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Fwd: [Outreach] download
by Nomi Harris 08 Apr '13

08 Apr '13

I went to try to download this dmg and see what was wrong, but I can't figure out where Loren even found it! The version on http://kbase.us/developer-zone/downloads/ is 20130219-prod-dmg-4.dmg and even the older version down in the gray zone is kb-v2013-01-17.dmg I can go ahead and reply and suggest that Loren download the latest version. Aren't we glad that we put version numbers in the dmg filenames so that we didn't have to have a long, frustrating dialog with Loren about the problem before realizing that he or she was using an out-of-date dmg? :-) Nomi Begin forwarded message: > From: "Hauser, Loren John" <hauserlj(a)ornl.gov> > Subject: [Outreach] download > Date: April 8, 2013 11:44:37 AM PDT > To: "help(a)kbase.us" <help(a)kbase.us> > > I downloaded the Mac OS X package kb-v2013-01-13.dmg and tried to open and install and got at OSStatus error 100030. > Any suggestions? > Loren Hauser, PhD > Computation Biology and Bioinformatics Group > BioSciences Division > Oak Ridge National Laboratory > One Bethel Valley Road > P.O. Box 6420 > Oak Ridge, TN 37831-6420 > work: 865-241-1960 > cell: 865-607-7143 > _______________________________________________ > Outreach mailing list > Outreach(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/outreach

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Re: [Release-team] Notebook in build
by Thomas Brettin 29 Mar '13

29 Mar '13

Hey Guys, I'm digging out of email from vacation. I'll get this on the next schedule. In general, emailing the release-team(a)lists.kbase.us is a more sure way, but usually sending me the email would work, except when vacation is involved … t On Mar 25, 2013, at 9:00 AM, Andreas Wilke <andreas.wilke(a)me.com> wrote: > Hi Tom, > > Can you add the KBNB iPython notebook to the build process? Travis did the Make file a while ago and I looked at it. Seems ok. > > Thanks, > > Andreas > > > Sent en route

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Re: [Release-team] [Kbase-devel] COMMANDS File and Minor Release Next Week
by Shiran Pasternak 21 Mar '13

21 Mar '13

I wasn't suggesting that a new format be adopted before next week's build. We're all capable of writing a COMMANDS file with the present file format to help the next build go smoothly. But well before the COMMANDS file goes "beyond just defining the set of commands" it would be good to change to a standard format. It might be useful having some sort of outlet (maybe an RFC, if you wanna get all formal) for discussing and planning these kinds of standards with a set of the KBase developers before valuable effort is pored into coding up handlers. Usually, we're notified on this list of conventions after the format is decided and its software written. Maybe fodder for discussion at next month's all-hands meeting. Shiran On Mar 21, 2013, at 4:48 PM, brettint(a)gmail.com wrote: > Also. While the suggestion here are fine, a change request usually lists all the code affected. a change might seem trivial to someone not familiar with the code base. And then someone needs to make the changes on the affected code. And it has to be fit into a schedule. And the value of the change needs to be weighed against the cost. Both the cost of making the change and the cost of not doing something else. > > For the release on monday we need the COMMANDS file in the specified format > > I already anticipate a more structured format will be necessary. > > Thanks all. > Sent from my Verizon Wireless BlackBerry > > -----Original Message----- > From: brettint(a)gmail.com > Date: Thu, 21 Mar 2013 20:34:30 > To: Travis Harrison<teharrison(a)anl.gov>; <kbase-devel-bounces(a)lists.kbase.us>; Thomas Brettin<brettin(a)mcs.anl.gov> > Reply-To: brettint(a)gmail.com > Cc: Kbase Devel<kbase-devel(a)lists.kbase.us>; release-team(a)lists.kbase.us<release-team(a)lists.kbase.us> > Subject: Re: [Kbase-devel] COMMANDS File and Minor Release Next Week > > All. Answers toi come in due time. I'm leaving town on family vacation. For now just create the file according to the existing format. We can evolve. We have existing code that will evolve. > Sent from my Verizon Wireless BlackBerry > > -----Original Message----- > From: Travis Harrison <teharrison(a)anl.gov> > Sender: kbase-devel-bounces(a)lists.kbase.usDate: Thu, 21 Mar 2013 14:52:11 > To: Thomas Brettin<brettin(a)mcs.anl.gov> > Cc: kbase-devel(a)lists.kbase.us devel<kbase-devel(a)lists.kbase.us>; release-team(a)lists.kbase.us<release-team(a)lists.kbase.us> > Subject: Re: [Kbase-devel] COMMANDS File and Minor Release Next Week > > _______________________________________________ > Kbase-devel mailing list > Kbase-devel(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/kbase-devel > > _______________________________________________ > Kbase-devel mailing list > Kbase-devel(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/kbase-devel

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Re: [Release-team] COMMANDS File and Minor Release Next Week
by Shiran Pasternak 21 Mar '13

21 Mar '13

On Mar 21, 2013, at 8:33 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > I've had a number of discussions with Rick on the issue of the COMMANDS file. We see this file going beyond just defining the set of commands deployed in IRIS. It in fact specifies what commands are in the KBase CLI. We plan to integrate the file with the release engineering process. > Tom, This was my concern at the get-go about just introducing a new file with an ad hoc, non-standard format. Even though Bob said at the time that the file will contain "a trivial amount of data that doesn't need a more complex encoding", your statement that the file will be going beyond just defining a set of commands (itself complex enough) should justify that the COMMANDS file now adopt a more standard format, such as JSON (cf. Shreyas's email). Shiran

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Re: [Release-team] COMMANDS File and Minor Release Next Week
by Thomas Brettin 21 Mar '13

21 Mar '13

Please look for your module in the list below. Git Module Command Line Interface Support assembly COMMANDS communities_api COMMANDS communities_qc COMMANDS experiment COMMANDS file_type_service COMMANDS genome_annotation COMMANDS idserver COMMANDS invocation COMMANDS jnomics COMMANDS kb_seed COMMANDS KBaseFBAModeling COMMANDS networks COMMANDS ontology_service COMMANDS phispy COMMANDS plant_expression_service COMMANDS probabilistic_annotation COMMANDS prom_service COMMANDS protein_info_service COMMANDS translation COMMANDS trees COMMANDS adapters COMMANDS: No such file or directory auth COMMANDS: No such file or directory auth_service COMMANDS: No such file or directory aux_store COMMANDS: No such file or directory bootstrap COMMANDS: No such file or directory cdd_service COMMANDS: No such file or directory cluster_service COMMANDS: No such file or directory communities_prospecting COMMANDS: No such file or directory communities_wizzard COMMANDS: No such file or directory concrete5 COMMANDS: No such file or directory datavis COMMANDS: No such file or directory dev_container COMMANDS: No such file or directory dev_container_tools COMMANDS: No such file or directory erdb_service COMMANDS: No such file or directory exchange_format_specs COMMANDS: No such file or directory exchange_format_support COMMANDS: No such file or directory expression COMMANDS: No such file or directory fastbitdb COMMANDS: No such file or directory fbaModelData COMMANDS: No such file or directory feature_selection COMMANDS: No such file or directory genome_data_browser COMMANDS: No such file or directory genotype_phenotype_api COMMANDS: No such file or directory kbapi_common COMMANDS: No such file or directory KBaseFBAModeling COMMANDS: No such file or directory kb_model_seed COMMANDS: No such file or directory matR COMMANDS: No such file or directory microbes_model_builder COMMANDS: No such file or directory micro_pheno COMMANDS: No such file or directory narrative COMMANDS: No such file or directory network_viewer COMMANDS: No such file or directory operon_service COMMANDS: No such file or directory otu_correlation COMMANDS: No such file or directory perl_runtime COMMANDS: No such file or directory persistent_store COMMANDS: No such file or directory plant COMMANDS: No such file or directory plant_network COMMANDS: No such file or directory plugin COMMANDS: No such file or directory prinseq COMMANDS: No such file or directory py_deploy_tools COMMANDS: No such file or directory registry COMMANDS: No such file or directory regprecise COMMANDS: No such file or directory release COMMANDS: No such file or directory ribo16s_pipeline COMMANDS: No such file or directory runtime COMMANDS: No such file or directory search COMMANDS: No such file or directory shock COMMANDS: No such file or directory sim_service COMMANDS: No such file or directory testing COMMANDS: No such file or directory typecomp COMMANDS: No such file or directory ui COMMANDS: No such file or directory widget_lib COMMANDS: No such file or directory workspace_browse COMMANDS: No such file or directory workspace_service COMMANDS: No such file or directory On Mar 21, 2013, at 7:33 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > On the Commands File > > We are going to do a minor release next week. If you have not created a COMMANDS file in your repo, please do so before the end of this week. Instructions are listed here: > > https://trac.kbase.us/projects/kbase/wiki/StandardDocuments > > I've had a number of discussions with Rick on the issue of the COMMANDS file. We see this file going beyond just defining the set of commands deployed in IRIS. It in fact specifies what commands are in the KBase CLI. We plan to integrate the file with the release engineering process. > > In the future, commands not listed in the COMMANDS file will not be included in the mac dmg, will not be included in the ubuntu image, and will not be deployed. This allows you to choose which commands are ready for deployment. I imagine the structure of the file could change in the future to contain more information about the commands, but for now lets just get them in our repos. > > I've created a number of them for folks to illustrate how easy it is. If anyone else needs help, I'll be available today. > > On the Upcoming Minor Release > > Any one wanting a new release pushed to production should let the release team know (release-team(a)lists.kbase.us) > > > > Thanks, > Tom

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COMMANDS File and Minor Release Next Week
by Thomas Brettin 21 Mar '13

21 Mar '13

On the Commands File We are going to do a minor release next week. If you have not created a COMMANDS file in your repo, please do so before the end of this week. Instructions are listed here: https://trac.kbase.us/projects/kbase/wiki/StandardDocuments I've had a number of discussions with Rick on the issue of the COMMANDS file. We see this file going beyond just defining the set of commands deployed in IRIS. It in fact specifies what commands are in the KBase CLI. We plan to integrate the file with the release engineering process. In the future, commands not listed in the COMMANDS file will not be included in the mac dmg, will not be included in the ubuntu image, and will not be deployed. This allows you to choose which commands are ready for deployment. I imagine the structure of the file could change in the future to contain more information about the commands, but for now lets just get them in our repos. I've created a number of them for folks to illustrate how easy it is. If anyone else needs help, I'll be available today. On the Upcoming Minor Release Any one wanting a new release pushed to production should let the release team know (release-team(a)lists.kbase.us) Thanks, Tom

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Re: [Release-team] release targets for next week
by Thomas Brettin 20 Mar '13

20 Mar '13

Yes on the workspace. I was sort of lumping a number of services in modeling. I should have the review of the COMMANDS files done this am for the invocation service. Tom On Mar 20, 2013, at 12:02 AM, Christopher Henry <chrisshenry(a)gmail.com> wrote: > Tom, > > Should we add: > 3.) Production deployment of workspaces > > Or is that lumped in the modeling? > The workspace may actually be the more important one to do. > > Chris > > On Mar 19, 2013, at 12:27 PM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > >> Hi folks, It's time to restart the release process. We'll plan on one per week until we get to a fully automated state. These are the highest priorities. >> >> 1) production deployment of invocation service (new COMMANDS files added to modules) >> 2) production deployment of fba modeling service >> >> Others to come. I'll post a request for release candidates later this week. >> >> Thanks, >> Tom >

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release targets for next week
by Thomas Brettin 19 Mar '13

19 Mar '13

Hi folks, It's time to restart the release process. We'll plan on one per week until we get to a fully automated state. These are the highest priorities. 1) production deployment of invocation service (new COMMANDS files added to modules) 2) production deployment of fba modeling service Others to come. I'll post a request for release candidates later this week. Thanks, Tom

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Re: [Release-team] [Kbase-devel] COMMANDS file
by Nomi Harris 08 Mar '13

08 Mar '13

On Mar 8, 2013, at 6:52 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > Nothing changed in the format of the Commands file, but the discussion was fun. > > There is the deploy.cfg file > > There is the DEPENDENCIES file. Right, those are both already on https://trac.kbase.us/projects/kbase/wiki/StandardDocuments but could use better descriptions/examples. Nomi > > Thanks Nomi! > Tom > > > On Mar 7, 2013, at 11:27 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > >> I added a description and examples of COMMANDS files to https://trac.kbase.us/projects/kbase/wiki/StandardDocuments >> Please check that I got it right--there was a lot of discussion about the format of this file so I'm not sure whether it changed after the examples I copied were sent out. >> >> Are there any other config files that need to be added to https://trac.kbase.us/projects/kbase/wiki/StandardDocuments ? >> >> Nomi >> >> On Mar 5, 2013, at 3:19 PM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: >> >>> Progress on this front. It takes about 120 seconds to create the file. We need this for the production IRIS deployment. >>> >>> Thanks to everyone that put one into their repo today. >>> >>> >>> 84 17:15 foreach d ( * ) >>> 85 17:15 ls -l $d/COMMANDS >> command.list >>> 86 17:15 end >>> >>> -rw-r--r-- 1 brettin staff 88 Mar 5 16:59 assembly/COMMANDS >>> -rw-r--r-- 1 brettin staff 72 Mar 5 17:01 communities_api/COMMANDS >>> -rw-r--r-- 1 brettin staff 57 Mar 5 17:01 communities_qc/COMMANDS >>> -rw-r--r-- 1 brettin staff 76 Mar 5 16:59 experiment/COMMANDS >>> -rw-r--r-- 1 brettin staff 103 Mar 5 16:59 genome_annotation/COMMANDS >>> -rw-r--r-- 1 brettin staff 79 Mar 5 17:01 idserver/COMMANDS >>> -rw-r--r-- 1 brettin staff 78 Mar 5 16:59 invocation/COMMANDS >>> -rw-r--r-- 1 brettin staff 83 Mar 5 17:00 jnomics/COMMANDS >>> -rw-r--r-- 1 brettin staff 294 Mar 5 17:01 kb_seed/COMMANDS >>> -rw-r--r-- 1 brettin staff 58 Mar 5 16:59 networks/COMMANDS >>> -rw-r--r-- 1 brettin staff 103 Mar 5 16:59 ontology_service/COMMANDS >>> -rw-r--r-- 1 brettin staff 71 Mar 5 16:58 phispy/COMMANDS >>> -rw-r--r-- 1 brettin staff 64 Mar 5 16:59 plant_expression_service/COMMANDS >>> >>> >>> MISSING: >>> >>> feature_selection >>> file_type_service >>> genotype_phenotype_api >>> KBaseFBAModeling >>> microphone >>> otu_correlation >>> prinseq >>> probabilistic_annotation >>> prom_service >>> protein_info_service >>> regprecise >>> sim_service >>> translation >>> trees >>> workspace_service >>> >>> I'll see what I can find from Bob's work, but anyone owning one of these repos should create their own. I shouldn't be checking these into your repos. >>> >>> Tom >> >

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Re: [Release-team] [Kbase-devel] COMMANDS file
by Thomas Brettin 08 Mar '13

08 Mar '13

Nothing changed in the format of the Commands file, but the discussion was fun. There is the deploy.cfg file There is the DEPENDENCIES file. Thanks Nomi! Tom On Mar 7, 2013, at 11:27 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > I added a description and examples of COMMANDS files to https://trac.kbase.us/projects/kbase/wiki/StandardDocuments > Please check that I got it right--there was a lot of discussion about the format of this file so I'm not sure whether it changed after the examples I copied were sent out. > > Are there any other config files that need to be added to https://trac.kbase.us/projects/kbase/wiki/StandardDocuments ? > > Nomi > > On Mar 5, 2013, at 3:19 PM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > >> Progress on this front. It takes about 120 seconds to create the file. We need this for the production IRIS deployment. >> >> Thanks to everyone that put one into their repo today. >> >> >> 84 17:15 foreach d ( * ) >> 85 17:15 ls -l $d/COMMANDS >> command.list >> 86 17:15 end >> >> -rw-r--r-- 1 brettin staff 88 Mar 5 16:59 assembly/COMMANDS >> -rw-r--r-- 1 brettin staff 72 Mar 5 17:01 communities_api/COMMANDS >> -rw-r--r-- 1 brettin staff 57 Mar 5 17:01 communities_qc/COMMANDS >> -rw-r--r-- 1 brettin staff 76 Mar 5 16:59 experiment/COMMANDS >> -rw-r--r-- 1 brettin staff 103 Mar 5 16:59 genome_annotation/COMMANDS >> -rw-r--r-- 1 brettin staff 79 Mar 5 17:01 idserver/COMMANDS >> -rw-r--r-- 1 brettin staff 78 Mar 5 16:59 invocation/COMMANDS >> -rw-r--r-- 1 brettin staff 83 Mar 5 17:00 jnomics/COMMANDS >> -rw-r--r-- 1 brettin staff 294 Mar 5 17:01 kb_seed/COMMANDS >> -rw-r--r-- 1 brettin staff 58 Mar 5 16:59 networks/COMMANDS >> -rw-r--r-- 1 brettin staff 103 Mar 5 16:59 ontology_service/COMMANDS >> -rw-r--r-- 1 brettin staff 71 Mar 5 16:58 phispy/COMMANDS >> -rw-r--r-- 1 brettin staff 64 Mar 5 16:59 plant_expression_service/COMMANDS >> >> >> MISSING: >> >> feature_selection >> file_type_service >> genotype_phenotype_api >> KBaseFBAModeling >> microphone >> otu_correlation >> prinseq >> probabilistic_annotation >> prom_service >> protein_info_service >> regprecise >> sim_service >> translation >> trees >> workspace_service >> >> I'll see what I can find from Bob's work, but anyone owning one of these repos should create their own. I shouldn't be checking these into your repos. >> >> Tom >

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