parsing of the web input to the cluster, so the creation of the histories and datasets is no longer the bottleneckHow do others deal with large sequencing projects on this list?Are there any groups that routinely do 100-200 pairs of FASTQ files from within galaxy?I would like to hear their experience...ThanksThonOn Feb 13, 2013, at 01:44 PM, Nate Coraor n...@bx.psu.edu wrote:On Feb 13, 2013, at 4:12 PM, Anthonius deBoer wrote: Would this problem go away if I only used ONE webserver in my proxy setting and not use a balancer? I may not need it and if it means I could not use the toolshed effectively, it may be worth it not to use balancing.. No, because your manager/handlers will still need to be restarted to pick up the new tools. The only way you can have it work without restarting is to have everything in a single process. What i really need is the manager being balanced, since submitting a workflow with 100's of BAM files can take hours just to get started...ANy change we can run multiple managers? I'm surprised the manager is the holdup here since all it does is assign a handler. Regardless, in the development branch (which will be the next stable/release branch), the manager has been killed, and handlers are assigned directly by the web processes. --nate ThanksOn Feb 13, 2013, at 07:59 AM, Nate Coraor n...@bx.psu.edu wrote:On Feb 7, 2013, at 2:43 PM, Anthonius deBoer wrote: That's very unfortunate... I have a ton of tools and I guess now I have to create a package for them in a local toolshed to update them in a running galaxy server? In any case...The toolshed installation also does not work for me...I still have to restart galaxy, even after using the toolshed approach to install a tool...It either does not show up at all or give a bunch of errors, about not being able to find the tool... Is this also related to the fact I have two webservers and am behind a proxy server as well?Hi Thon,Essentially yes, there is no way for one web process to communicate with others that it has installed a tool. We'd like to allow for this sort of notification via a message queue, but we don't have a proper message queue in Galaxy right now.--nateThon On Feb 07, 2013, at 05:29 AM, Dannon Baker dannonba...@me.com wrote: Unfortunately not, and with the migration of tools to the toolshed installation mechanism I don't imagine this will be addressed (at least by the team) anytime soon. If you wanted you could probably write a script that would reload a specified tool in each of the separate web processes, or just implement a complete rolling restart of your web processes to avoid service disruption while still loading the tool updates. -Dannon On Feb 6, 2013, at 8:40 PM, Anthonius deBoer thondeb...@me.com wrote: I am indeed using multiple web processes and I guess I am talking about the "old" admine tool reloader...Is there any other way to do this for your own tools that you just manually place in tools etc.?ThonOn Feb 05, 2013, at 06:22 PM, Dannon Baker dannonba...@me.com wrote:Are you using multiple web processes, and are you referring to the old admin tool reloader or the toolshed reloading interface?-DannonOn Feb 5, 2013, at 9:13 PM, Anthonius deBoer thondeb...@me.com wrote: Hi, I find that reloading a tool's configuration file does not really work. First, you have to click the reload buttow twice to actually have it update the VERSION number (so it does read something)... But when I try to run my tool, the old bug is still there... I am using proxy server so something may still be cached, but I have to restart my server for it actually to pick up the changes... Any ideas? Thon ___ 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
Re: [galaxy-dev] Reloading a tools configuration does not seem to actually work
Unfortunately not, and with the migration of tools to the toolshed installation mechanism I don't imagine this will be addressed (at least by the team) anytime soon. If you wanted you could probably write a script that would reload a specified tool in each of the separate web processes, or just implement a complete rolling restart of your web processes to avoid service disruption while still loading the tool updates. -Dannon On Feb 6, 2013, at 8:40 PM, Anthonius deBoer thondeb...@me.com wrote: I am indeed using multiple web processes and I guess I am talking about the old admine tool reloader... Is there any other way to do this for your own tools that you just manually place in tools etc.? Thon On Feb 05, 2013, at 06:22 PM, Dannon Baker dannonba...@me.com wrote: Are you using multiple web processes, and are you referring to the old admin tool reloader or the toolshed reloading interface? -Dannon On Feb 5, 2013, at 9:13 PM, Anthonius deBoer thondeb...@me.com wrote: Hi, I find that reloading a tool's configuration file does not really work. First, you have to click the reload buttow twice to actually have it update the VERSION number (so it does read something)... But when I try to run my tool, the old bug is still there... I am using proxy server so something may still be cached, but I have to restart my server for it actually to pick up the changes... Any ideas? Thon ___ 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] Reloading a tools configuration does not seem to actually work
That's very unfortunate...I have a ton of tools and I guess now I have to create a package for them in a local toolshed to update them in a running galaxy server?In any case...The toolshed installation also does not work for me...I still have to restart galaxy, even after using the toolshed approach to install a tool...It either does not show up at all or give a bunch of errors, about not being able to find the tool...Is this also related to the fact I have two webservers and am behind a proxy server as well?ThonOn Feb 07, 2013, at 05:29 AM, Dannon Baker dannonba...@me.com wrote:Unfortunately not, and with the migration of tools to the toolshed installation mechanism I don't imagine this will be addressed (at least by the team) anytime soon. If you wanted you could probably write a script that would reload a specified tool in each of the separate web processes, or just implement a complete rolling restart of your web processes to avoid service disruption while still loading the tool updates. -Dannon On Feb 6, 2013, at 8:40 PM, Anthonius deBoer thondeb...@me.com wrote: I am indeed using multiple web processes and I guess I am talking about the "old" admine tool reloader... Is there any other way to do this for your own tools that you just manually place in tools etc.?ThonOn Feb 05, 2013, at 06:22 PM, Dannon Baker dannonba...@me.com wrote:Are you using multiple web processes, and are you referring to the old admin tool reloader or the toolshed reloading interface?-DannonOn Feb 5, 2013, at 9:13 PM, Anthonius deBoer thondeb...@me.com wrote: Hi, I find that reloading a tool's configuration file does not really work. First, you have to click the reload buttow twice to actually have it update the VERSION number (so it does read something)... But when I try to run my tool, the old bug is still there... I am using proxy server so something may still be cached, but I have to restart my server for it actually to pick up the changes... Any ideas? Thon ___ 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] Reloading a tools configuration does not seem to actually work
I am indeed using multiple web processes and I guess I am talking about the "old" admine tool reloader...Is there any other way to do this for your own tools that you just manually place in tools etc.?ThonOn Feb 05, 2013, at 06:22 PM, Dannon Baker dannonba...@me.com wrote:Are you using multiple web processes, and are you referring to the old admin tool reloader or the toolshed reloading interface? -Dannon On Feb 5, 2013, at 9:13 PM, Anthonius deBoer thondeb...@me.com wrote: Hi,I find that reloading a tool's configuration file does not really work. First, you have to click the reload buttow twice to actually have it update the VERSION number (so it does read something)... But when I try to run my tool, the old bug is still there...I am using proxy server so something may still be cached, but I have to restart my server for it actually to pick up the changes...Any ideas?Thon ___ 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/
