WPWG-20100622-transcript

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- Tuesday June 22 2010, 08:27 -

- rama has joined the room

rama: morning

sjcarbon: morning

rama: Seth-

rama: about the refresh.pl sccript

sjcarbon: ah, yeah.

ben: howdy

sjcarbon: howdy

sjcarbon: https://sourceforge.net/tracker/?func=detail&aid=3013383&group_id=36855&atid=908269

sjcarbon: ben: from that bug it looks like the refresh scripts aren't running very frequently (the ids have gone out of sync).

ben: hmm

sjcarbon: Is refresh.pl run periodically? And if so, what schedule?

- 08:33 -

- ben has disconnected (Read error: Operation timed out)

sjcarbon: He escaped!

rama: no Ben yet

rama: no body else on the chat

sjcarbon: Ah well.

rama: about testing

sjcarbon: I was going to see what people's schedule looked like for the next couple of weeks.

rama: i am going on vacation on june 24th

rama: i am out for 3 weeks.

sjcarbon: zing!

sjcarbon: Have fun!

rama: I will have email access and will be able to test if there are no firewall issues/connectivity issues

sjcarbon: I'd hate to have you test while you're trying to relax.

sjcarbon: We can see who else will be around.

rama: (relax in India?? with inlaws and family??

rama: i need a break from family. so escaping with work as excuse is a good thing

sjcarbon: Okay with me then.

sjcarbon: I hope it's not too hot where you're going.

- 08:39 -

sjcarbon: I'm hoping to scoop up the last two bugs while we're testing.

rama: it is hot there 35C

sjcarbon: Ugh.

rama: that will force me to stay home

sjcarbon: I can understand the need for internal escape then.

sjcarbon: There were some caching issues that I want to talk to Ben about, but I can get him on email.

rama: okay

rama: i will sign off

sjcarbon: And follow up with the refresh.pl calling.

rama: thanks a lot

sjcarbon: Cheers--I'll talk to you later.

rama: btw

sjcarbon: ?

rama: one more question

sjcarbon: Yeah.

- Zenbitz has joined the room

rama: how is the new PANTHEr family display going to work with the existing Homolog set displays

- Zenbitz is now known as ben

rama: welcome back Ben

ben: uh... what did I miss...

sjcarbon: Secrets.

rama: nothing much

ben: should I change the cache script command invocation/timing?

sjcarbon: Rama: I don't know how the displays will integrate.

sjcarbon: Ben: What's it at now?

ben: 00 12 * * 1,3,5 /share/goweb/www-data/html/dev/amigo/refresh.pl -c

sjcarbon: Rama: I thiought the news ones were to replace the old ones?

ben: that was the last thing I chatted... I think I got discon'd when I turned on vpn to check crontab on goweb1 from home!

- gwg has joined the room

- 08:45 -

sjcarbon: Ben: Hmmm...I'll have to check the version that you're running, but I think that you'll need to get rid of the "-c" to regenerate the RG stuff with a new database.

ben: I meant to change this when we went to weekly (since the wed/fri runs don't do anything... doesn't the RG stuff take a long time?)

rama: Seth- about ref.genome data

rama: the new thing can't replace the old ones i think

rama: data needs to be merged somehow

sjcarbon: Ben: I think on the order of five or six hours--but it could be speeded up significantly (for you and the user) by redoing the cache.

sjcarbon: And to connect this to Rama's point...

rama: i am clueless about how all the ref.genome data are going to come together in amigo

sjcarbon: I didn't do that because I thought that Sven's stuff was a replacement.

sjcarbon: We can cover that with Chris at the next AHWG.

rama: need to talk to Pascale/Kara and Chris

sjcarbon: Or next RG meeting.

rama: sure. i will let pascale know

sjcarbon: Next RG then? Okay, thanks.

rama: hopefully

- 08:50 -

sjcarbon: The cache redo for RG would take a little elbow grease, so let's not worry about it right now.

rama: not worry about ? (sorry i did not follow)

sjcarbon: Rewriting the caching mechanism for the RG stuff (which would speed up refresh.pl).

ben: well I will wait until you send me the command

ben: I think we discussed priming it priot to load? or by flipping servers?

sjcarbon: I think that was in reference to the Lucene stuff.

ben: yeah, you are right

sjcarbon: The RG regenerations can be done on a live machine.

sjcarbon: Could anyways.

rama: (okay got it)

rama: i have to go now.

sjcarbon: see ya!

rama: Seth- did you have any questions for me?

sjcarbon: no,. I'm good--have fun!

- 08:56 -

rama: okay.

rama: bye

sjcarbon: bye

sjcarbon: Ben: the RG data will fall out of sync unless the script is run without the "-c" (or wit hthe addition of "-s -p -g").

ben: we good?

ben: we need to run -c after every load

ben: should we just run "no opts" (which is everything I recall) after loading?

sjcarbon: that would be great.

ben: I could make it earlier on monday (load usually finishes ca. 6 am, so I could make it 9)

ben: I will run it right now manually to check timing.

sjcarbon: okay,great--let me know how long it takes.

ben: running... brb

sjcarbon: if it's insane on your machine, maybe i'll try and redo the caching right now.

ben: well if it takes more than 30 min, then I won't be able to report back...

ben: today

sjcarbon: i'll no doubt be talking to you later then ;-)

sjcarbon: definitely slower than that.

sjcarbon: I think that covers everything that we can here...

sjcarbon: anybody else with anything?

- 09:01 -

sjcarbon: all good then--thanks everybody!

ben: Oh, sure is.

ben: I better put it in background.

sjcarbon: definitely.

ben: it might bomb anyway when I kill my terminal

ben: I think linux is more forgiving of leaving off the nohup though

ben: or I could leave my lap top here and let it go

ben: prolly do that

sjcarbon: You can rerun under screen too--that's usually what I do for things like this.

sjcarbon: Nicer than nohup.

ben: yeah but I can never remember all the screen commands

sjcarbon: byobu is a great wrapper if you have it.

sjcarbon: much simpler and with menus if necessary (it actually what I use).

- 09:07 -

sjcarbon: i'm good here, anybody with anything else?

- rama has disconnected (Quit: Computer goes to sleep!)

ben: good

sjcarbon: okay--thanks all!

- gwg has disconnected (Read error: EOF from client)