- Release-team - mailman3.cels.anl.gov

Re: [Release-team] Defunct services
by Nomi Harris 12 Mar '14

12 Mar '14

Latest list of services that are presumed defunct: feature_selection (fizzy) file_type_service genotype_phenotype experiment prom_service regulation (regprecise) Any changes before we send the list to the devel team? Nomi On Feb 26, 2014, at 6:34 AM, Land, Miriam L. <landml(a)ornl.gov> wrote: > Nomi, > > Andreas has been working on JIRA tickets this week for communities_qc and feature_selection. He may not consider them defunct. > > Miriam > > From: Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> > Date: Tuesday, February 25, 2014 4:07 PM > To: Shane Canon <scanon(a)lbl.gov<mailto:[email protected]>> > Cc: "release-team(a)kbase.us<mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]>> > Subject: Re: [Release-team] Defunct services > > Ok, thanks for checking. Sounds like ERDB is still needed. So the revised list of services that can go is: > feature_selection (fizzy) > file_type_service > genotype_phenotype > experiment > prom_service > communities_qc > regulation (regprecise) > > On Feb 25, 2014, at 12:54 PM, Shane Canon <scanon(a)lbl.gov<mailto:[email protected]>> wrote: > > > So ERDB may still be needed by translation and trees. > > --Shane > > root@t1:/kbase/deployments/20140214-prod/dev_container/modules# grep -i erdb */DEP* > experiment/DEPENDENCIES:erdb_service > prom_service/DEPENDENCIES:erdb_service > translation/DEPENDENCIES:erdb_service > trees/DEPENDENCIES:erdb_service > > On Feb 25, 2014, at 12:09 PM, "Brettin, Thomas S." <brettin(a)anl.gov<mailto:[email protected]>> wrote: > > I think the list is accurate. The only exception might be ERDB service. A recursive grep might be needed for that one. > > Sent from my Verizon Wireless 4G LTE DROID > > > Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> wrote: > > Sure. We can follow up on it during tomorrow's devel call if needed. > > > On Tue, Feb 25, 2014 at 11:57 AM, Shane Canon <scanon(a)lbl.gov<mailto:[email protected]>> wrote: > > This is very helpful. Should we notify the devel list as well? > > --Shane > > > On Feb 25, 2014, at 11:38 AM, Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> wrote: > >> I believe the following services are not currently supported and can be shut down (if they haven’t been already): >> >> feature_selection (fizzy) >> file_type_services >> genotype_phenotype >> experiment >> prom_service >> communities_qc >> regulation (regprecise) >> erdb_service >> >> Ccing the release team in case they have any adjustments to that list. >> >> Nomi >> >> On Feb 24, 2014, at 5:54 PM, Shane Canon <scanon(a)lbl.gov<mailto:[email protected]>> wrote: >> >>> >>> So we can retire this service? Are there other services we can shutdown? >>> >>> Shane >>> >>> Sent from my iPhone >>> >>>> On Feb 24, 2014, at 11:56 AM, Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> wrote: >>>> >>>> I forgot to forward this to you. Ranjan says to leave the genotype/phenotype service out of this release. >>>> Nomi >>>> >>>> Begin forwarded message: >>>> >>>>> From: "Ranjan, Priya" <pranjan(a)utk.edu<mailto:[email protected]>> >>>>> Subject: Re: Genotype/Phenotype service repo? >>>>> Date: February 18, 2014 at 2:59:58 PM PST >>>>> To: Nomi Harris <nlharris(a)gmail.com<mailto:[email protected]>> >>>>> >>>>> Yes. Thanks. >>>>> Ranjan >>>>> >>>>> >>>>>> On Feb 18, 2014, at 5:40 PM, "Nomi Harris" <nlharris(a)gmail.com<mailto:[email protected]>> wrote: >>>>>> >>>>>> Ok—so the release of IRIS we’re doing this week should not include Genotype/Phenotype commands, and I should remove it from the Services web page? >>>>>> Nomi >>>>>> >>>>>>> On Feb 18, 2014, at 12:03 PM, Ranjan, Priya <pranjan(a)utk.edu<mailto:[email protected]>> wrote: >>>>>>> >>>>>>> Hi Nomi, >>>>>>> Both these services are obsolete and their functionality are being incorporated into gwas service. >>>>>>> I will request them to be deleted in few weeks. >>>>>>> Thanks >>>>>>> Ranjan >>>>>>> >>>>>>> >>>>>>> ________________________________________ >>>>>>> From: Nomi Harris [nlharris(a)gmail.com<mailto:[email protected]>] >>>>>>> Sent: Tuesday, February 18, 2014 3:00 PM >>>>>>> To: pranjan77(a)gmail.com<mailto:[email protected]>; Ranjan, Priya >>>>>>> Cc: release-team(a)kbase.us<mailto:[email protected]> >>>>>>> Subject: Genotype/Phenotype service repo? >>>>>>> >>>>>>> Hi Ranjan, >>>>>>> What is the correct repo for the Genotype/Phenotype service? >>>>>>> There’s a repo called genotype_phenotype, which hasn’t been updated since Sept. >>>>>>> There’s one called genotype_phenotype_api, which I think is the current repo. >>>>>>> The Master tab of the Services repo (https://docs.google.com/spreadsheet/ccc?key=0AriSbOyynCz1dDdJRHJBcGszaldlUE…) claims that the repo is called geno_pheno_service, which I guess is just wrong. >>>>>>> If genotype_phenotype_api is the live repo, then I would suggest deleting genotype_phenotype to avoid confusion. >>>>>>> Thanks, >>>>>>> Nomi >> > > > >

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Re: [Release-team] Question about testing environment
by Brettin, Thomas S. 10 Mar '14

10 Mar '14

Hi Roman. There are a couple things in your email. a) the why don't we -- we are working on this right now. I just came out of a design session that will make standing up development enviornments easier. Until now, our services were not that complex. As things on the project are maturing, we now see developers requiring more complex dev environments. b) on continous integration, we are well aware of jenkins and other tools for doing this. We had CI running before christmas as a prototype, and then took it off line. We are working on bringing this back on line and have a target timeline to have this in place for the next major build. Tom On Mar 10, 2014, at 4:11 PM, Roman Sutormin <rsutormin(a)lbl.gov<mailto:[email protected]>> wrote: Hello everybody, I have little bit strange question. Why don't we make testing environment for tests in our projects? My problem is that now I need to install local workspace service (and shock server + mongo that are used in WS) and job status service in order to be able to run tests for my service (genome comparison). But I'm sure that everybody who is developing services would be glad to have testing services and dbs that are necessary for running tests without installing all necessary parts on some random magellan instances or even locally. Another useful outcome of testing env will be ability to install automation testing software like https://wiki.jenkins-ci.org/display/JENKINS/Unit+Test . Thanks for your ideas and suggestions. -Roman. _______________________________________________ Release-team mailing list Release-team(a)lists.kbase.us<mailto:[email protected]> https://lists.kbase.us/mailman/listinfo/release-team

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Fwd: Question about testing environment
by Nomi Harris 10 Mar '14

10 Mar '14

Forwarding this question to the release-team mailing list because Roman isn’t a member of that list (and I’m not an admin of it, so I can’t approve his post). Nomi Begin forwarded message: > From: Roman Sutormin <rsutormin(a)lbl.gov> > Date: Mon, Mar 10, 2014 at 2:11 PM > Subject: Question about testing environment > To: Release-team(a)lists.kbase.us > Cc: Adam Arkin <aparkin(a)lbl.gov> > > > Hello everybody, > > I have little bit strange question. Why don't we make testing environment for tests in our projects? > > My problem is that now I need to install local workspace service (and shock server + mongo that are used in WS) and job status service in order to be able to run tests for my service (genome comparison). But I'm sure that everybody who is developing services would be glad to have testing services and dbs that are necessary for running tests without installing all necessary parts on some random magellan instances or even locally. > > Another useful outcome of testing env will be ability to install automation testing software like https://wiki.jenkins-ci.org/display/JENKINS/Unit+Test . > > Thanks for your ideas and suggestions. > > -Roman.

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Question about testing environment
by Roman Sutormin 10 Mar '14

10 Mar '14

Hello everybody, I have little bit strange question. Why don't we make testing environment for tests in our projects? My problem is that now I need to install local workspace service (and shock server + mongo that are used in WS) and job status service in order to be able to run tests for my service (genome comparison). But I'm sure that everybody who is developing services would be glad to have testing services and dbs that are necessary for running tests without installing all necessary parts on some random magellan instances or even locally. Another useful outcome of testing env will be ability to install automation testing software like https://wiki.jenkins-ci.org/display/JENKINS/Unit+Test. Thanks for your ideas and suggestions. -Roman.

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Re: [Release-team] [Kbase-devel] Authenticated Shock access from service
by Wei Tang 07 Mar '14

07 Mar '14

Hi Shane The new token passing feature requires the version of AWE server and clients match. Thus it would be good to update the AWE server to the latest version so that people who use the latest client code can work with that server. Thanks Wei On Fri, Mar 7, 2014 at 10:07 AM, Shane Canon <scanon(a)lbl.gov> wrote: > > Should I go ahead and redeploy AWE in production? > > --Shane > > On Mar 7, 2014, at 7:59 AM, Jared Bischof <jbischof(a)gmail.com> wrote: > > Wei's going to send an example. Since AWE has many more features now than > the last time it was presented, it's probably a good time to go over the > status of AWE on a conference call. > > -Jared > > > On Fri, Mar 7, 2014 at 9:54 AM, Wei Tang <wtang(a)anl.gov> wrote: > >> by default it is: KB_AUTH_TOKEN >> >> On Fri, Mar 7, 2014 at 9:51 AM, Shane Canon <scanon(a)lbl.gov> wrote: >> >>> >>> Awesome. What is the variable name? >>> >>> Shane >>> >>> Sent from my iPhone >>> >>> On Mar 7, 2014, at 7:43 AM, Wei Tang <wtang(a)anl.gov> wrote: >>> >>> The feature that awe client sets kbase token as env variable before >>> dispatching the actual script has been implemented and committed, which >>> means AWE tasks can now access other kbase services using tokens previously >>> set at job submission. >>> >>> Thanks >>> Wei >>> >>> >>> On Tue, Mar 4, 2014 at 5:17 PM, Shane Canon <scanon(a)lbl.gov> wrote: >>> >>>> >>>> These sounds like good suggestions. I think it is important that AWE >>>> tasks should be able to easily interact with KBase services, especially >>>> workspace. But we should spend some >>>> time thinking about the best model for doing this. >>>> >>>> --Shane >>>> >>>> On Mar 4, 2014, at 2:49 PM, Wei Tang <wtang(a)anl.gov> wrote: >>>> >>>> Putting aside the security issue, AWE can be enhanced to support >>>> following: >>>> >>>> In the task description section of the workflow document, we add a >>>> field as ENV_VARS (along the cmd name/arg list), and let awe-client to set >>>> environmental variables based on that field before dispatch the actual >>>> script. In this way, we can pass needed token for certain tasks to access >>>> other kbase services (other than shock). This works for some scripts that >>>> retrieves token from environmental variables instead of command line args. >>>> The job submitter will need to define the needed token for each task in >>>> workflow template. >>>> >>>> Pls let me know if this feature is useful. We can add it to the feature >>>> list. >>>> >>>> Thanks >>>> Wei >>>> >>>> >>>> On Tue, Mar 4, 2014 at 4:33 PM, Jared Bischof <jbischof(a)gmail.com>wrote: >>>> >>>>> You could pass the KBase token as a command line argument for a given >>>>> task or we could even create another option for setting an environment >>>>> variable for a task. This isn't a secure way of handling things but I >>>>> haven't seen a better solution for this yet in the KBase infrastructure. >>>>> Suggestions are welcome. >>>>> >>>>> -Jared >>>>> >>>>> >>>>> On Tue, Mar 4, 2014 at 4:26 PM, Desai, Narayan <desai(a)mcs.anl.gov>wrote: >>>>> >>>>>> The task isn't exposed to the runtime environment for tasks, it is >>>>>> only used for data movement. We do all of this with restricted use tokens >>>>>> that are only good for a single shock object, so it wouldn't be useful for >>>>>> the workspace, etc. >>>>>> -nld >>>>>> >>>>>> On Mar 4, 2014, at 3:56 PM, Shane Canon wrote: >>>>>> >>>>>> >>>>>> Wei, >>>>>> >>>>>> If a worker task needed to use the token to access another KBase >>>>>> service (i.e. the workspace), how could the task access the token? Or is >>>>>> this allowed? >>>>>> >>>>>> --Shane >>>>>> >>>>>> On Feb 28, 2014, at 1:56 PM, Wei Tang <wtang(a)mcs.anl.gov> wrote: >>>>>> >>>>>> Yes, AWE can pass tokens to use authenticated shock, following is >>>>>> the how it currently working. >>>>>> >>>>>> When a AWE job is submitted and it need to use private shock data, >>>>>> one need to specify the shock token for that data in the header of the POST >>>>>> call for job submission. And the token (associated with the job) will be >>>>>> stored in mongodb at awe server. >>>>>> >>>>>> When a awe-client checks out a workunit from AWE, the workunit >>>>>> description tells whether this workunit needs token to get input data. if >>>>>> yes, the awe-client will issue another GET request to get the token from >>>>>> the AWE server, and continue to use that token to talk to shock, either >>>>>> for file downloading and uploading. >>>>>> >>>>>> Thanks >>>>>> Wei >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On Fri, Feb 28, 2014 at 3:40 PM, Narayan Desai <desai(a)mcs.anl.gov>wrote: >>>>>> >>>>>>> Wei has done this for AWE. Wei? >>>>>>> -nld >>>>>>> >>>>>>> On Feb 28, 2014, at 2:47 PM, Olson, Robert D. wrote: >>>>>>> >>>>>>> Does anyone have a service backend working that accesses >>>>>>> authenticated Shock based on the credentials coming in from an >>>>>>> authenticated service call? I seem to recall that when Tom and I tried >>>>>>> this during our last bootcamp we had a lot of trouble with it. >>>>>>> >>>>>>> thanks, >>>>>>> --bob >>>>>>> _______________________________________________ >>>>>>> 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 >>>>>>> >>>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>> >>>>> >>>> _______________________________________________ >>>> 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 >>>> >>>> >>> >>> _______________________________________________ >>> 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] [Kbase-devel] Authenticated Shock access from service
by Shane Canon 07 Mar '14

07 Mar '14

Should I go ahead and redeploy AWE in production? --Shane On Mar 7, 2014, at 7:59 AM, Jared Bischof <jbischof(a)gmail.com> wrote: > Wei's going to send an example. Since AWE has many more features now than the last time it was presented, it's probably a good time to go over the status of AWE on a conference call. > > -Jared > > > On Fri, Mar 7, 2014 at 9:54 AM, Wei Tang <wtang(a)anl.gov> wrote: > by default it is: KB_AUTH_TOKEN > > On Fri, Mar 7, 2014 at 9:51 AM, Shane Canon <scanon(a)lbl.gov> wrote: > > Awesome. What is the variable name? > > Shane > > Sent from my iPhone > > On Mar 7, 2014, at 7:43 AM, Wei Tang <wtang(a)anl.gov> wrote: > >> The feature that awe client sets kbase token as env variable before dispatching the actual script has been implemented and committed, which means AWE tasks can now access other kbase services using tokens previously set at job submission. >> >> Thanks >> Wei >> >> >> On Tue, Mar 4, 2014 at 5:17 PM, Shane Canon <scanon(a)lbl.gov> wrote: >> >> These sounds like good suggestions. I think it is important that AWE tasks should be able to easily interact with KBase services, especially workspace. But we should spend some >> time thinking about the best model for doing this. >> >> --Shane >> >> On Mar 4, 2014, at 2:49 PM, Wei Tang <wtang(a)anl.gov> wrote: >> >>> Putting aside the security issue, AWE can be enhanced to support following: >>> >>> In the task description section of the workflow document, we add a field as ENV_VARS (along the cmd name/arg list), and let awe-client to set environmental variables based on that field before dispatch the actual script. In this way, we can pass needed token for certain tasks to access other kbase services (other than shock). This works for some scripts that retrieves token from environmental variables instead of command line args. The job submitter will need to define the needed token for each task in workflow template. >>> >>> Pls let me know if this feature is useful. We can add it to the feature list. >>> >>> Thanks >>> Wei >>> >>> >>> On Tue, Mar 4, 2014 at 4:33 PM, Jared Bischof <jbischof(a)gmail.com> wrote: >>> You could pass the KBase token as a command line argument for a given task or we could even create another option for setting an environment variable for a task. This isn't a secure way of handling things but I haven't seen a better solution for this yet in the KBase infrastructure. Suggestions are welcome. >>> >>> -Jared >>> >>> >>> On Tue, Mar 4, 2014 at 4:26 PM, Desai, Narayan <desai(a)mcs.anl.gov> wrote: >>> The task isn't exposed to the runtime environment for tasks, it is only used for data movement. We do all of this with restricted use tokens that are only good for a single shock object, so it wouldn't be useful for the workspace, etc. >>> -nld >>> >>> On Mar 4, 2014, at 3:56 PM, Shane Canon wrote: >>> >>>> >>>> Wei, >>>> >>>> If a worker task needed to use the token to access another KBase service (i.e. the workspace), how could the task access the token? Or is this allowed? >>>> >>>> --Shane >>>> >>>> On Feb 28, 2014, at 1:56 PM, Wei Tang <wtang(a)mcs.anl.gov> wrote: >>>> >>>>> Yes, AWE can pass tokens to use authenticated shock, following is the how it currently working. >>>>> >>>>> When a AWE job is submitted and it need to use private shock data, one need to specify the shock token for that data in the header of the POST call for job submission. And the token (associated with the job) will be stored in mongodb at awe server. >>>>> >>>>> When a awe-client checks out a workunit from AWE, the workunit description tells whether this workunit needs token to get input data. if yes, the awe-client will issue another GET request to get the token from the AWE server, and continue to use that token to talk to shock, either for file downloading and uploading. >>>>> >>>>> Thanks >>>>> Wei >>>>> >>>>> >>>>> >>>>> >>>>> On Fri, Feb 28, 2014 at 3:40 PM, Narayan Desai <desai(a)mcs.anl.gov> wrote: >>>>> Wei has done this for AWE. Wei? >>>>> -nld >>>>> >>>>> On Feb 28, 2014, at 2:47 PM, Olson, Robert D. wrote: >>>>> >>>>>> Does anyone have a service backend working that accesses authenticated Shock based on the credentials coming in from an authenticated service call? I seem to recall that when Tom and I tried this during our last bootcamp we had a lot of trouble with it. >>>>>> >>>>>> thanks, >>>>>> --bob >>>>>> _______________________________________________ >>>>>> 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 >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>> >>> >>> _______________________________________________ >>> 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 >> >> > > _______________________________________________ > 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] Release and dmg
by Shane Canon 05 Mar '14

05 Mar '14

I still need to update FBA. I will try to do that now. I haven't done anything to IRIS yet since I'm unclear what needs to be fixed and the deployment is a little more involved. --Shane On Mar 5, 2014, at 2:53 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > Bob Olson wrote (in response to https://atlassian.kbase.us/browse/KBASE-198) >> I am awaiting information from the release folks about building a new [dmg]. > > I think we’re almost ready for that. The FBA and workspace services are now working in IRIS—right? There are some issues with CBD and Shock (and a few other issues with some services), but I don’t think we have to wait for those to be fixed before putting together a new dmg. > > Thanks, > Nomi > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team

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Release and dmg
by Nomi Harris 05 Mar '14

05 Mar '14

Bob Olson wrote (in response to https://atlassian.kbase.us/browse/KBASE-198) > I am awaiting information from the release folks about building a new [dmg]. I think we’re almost ready for that. The FBA and workspace services are now working in IRIS—right? There are some issues with CBD and Shock (and a few other issues with some services), but I don’t think we have to wait for those to be fixed before putting together a new dmg. Thanks, Nomi

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Re: [Release-team] Empty or obsolete git repos--can we get rid of some of them?
by Nomi Harris 03 Mar '14

03 Mar '14

Fair enough. Does anyone want to defend any of the other listed repos before I send the list to dev? Nomi On Feb 25, 2014, at 2:38 PM, Robert Olson <olson(a)mcs.anl.gov> wrote: > strep_repeats is untouched because it is stable and working. > > > On Feb 25, 2014, at 4:20 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > >> By the way, while we’re talking about defunct services, there are some repos that we could probably get rid of. >> >> Here are repos that are empty: >> Empty: prinseq.git support%40kbase.us >> Empty: coexpression.git gang.fang%40yale.edu >> Empty: fat_cat.git dave.dineen%40gmail.com >> Empty: kmer_annotation_function.git olson%40mcs.anl.gov >> Empty: kbtypedef_common_proposals.git msneddon%40lbl.gov >> Empty: fbaModelData.git support%40kbase.us >> Empty: kbtyped_obj_service.git msneddon%40lbl.gov >> >> And here are some repos that haven’t been touched in 7 months or more (see https://git.kbase.us/?o=age) and may no longer be needed: >> >> structured_assertions.git repo for structured assertions... psdehal(a)lbl.gov 7 months ago >> genome_data_browser.git a kbase lab project to browse... wjriehl(a)lbl.gov 8 months ago >> registry.git "service registry" brettin(a)anl.gov 8 months ago >> seq_search.git sequence search nconrad(a)mcs.anl.gov 8 months ago >> # erdb_service.git service to query cs via erdb... gaprice(a)lbl.gov 9 months ago # erdb_service is apparently still in use >> user_page.git repo for a user page wjriehl(a)lbl.gov 9 months ago >> askkb.git natural language interface... disz 9 months ago >> data_scatter_plot.git js for displaying data in... psdehal(a)lbl.gov 9 months ago >> strep_repeats.git Unnamed repository; edit this... olson(a)mcs.anl.gov 9 months ago >> plant.git repository for all things... shiran(a)cshl.edu 10 months ago >> adapters.git adapters repo brettin(a)mcs.anl.gov 10 months ago >> network_viewer.git browser for networks jmchandonia(a)lbl.gov 11 months ago >> otu_correlation.git generate correlations between... wjriehl(a)lbl.gov 11 months ago >> exchange_format_specs.git data exchange formats for... disz(a)mcs.anl.gov 11 months ago >> regprecise.git things related to regulons... psnovichkov(a)lbl.gov 12 months ago >> prinseq.git one of Rob Edwards services support(a)kbase.us 13 months ago >> core_model.git old code for gui nconrad(a)mcs.anl.gov 13 months ago >> fbaModelData.git "new module for storing fba... support(a)kbase.us 13 months ago >> _______________________________________________ >> Release-team mailing list >> Release-team(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/release-team >

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Metagenomic Sequence QC service--is it working again?
by Nomi Harris 03 Mar '14

03 Mar '14

Can someone update me on the status of the Metagenomic Sequence QC service? It is visible in IRIS, and I can run the commands with —help but I don’t have the right input files to test it more thoroughly. Miriam, could you do that? We had taken that service off the services page and taken down its tutorial (http://kbase.us/for-users/tutorials/analyzing-data/metagenome-analysis/sequ…) because the service wasn’t working. I need to know if those should be restored. Thanks, Nomi

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