Re: [galaxy-dev] Reload .loc files without restarting Galaxy system?
On Wed, Apr 6, 2011 at 10:30 PM, Luobin Yang yangl...@isu.edu wrote: Hi, The reload a tool's configuration menu avoids restarting Galaxy system when a tool's web interface changed, but it doesn't seem to reload the .loc files that a tool's XML file uses. I am wondering if it's possible to reload the .loc file also? Thanks, Luobin I'd like to be able to do this too. I filed an enhancement bug: https://bitbucket.org/galaxy/galaxy-central/issue/538 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/
[galaxy-dev] Wrapper generator.
Dear, I need to add a number of tools to my local Galaxy installation, but the size of the wrappers I've seen keep me from writing one. Are there wrapper generators to make this task easier? If not, I might want to make one. A possible implementation I'm considering is to first make a (WSDL) description of any command line tool (using soaplab2 for example) and by making a general wrapper builder that takes WSDL as input. Does something similar already exist and if not, does this idea sound okay? With kind regards, Jeroen. -- Jeroen F. J. Laros - j.f.j.la...@lumc.nl ___ 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] Wrapper generator.
Hi Jeroen, You can use web services thanks to the work from Sumedha Ganjoo et al. from the University of Georgia. You can find that on the community site: Tools Shed - Data Source - Suite of Web service addition tools. http://community.g2.bx.psu.edu/common/view_tool?sort=suitecntrller=toolwebapp=communityoperation=view_toolid=1766c85c07803d78 Cheers, Pi On May 13, 2011, at 1:41 PM, J. F. J. Laros wrote: Dear, I need to add a number of tools to my local Galaxy installation, but the size of the wrappers I've seen keep me from writing one. Are there wrapper generators to make this task easier? If not, I might want to make one. A possible implementation I'm considering is to first make a (WSDL) description of any command line tool (using soaplab2 for example) and by making a general wrapper builder that takes WSDL as input. Does something similar already exist and if not, does this idea sound okay? With kind regards, Jeroen. -- Jeroen F. J. Laros - j.f.j.la...@lumc.nl ___ 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/
[galaxy-dev] select menu in conditional tag cannot be set at runtime in workflow editor
Hi all, In a tool XML I have a select menu param within/driving a conditional tag and in the workflow editor it doesn't let me choose to allow the user to set this select menu at runtime? Is this a bug? best, leandro ___ 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] Wrapper generator.
Hi Pieter, Thanks for the reply, but from the looks of it, this is a way to incorporate webservice clients into galaxy. What I want is slightly different. I'm talking about adding a normal command line tool (an aligner for example) but I'm not willing to write a wrapper each time (the wrapper for BWA for example is 327 lines). If a computer readable description of the interface exists, this description can be used to generate a python wrapper. I mentioned WSDL because this also gives a description of an interface, but any equivalent description would of course be fine. Ideally, such a description is maintained by the developer of the tool in question. With kind regards, Jeroen. On Fri, May 13, 2011 at 02:16:37PM +0200, Pieter Neerincx wrote: Hi Jeroen, You can use web services thanks to the work from Sumedha Ganjoo et al. from the University of Georgia. You can find that on the community site: Tools Shed - Data Source - Suite of Web service addition tools. http://community.g2.bx.psu.edu/common/view_tool?sort=suitecntrller=toolwebapp=communityoperation=view_toolid=1766c85c07803d78 Cheers, Pi On May 13, 2011, at 1:41 PM, J. F. J. Laros wrote: Dear, I need to add a number of tools to my local Galaxy installation, but the size of the wrappers I've seen keep me from writing one. Are there wrapper generators to make this task easier? If not, I might want to make one. A possible implementation I'm considering is to first make a (WSDL) description of any command line tool (using soaplab2 for example) and by making a general wrapper builder that takes WSDL as input. Does something similar already exist and if not, does this idea sound okay? With kind regards, Jeroen. -- Jeroen F. J. Laros - j.f.j.la...@lumc.nl ___ 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/ -- Jeroen F. J. Laros - j.f.j.la...@lumc.nl ___ 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] Wrapper generator.
On Fri, May 13, 2011 at 2:12 PM, J. F. J. Laros j.f.j.la...@lumc.nl wrote: Hi Pieter, Thanks for the reply, but from the looks of it, this is a way to incorporate webservice clients into galaxy. What I want is slightly different. I'm talking about adding a normal command line tool (an aligner for example) but I'm not willing to write a wrapper each time (the wrapper for BWA for example is 327 lines). If a computer readable description of the interface exists, this description can be used to generate a python wrapper. I mentioned WSDL because this also gives a description of an interface, but any equivalent description would of course be fine. Ideally, such a description is maintained by the developer of the tool in question. With kind regards, Jeroen. How many tools can you name that come with such a machine readable file describing their command line interface? I can think of only one - the EMBOSS tool suite and their ACD files (used internally by EMBOSS to generate the command line help, documentation, and do the command line option parsing). Unfortunately I don't think there is an easy answer - even if wrapping a tool where all the input and output formats are already supported in 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] Wrapper generator.
An alternative might be to have something like GenePattern has. It's not as seamless for the person who wants the wrapper as what's been suggested here, but it's easier than creating a lengthy XML file. GenePattern has an HTML Form interface for entering all the components of your tool, including the command-line you want to expose and the parameters you want to make available, and then it generates the back-end. There are definite down-sides to this. I've never tested what keeps the tool in GenePattern from letting you do destructive things. Dave On 5/13/11 9:41 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Fri, May 13, 2011 at 2:12 PM, J. F. J. Laros j.f.j.la...@lumc.nl wrote: Hi Pieter, Thanks for the reply, but from the looks of it, this is a way to incorporate webservice clients into galaxy. What I want is slightly different. I'm talking about adding a normal command line tool (an aligner for example) but I'm not willing to write a wrapper each time (the wrapper for BWA for example is 327 lines). If a computer readable description of the interface exists, this description can be used to generate a python wrapper. I mentioned WSDL because this also gives a description of an interface, but any equivalent description would of course be fine. Ideally, such a description is maintained by the developer of the tool in question. With kind regards, Jeroen. How many tools can you name that come with such a machine readable file describing their command line interface? I can think of only one - the EMBOSS tool suite and their ACD files (used internally by EMBOSS to generate the command line help, documentation, and do the command line option parsing). Unfortunately I don't think there is an easy answer - even if wrapping a tool where all the input and output formats are already supported in 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/ ___ 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] Wrapper generator.
Dear Dave, This indeed sounds like an interesting alternative. I'll look into it. With kind regards, Jeroen. On Fri, May 13, 2011 at 01:48:12PM +, Dave Walton wrote: An alternative might be to have something like GenePattern has. It's not as seamless for the person who wants the wrapper as what's been suggested here, but it's easier than creating a lengthy XML file. GenePattern has an HTML Form interface for entering all the components of your tool, including the command-line you want to expose and the parameters you want to make available, and then it generates the back-end. There are definite down-sides to this. I've never tested what keeps the tool in GenePattern from letting you do destructive things. Dave On 5/13/11 9:41 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Fri, May 13, 2011 at 2:12 PM, J. F. J. Laros j.f.j.la...@lumc.nl wrote: Hi Pieter, Thanks for the reply, but from the looks of it, this is a way to incorporate webservice clients into galaxy. What I want is slightly different. I'm talking about adding a normal command line tool (an aligner for example) but I'm not willing to write a wrapper each time (the wrapper for BWA for example is 327 lines). If a computer readable description of the interface exists, this description can be used to generate a python wrapper. I mentioned WSDL because this also gives a description of an interface, but any equivalent description would of course be fine. Ideally, such a description is maintained by the developer of the tool in question. With kind regards, Jeroen. How many tools can you name that come with such a machine readable file describing their command line interface? I can think of only one - the EMBOSS tool suite and their ACD files (used internally by EMBOSS to generate the command line help, documentation, and do the command line option parsing). Unfortunately I don't think there is an easy answer - even if wrapping a tool where all the input and output formats are already supported in 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/ -- Jeroen F. J. Laros - j.f.j.la...@lumc.nl ___ 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 with SGE cluster
On May 12, 2011, at 3:43 PM, Nate Coraor wrote: Shantanu Pavgi wrote: I need some help in configuring galaxy with SGE scheduler using unified method. The galaxy is running on a system distinct from SGE scheduler install. The cluster nodes can access galaxy install, galaxy-tools and dataset files using NFS. I am not sure how drmaa works and how galaxy submits jobs to the cluster/scheduler. Do we need specify some type of connection string or ssh-config to connect with the cluster/scheduler? Does it need any configuration changes on the SGE scheduler side? Any explanation regarding this will be really helpful. Hi Shantanu, You'll need to locate your drmaa library, it can be found wherever SGE is installed. For example, if SGE is installed for 64-bit Linux in /galaxy/sge, then the drmaa library should be located at: /galaxy/sge/lib/lx24-amd64/libdrmaa.so.1.0 Once you have the path, do the following (adjusting the value for the path to libdrmaa.so.1.0 at your site): export DRMAA_LIBRARY_PATH=/galaxy/sge/lib/lx24-amd64/libdrmaa.so.1.0 Then in universe_wsgi.ini, set: start_job_runners = drmaa default_cluster_job_runner = drmaa:/// This should be all you need. Thanks for the explanation Nate. I will try it out. Also, after integrating with the cluster is there any pre-processing or post-processing done on the galaxy system locally? I would like to get some sense on how much RAM and other system resources will be required for the galaxy system itself. I am assuming it can be fairly thin system for running web server, database and job submission processes. Is it a correct assumption or am I missing something here? -- Shantanu. ___ 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/
