Re: [galaxy-dev] Managing large database lists in tool wrappers?
On 31.03.2014 22:58, Smithies, Russell: Does anyone have a workable solution to managing and displaying large lists in tool wrappers? eg. a database list containing hundreds of enteries in the blast+ tool? (we have 1,056 different blast databases). On Mon, Mar 31, 2014 at 10:18 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Russell, would something like a http://ivaynberg.github.io/select2/ field work for you? Which bit of that do you mean Bjoern? Galaxy already does searching within the drop down box (when the list is above some threshold in length) which is very handy. Mind you, we currently have under a hundred BLAST databases defined in our *.loc files, so this is an order of magnitude less than Russell's setup. What do you mean with include tags? Are you aware of Galaxy macros? https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#Direct_XML_Macros Cheers, Bjoern Since it looks like you are modifying the BLAST+ wrappers, they are already using Galaxy macros - you probably only need to change the ncbi_macros.xml file once and have this work on all of BLASTP, BLASTN, etc. i.e. Modify the input_conditional_nucleotide_db and input_conditional_protein_db definitions (and potentially the token @BLAST_DB_SUBJECT@ where those parameters are inserted in the the Cheetah command line template): https://github.com/peterjc/galaxy_blast/blob/master/tools/ncbi_blast_plus/ncbi_macros.xml Regards, 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] restarting multiple web workers
Hi, I’m using the multiple web server stuff described here: https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling that seems to address the responsiveness issues i see when many users are active. However, when i add a new tool - it does not alway show up (only for one of the workers maybe?) Right now I’m restarting, but this costs a minute or two of downtime as the server starts up. Has anyone experimented with rolling restarts of web server processes? Alternatively, has anyone found a good way to speed up the startup process? Thanks! Brad -- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] restarting multiple web workers
On Tue, Apr 1, 2014 at 2:48 PM, Langhorst, Brad langho...@neb.com wrote: However, when i add a new tool - it does not alway show up (only for one of the workers maybe?) I don't have good answers for the rest of your questions (I'm sure someone else can chime in), but I do have some information about this. You're correct in that, currently, the only process that will reflect the new or reloaded tool is the one the admin user was actually interacting with. While it doesn't solve your problem right now, I've been working on new mechanisms for reloading tools and generally interacting with multiple processes that will be available soon. -Dannon ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Managing large database lists in tool wrappers?
Hi, On 31.03.2014 22:58, Smithies, Russell: Does anyone have a workable solution to managing and displaying large lists in tool wrappers? eg. a database list containing hundreds of enteries in the blast+ tool? (we have 1,056 different blast databases). On Mon, Mar 31, 2014 at 10:18 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Russell, would something like a http://ivaynberg.github.io/select2/ field work for you? Which bit of that do you mean Bjoern? Galaxy already does searching within the drop down box (when the list is above some threshold in length) which is very handy. Yes, that was my intention. To point out that something like that should be possible. It new for me that there is a threshold to enable that mechanism. Mind you, we currently have under a hundred BLAST databases defined in our *.loc files, so this is an order of magnitude less than Russell's setup. We also have only 3x. So no problem until now. Ciao, Bjoern What do you mean with include tags? Are you aware of Galaxy macros? https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#Direct_XML_Macros Cheers, Bjoern Since it looks like you are modifying the BLAST+ wrappers, they are already using Galaxy macros - you probably only need to change the ncbi_macros.xml file once and have this work on all of BLASTP, BLASTN, etc. i.e. Modify the input_conditional_nucleotide_db and input_conditional_protein_db definitions (and potentially the token @BLAST_DB_SUBJECT@ where those parameters are inserted in the the Cheetah command line template): https://github.com/peterjc/galaxy_blast/blob/master/tools/ncbi_blast_plus/ncbi_macros.xml Regards, 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Bowtie2 and tophat2 data library set up
Hi Huayan, these tools should mostly be available from the Tool Shed (Galaxy's appstore). You can install them easily into any Galaxy that you are an admin of. Please see more information here: https://wiki.galaxyproject.org/Admin/Tools Martin, galaxy team On Thu, Mar 20, 2014 at 1:57 AM, Huayan Gao huayan...@gmail.com wrote: Hi Martin, Actually I want a NGS Toolbox Beta tool panel exactly like the usegalaxy.org. How can I achieve this? I found myself looking for the tools and put them to tool_conf.xml which is very tedious. Is there a better way to do it? Best, Huayan On Thu, Mar 20, 2014 at 11:43 AM, Huayan Gao huayan...@gmail.com wrote: Thanks Martin! One more question, I want to install all the migrated tools from stage 9, that is NGS tools to my local galaxy. I tried but always got some problems. Do you have the instructions on wiki too? Thanks, Huayan On Thu, Mar 20, 2014 at 10:27 AM, Martin Čech mar...@bx.psu.edu wrote: Hello again Huayan, the page got renamed and redirect was not in place. I have put it there and the new page has even more info on it! :) thank you for using Galaxy! Martin On Wed, Mar 19, 2014 at 10:18 PM, Martin Čech mar...@bx.psu.edu wrote: Hello Huayan, I don't know why the wiki page disappeared and I will investigate it. In the meantime I have found a cached copy for you: http://webcache.googleusercontent.com/search?q=cache:SWWpt6XsmCkJ:https://wiki.galaxyproject.org/Admin/NGS%2520Local%2520Setup+cd=1hl=enct=clnkgl=us Martin, Galaxy team On Wed, Mar 19, 2014 at 9:44 PM, Huayan Gao huayan...@gmail.comwrote: Hi, I wanted to use bowtie2 and tophat2 locally. I remembered you have instructions about how to set up the library here, but it is not accessible any more. https://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Can you direct me to the right page or send me the documents please? Thanks, Huayan ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
