[galaxy-dev] planemo with --docker and --conda_dependency_resolution
Hi, I’m trying to test a few tools, one of which uses a docker container, the others use dependencies that can be found in conda. I can test each one by using either —docker or —conda_dependency_resolution with planemo, but when I try to give both of these, it seems to want to only use docker and fails because it can’t find a usable container. I’ve hunted around the planemo sources but i can’t see what magic is creating this problem. Am I just asking too much? Any pointers appreciated. Thanks, Steve — Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Elastic Bean Stalk
Hi Ryan, if you are planning to use Galaxy on AWS I recommend you to have a look at the CloudMan (https://wiki.galaxyproject.org/CloudMan). It will help you orchestrate the instances and scale to meet the needs of your users. It has been a while since I used the EB, but generally when scaling Galaxy you do not want to scale the whole webserver/app stack because you only need the worker nodes for jobs. Cloudman brings this setup to you with no strings attached. How many users and what type of jobs/load are we talking about? Thanks. Martin On Tue, Nov 15, 2016 at 11:26 AM Ryan G wrote: > Hi all - I was wondering, if we deploy Galaxy in AWS, can we take > advantage of Elastic BeanStalk to scale our instances based on demand > instead of trying to configure Galaxy to perform well for our users? > > Ryan > > ___ > 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: > https://lists.galaxyproject.org/ > > 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Elastic Bean Stalk
Hi all - I was wondering, if we deploy Galaxy in AWS, can we take advantage of Elastic BeanStalk to scale our instances based on demand instead of trying to configure Galaxy to perform well for our users? Ryan ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Reporting issues for the wiki? e.g. universe_wgsi.ini still widely used
Unfortunately we weren't able to use pandoc, coming from Moin. Regarding edit links, yes, that's exactly what we have implemented. -Dannon On Tue, Nov 15, 2016 at 10:26 AM, Peter Cock wrote: > Thanks Dannon, > > I've logged the universe_wsgi.ini issue there as > https://github.com/galaxyproject/galaxy-site/issues/16 > > Interesting to see yet another MediaWiki site being moved to > GitHub with Markdown - although not with GitHub pages in this > case. I'd guess you guys used the wonderful pandoc for the > conversion? > > I assume you'll be able to add "edit" buttons to pages pointing > at the markdown pages on GitHub? While it could be prettier, > this works pretty well for us using GitHub Pages: > > https://github.com/biopython/biopython.github.io/pull/78 > > Regards, > > Peter > > On Tue, Nov 15, 2016 at 3:10 PM, Dannon Baker > wrote: > > Hi Peter, > > > > We're in the middle of migrating the wiki right now -- you may notice > that > > the current wiki is in read-only mode. Going forward, the place to > report > > (and fix) issues like that will be > > https://github.com/galaxyproject/galaxy-site. > > > > -Dannon > > > > On Tue, Nov 15, 2016 at 10:06 AM, Peter Cock > > wrote: > >> > >> Hello all, > >> > >> Is there a specific issue tracker for the wiki? It seems wrong to > >> open an issue on the main GitHub code repository... > >> > >> e.g. Many of the documentation pages still refer to the legacy > >> configuration filename universe_wgsi.ini rather than the new > >> name of config/galaxy.ini > >> > >> Problem pages include: > >> > >> https://wiki.galaxyproject.org/Learn/SecurityFeatures > >> https://wiki.galaxyproject.org/Admin/DiskQuotas > >> https://wiki.galaxyproject.org/Admin/SampleTracking/Demo > >> https://wiki.galaxyproject.org/Admin/Tools/MultipleOutputFiles > >> https://wiki.galaxyproject.org/Admin/Config/GenomeSpace > >> https://wiki.galaxyproject.org/Admin/Config/ApacheExternalUserAuth > >> https://wiki.galaxyproject.org/VisualizationSetup > >> https://wiki.galaxyproject.org/ToolShedApi > >> > >> Other pages would benefit from minor edits to at least put the old form > >> second and in brackets: > >> > >> https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster > >> https://wiki.galaxyproject.org/Admin/Interface > >> https://wiki.galaxyproject.org/ToolShed/InstallingRepositoriesToGalaxy > >> Some pages look fine, e.g. > >> > >> https://wiki.galaxyproject.org/ToolShed/InstallingAndCompilingPackages > >> > >> Or are clearly dated and appropriate for the time, e.g. Dev news briefs > >> > >> https://wiki.galaxyproject.org/DevNewsBriefs/2010_07_16 > >> > >> This means lots of pages with the term which are fine: > >> > >> > >> https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax?action= > fullsearch&titlesearch=0&from=0&value=universe_wsgi.ini > >> > >> 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: > >> https://lists.galaxyproject.org/ > >> > >> 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Reporting issues for the wiki? e.g. universe_wgsi.ini still widely used
Thanks Dannon, I've logged the universe_wsgi.ini issue there as https://github.com/galaxyproject/galaxy-site/issues/16 Interesting to see yet another MediaWiki site being moved to GitHub with Markdown - although not with GitHub pages in this case. I'd guess you guys used the wonderful pandoc for the conversion? I assume you'll be able to add "edit" buttons to pages pointing at the markdown pages on GitHub? While it could be prettier, this works pretty well for us using GitHub Pages: https://github.com/biopython/biopython.github.io/pull/78 Regards, Peter On Tue, Nov 15, 2016 at 3:10 PM, Dannon Baker wrote: > Hi Peter, > > We're in the middle of migrating the wiki right now -- you may notice that > the current wiki is in read-only mode. Going forward, the place to report > (and fix) issues like that will be > https://github.com/galaxyproject/galaxy-site. > > -Dannon > > On Tue, Nov 15, 2016 at 10:06 AM, Peter Cock > wrote: >> >> Hello all, >> >> Is there a specific issue tracker for the wiki? It seems wrong to >> open an issue on the main GitHub code repository... >> >> e.g. Many of the documentation pages still refer to the legacy >> configuration filename universe_wgsi.ini rather than the new >> name of config/galaxy.ini >> >> Problem pages include: >> >> https://wiki.galaxyproject.org/Learn/SecurityFeatures >> https://wiki.galaxyproject.org/Admin/DiskQuotas >> https://wiki.galaxyproject.org/Admin/SampleTracking/Demo >> https://wiki.galaxyproject.org/Admin/Tools/MultipleOutputFiles >> https://wiki.galaxyproject.org/Admin/Config/GenomeSpace >> https://wiki.galaxyproject.org/Admin/Config/ApacheExternalUserAuth >> https://wiki.galaxyproject.org/VisualizationSetup >> https://wiki.galaxyproject.org/ToolShedApi >> >> Other pages would benefit from minor edits to at least put the old form >> second and in brackets: >> >> https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster >> https://wiki.galaxyproject.org/Admin/Interface >> https://wiki.galaxyproject.org/ToolShed/InstallingRepositoriesToGalaxy >> Some pages look fine, e.g. >> >> https://wiki.galaxyproject.org/ToolShed/InstallingAndCompilingPackages >> >> Or are clearly dated and appropriate for the time, e.g. Dev news briefs >> >> https://wiki.galaxyproject.org/DevNewsBriefs/2010_07_16 >> >> This means lots of pages with the term which are fine: >> >> >> https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax?action=fullsearch&titlesearch=0&from=0&value=universe_wsgi.ini >> >> 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: >> https://lists.galaxyproject.org/ >> >> 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Reporting issues for the wiki? e.g. universe_wgsi.ini still widely used
Hi Peter, We're in the middle of migrating the wiki right now -- you may notice that the current wiki is in read-only mode. Going forward, the place to report (and fix) issues like that will be https://github.com/galaxyproject/galaxy-site. -Dannon On Tue, Nov 15, 2016 at 10:06 AM, Peter Cock wrote: > Hello all, > > Is there a specific issue tracker for the wiki? It seems wrong to > open an issue on the main GitHub code repository... > > e.g. Many of the documentation pages still refer to the legacy > configuration filename universe_wgsi.ini rather than the new > name of config/galaxy.ini > > Problem pages include: > > https://wiki.galaxyproject.org/Learn/SecurityFeatures > https://wiki.galaxyproject.org/Admin/DiskQuotas > https://wiki.galaxyproject.org/Admin/SampleTracking/Demo > https://wiki.galaxyproject.org/Admin/Tools/MultipleOutputFiles > https://wiki.galaxyproject.org/Admin/Config/GenomeSpace > https://wiki.galaxyproject.org/Admin/Config/ApacheExternalUserAuth > https://wiki.galaxyproject.org/VisualizationSetup > https://wiki.galaxyproject.org/ToolShedApi > > Other pages would benefit from minor edits to at least put the old form > second and in brackets: > > https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster > https://wiki.galaxyproject.org/Admin/Interface > https://wiki.galaxyproject.org/ToolShed/InstallingRepositoriesToGalaxy > Some pages look fine, e.g. > > https://wiki.galaxyproject.org/ToolShed/InstallingAndCompilingPackages > > Or are clearly dated and appropriate for the time, e.g. Dev news briefs > > https://wiki.galaxyproject.org/DevNewsBriefs/2010_07_16 > > This means lots of pages with the term which are fine: > > https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax?action= > fullsearch&titlesearch=0&from=0&value=universe_wsgi.ini > > 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: > https://lists.galaxyproject.org/ > > 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Reporting issues for the wiki? e.g. universe_wgsi.ini still widely used
Hello all, Is there a specific issue tracker for the wiki? It seems wrong to open an issue on the main GitHub code repository... e.g. Many of the documentation pages still refer to the legacy configuration filename universe_wgsi.ini rather than the new name of config/galaxy.ini Problem pages include: https://wiki.galaxyproject.org/Learn/SecurityFeatures https://wiki.galaxyproject.org/Admin/DiskQuotas https://wiki.galaxyproject.org/Admin/SampleTracking/Demo https://wiki.galaxyproject.org/Admin/Tools/MultipleOutputFiles https://wiki.galaxyproject.org/Admin/Config/GenomeSpace https://wiki.galaxyproject.org/Admin/Config/ApacheExternalUserAuth https://wiki.galaxyproject.org/VisualizationSetup https://wiki.galaxyproject.org/ToolShedApi Other pages would benefit from minor edits to at least put the old form second and in brackets: https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster https://wiki.galaxyproject.org/Admin/Interface https://wiki.galaxyproject.org/ToolShed/InstallingRepositoriesToGalaxy Some pages look fine, e.g. https://wiki.galaxyproject.org/ToolShed/InstallingAndCompilingPackages Or are clearly dated and appropriate for the time, e.g. Dev news briefs https://wiki.galaxyproject.org/DevNewsBriefs/2010_07_16 This means lots of pages with the term which are fine: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax?action=fullsearch&titlesearch=0&from=0&value=universe_wsgi.ini 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
