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

Re: [Release-team] New genome_annotation update.
by Brettin, Thomas S. 30 Jan '14

30 Jan '14

Nice work! Lookin forward to a test drive. Sent from my Verizon Wireless 4G LTE DROID Robert Olson <olson(a)mcs.anl.gov> wrote: I’ve pushed the updated genome_annotation and kb_seed code needed for the new RAST2 integration and the updated CDM schema routines. The genome annotation service will need to go onto a machine with at least 24GB of RAM, and also requires the download and installation of a kmer data file; I don’t know if we have a standard procedure for the installation of such tools. The data directory is 32GB in size. Its location needs to be in the deployment configuration file; e.g: [genome_annotation] kmer_v2_data_directory = /data/Data.6 [GenomeAnnotation] kmer_v2_data_directory = /data/Data.6 Both clauses there need to be included for now. The data to be installed is: ftp://ftp.theseed.org/KmerClassification/Data.6.tar.gz and unpacks into that Data.6 directory. Let me know if you have any questions. —bob

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New genome_annotation update.
by Robert Olson 30 Jan '14

30 Jan '14

I’ve pushed the updated genome_annotation and kb_seed code needed for the new RAST2 integration and the updated CDM schema routines. The genome annotation service will need to go onto a machine with at least 24GB of RAM, and also requires the download and installation of a kmer data file; I don’t know if we have a standard procedure for the installation of such tools. The data directory is 32GB in size. Its location needs to be in the deployment configuration file; e.g: [genome_annotation] kmer_v2_data_directory = /data/Data.6 [GenomeAnnotation] kmer_v2_data_directory = /data/Data.6 Both clauses there need to be included for now. The data to be installed is: ftp://ftp.theseed.org/KmerClassification/Data.6.tar.gz and unpacks into that Data.6 directory. Let me know if you have any questions. —bob

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Re: [Release-team] Fwd: KBase: HUGE ROADBLOCK
by Land, Miriam L. 30 Jan '14

30 Jan '14

I think Pavel is in serious need of a contingency plan. The odds of getting an updated Networks and 4 brand new modules all deployed, tested, and released ready next week are not in his favor. From: Shane Canon <scanon(a)lbl.gov<mailto:[email protected]>> Date: Thursday, January 30, 2014 4:35 PM To: "release-team(a)kbase.us<mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]>> Subject: [Release-team] Fwd: KBase: HUGE ROADBLOCK FYI. Apparently I was totally wrong on this. Trying to figure out a workaround now. Stay tuned. --Shane Begin forwarded message: From: Pavel Novichkov <psnovichkov(a)lbl.gov<mailto:[email protected]>> Subject: KBase: HUGE ROADBLOCK Date: January 30, 2014 1:17:05 PM PST To: Shane Canon <scanon(a)lbl.gov<mailto:[email protected]>> Cc: Adam Arkin <APArkin(a)lbl.gov<mailto:[email protected]>>, Nomi Harris <NLHarris(a)lbl.gov<mailto:[email protected]>> Hi Shane, I am cc-ing to Adam… I mentioned this at the build, I do not know anything about it… You probably said it to somebody else, but not to me… If I knew that, believe me, I would take care about it because of two reasons: 1. We use it for Networks API as well, that WILL be used in narrative (demo).. 2. Meme, cmonkey, inferelator and bambi are developed as a part ENIGMA-KBASE integration project. During the recent ENIMGA SAC Adam explicitly promised to DOE managers that these services will be ready by Feb meeting in DC. Thus they MSUT be deployed to production somehow. P. On Jan 30, 2014, at 9:47 AM, Shane Canon <scanon(a)lbl.gov<mailto:[email protected]>> wrote: Pavel, I mentioned this at the build, but I just wanted to say it again so you weren't surprised. We are delaying the deployment of meme, monkey, inferelator, and bambi because we are trying to focus on services that will be used during the demos and their are some issues to work out with these services. I'm hoping we can turn to these after the demos. BTW, the issue is the service is relying on a branch of the type compiler which isn't part of our deployment. To get around this we could: a) try to get Bob to accept some of the changes into master (difficult) b) try to convince whomever that we should adopt the branch as the primary (also difficult) c) create some mechanism for you to run a branch of the type compiler as part of the deploy process (possible with some work). After the demos, you and I can get together to figure out what to do. --Shane

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Fwd: KBase: HUGE ROADBLOCK
by Shane Canon 30 Jan '14

30 Jan '14

FYI. Apparently I was totally wrong on this. Trying to figure out a workaround now. Stay tuned. --Shane Begin forwarded message: > From: Pavel Novichkov <psnovichkov(a)lbl.gov> > Subject: KBase: HUGE ROADBLOCK > Date: January 30, 2014 1:17:05 PM PST > To: Shane Canon <scanon(a)lbl.gov> > Cc: Adam Arkin <APArkin(a)lbl.gov>, Nomi Harris <NLHarris(a)lbl.gov> > > Hi Shane, > > I am cc-ing to Adam… > >> I mentioned this at the build, > > I do not know anything about it… You probably said it to somebody else, but not to me… If I knew that, believe me, I would take care about it because of two reasons: > > 1. We use it for Networks API as well, that WILL be used in narrative (demo).. > > 2. Meme, cmonkey, inferelator and bambi are developed as a part ENIGMA-KBASE integration project. During the recent ENIMGA SAC Adam explicitly promised to DOE managers that these services will be ready by Feb meeting in DC. Thus they MSUT be deployed to production somehow. > > P. > > > > > > On Jan 30, 2014, at 9:47 AM, Shane Canon <scanon(a)lbl.gov> wrote: > >> >> Pavel, >> >> I mentioned this at the build, but I just wanted to say it again so you weren't surprised. We are delaying the deployment >> of meme, monkey, inferelator, and bambi because we are trying to focus on services that will be used during the demos >> and their are some issues to work out with these services. I'm hoping we can turn to these after the demos. BTW, the >> issue is the service is relying on a branch of the type compiler which isn't part of our deployment. To get around this >> we could: a) try to get Bob to accept some of the changes into master (difficult) b) try to convince whomever that we >> should adopt the branch as the primary (also difficult) c) create some mechanism for you to run a branch of the type >> compiler as part of the deploy process (possible with some work). After the demos, you and I can get together to >> figure out what to do. >> >> --Shane >

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search is ready for testing
by Shane Canon 30 Jan '14

30 Jan '14

see subject. --Shane

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RELEASE NOTES added for id_map
by Brettin, Thomas S. 30 Jan '14

30 Jan '14

do a git pull t

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Action Items from release call
by Gordon, India S. 30 Jan '14

30 Jan '14

Action items from release call: Shane – work with Matt (Henderson) to ensure Search is deployable not being run as root Tom – will keep the release team up to date with each advance on the new database India – schedule release team follow-up telecon on Monday 2/3/2014 On the call: Nomi Miriam Dantong Tom Dan

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latest commit on id_map seems good
by Brettin, Thomas S. 30 Jan '14

30 Jan '14

commit 2b18e4ec166b2fb6006521d8f6ffbc2ff2591559 Author: brettin <brettin(a)mcs.anl.gov> Date: Mon Jan 20 19:07:13 2014 +0000 added test for empty return value on lookup_feature_synonyms

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Re: [Release-team] Do we need to touch base?
by Gordon, India S. 30 Jan '14

30 Jan '14

Please use 866.740.1260 Access Code: 9026516 On 1/30/14, 10:54 AM, "Brettin, Thomas S." <brettin(a)cels.anl.gov> wrote: >Lets do 11am CT. We can use the regularly scheduled slot that I set up >for repeating calls re: demo. > >India will send info. > >Tom > > >________________________________________ >From: release-team-bounces(a)lists.kbase.us >[release-team-bounces(a)lists.kbase.us] on behalf of Land, Miriam L. >[landml(a)ornl.gov] >Sent: Thursday, January 30, 2014 9:05 AM >To: Murphy-Olson, Daniel E.; release-team(a)kbase.us >Subject: Re: [Release-team] Do we need to touch base? > >I can do noon ET, 11am CT,and 9am PT. I'd like to hear from Tom and the >west coast before we confirm a time. > >Miriam > >From: <Murphy-Olson>, Dan Olson ><dolson(a)mcs.anl.gov<mailto:[email protected]>> >Date: Thursday, January 30, 2014 10:02 AM >To: Miriam Land <landml(a)ornl.gov<mailto:[email protected]>>, >"release-team(a)kbase.us<mailto:[email protected]>" ><release-team(a)kbase.us<mailto:[email protected]>> >Subject: RE: Do we need to touch base? > >Yes, can we do 11AM? We can use my callin number if needed. > > >---- >Daniel Murphy-Olson >Systems Administrator >Mathematics & Computer Science Division >Argonne National Laboratory >630-252-0055 > >________________________________________ >From: >release-team-bounces(a)lists.kbase.us<mailto:[email protected] >e.us> >[release-team-bounces(a)lists.kbase.us<mailto:[email protected] >se.us>] on behalf of Land, Miriam L. >[landml(a)ornl.gov<mailto:[email protected]>] >Sent: Thursday, January 30, 2014 8:40 AM >To: release-team(a)kbase.us<mailto:[email protected]> >Subject: [Release-team] Do we need to touch base? > >All, > >The final version of all the modules are due by Monday morning. I know >that Dan is off on Fridays. Do we need to touch base today to make sure >we will be in sync Monday? > >Should we go ahead and deploy id_map and Search to the test VM so I can >check off the testing those two before Monday? > >We only have one submitted contingency plan. Someone will be late and >someone will fail to deploy/test. Do we need to agree on how we will >deal with these or will it be a case-by-case basis? > >Miriam >_______________________________________________ >Release-team mailing list >Release-team(a)lists.kbase.us<mailto:[email protected]> >https://lists.kbase.us/mailman/listinfo/release-team > >_______________________________________________ >Release-team mailing list >Release-team(a)lists.kbase.us >https://lists.kbase.us/mailman/listinfo/release-team

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Re: [Release-team] Do we need to touch base?
by Brettin, Thomas S. 30 Jan '14

30 Jan '14

Lets do 11am CT. We can use the regularly scheduled slot that I set up for repeating calls re: demo. India will send info. Tom ________________________________________ From: release-team-bounces(a)lists.kbase.us [release-team-bounces(a)lists.kbase.us] on behalf of Land, Miriam L. [landml(a)ornl.gov] Sent: Thursday, January 30, 2014 9:05 AM To: Murphy-Olson, Daniel E.; release-team(a)kbase.us Subject: Re: [Release-team] Do we need to touch base? I can do noon ET, 11am CT,and 9am PT. I'd like to hear from Tom and the west coast before we confirm a time. Miriam From: <Murphy-Olson>, Dan Olson <dolson(a)mcs.anl.gov<mailto:[email protected]>> Date: Thursday, January 30, 2014 10:02 AM To: Miriam Land <landml(a)ornl.gov<mailto:[email protected]>>, "release-team(a)kbase.us<mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]>> Subject: RE: Do we need to touch base? Yes, can we do 11AM? We can use my callin number if needed. ---- Daniel Murphy-Olson Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055 ________________________________________ From: release-team-bounces(a)lists.kbase.us<mailto:[email protected]> [release-team-bounces(a)lists.kbase.us<mailto:[email protected]>] on behalf of Land, Miriam L. [landml(a)ornl.gov<mailto:[email protected]>] Sent: Thursday, January 30, 2014 8:40 AM To: release-team(a)kbase.us<mailto:[email protected]> Subject: [Release-team] Do we need to touch base? All, The final version of all the modules are due by Monday morning. I know that Dan is off on Fridays. Do we need to touch base today to make sure we will be in sync Monday? Should we go ahead and deploy id_map and Search to the test VM so I can check off the testing those two before Monday? We only have one submitted contingency plan. Someone will be late and someone will fail to deploy/test. Do we need to agree on how we will deal with these or will it be a case-by-case basis? Miriam _______________________________________________ Release-team mailing list Release-team(a)lists.kbase.us<mailto:[email protected]> https://lists.kbase.us/mailman/listinfo/release-team _______________________________________________ Release-team mailing list Release-team(a)lists.kbase.us https://lists.kbase.us/mailman/listinfo/release-team

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