These are chat archives for elsiklab/bovinemine

3rd
Nov 2015
Aditi
@tayala
Nov 03 2015 16:08
Hey you guys , which folder is hosting bovinemine on genomes? is there a folder that you are using for development
Deepak
@deepakunni3
Nov 03 2015 16:09
Hey, glad to see you on gitter
Hymenopteramine (live) is at : /db/intermine/hymenopteramine_release_1.0/beemine_main/beemine
Aditi
@tayala
Nov 03 2015 16:11
and for bovinemine. I am guessing bovinemine needs more work right now
Deepak
@deepakunni3
Nov 03 2015 16:12
bovinemine is in colin’s directory
Aditi
@tayala
Nov 03 2015 16:13
ok good.. i guess i wont mess things up then. Can I make a pull from github
Deepak
@deepakunni3
Nov 03 2015 16:13
are you planning to start with the KEGG?
Aditi
@tayala
Nov 03 2015 16:13
we dont have a file for KEGG
Deepak
@deepakunni3
Nov 03 2015 16:14
oh, right.
so what are you planning on starting with?
Aditi
@tayala
Nov 03 2015 16:14
i am almost done fixing the importer for sequences
in upper case
Deepak
@deepakunni3
Nov 03 2015 16:15
oh wow. thats great!
so you started with a clone of our up-to-date repo, right?
Aditi
@tayala
Nov 03 2015 16:16
i just took the bovinemine folder that was on genomes and worked with it. but i will update to the uptodate repo
Deepak
@deepakunni3
Nov 03 2015 16:16
yeah, its best to clone the repo and then make the changes and then push
Aditi
@tayala
Nov 03 2015 16:16
good it will force me to use it too
Deepak
@deepakunni3
Nov 03 2015 16:17
yes :+1:
Colin Diesh
@cmdcolin
Nov 03 2015 16:20
hellooooo
Aditi
@tayala
Nov 03 2015 16:21
hii colin
Colin Diesh
@cmdcolin
Nov 03 2015 16:25
:)
Aditi
@tayala
Nov 03 2015 17:19
bovinemine down?
Deepak
@deepakunni3
Nov 03 2015 17:20
tomcat is being restarted.
Aditi
@tayala
Nov 03 2015 17:21
ok
Deepak
@deepakunni3
Nov 03 2015 17:48
Hey, I think it would be best to use george for development, testing and deploying new test instances
Aditi
@tayala
Nov 03 2015 17:49
ok kool. i am testing somethng out. I will move there right after.
Deepak
@deepakunni3
Nov 03 2015 17:50
yeah. Deploy and undeploy has a tendency of making tomcat unstable. Since genomes is live, its best to minimize webapp deploy.
Aditi
@tayala
Nov 03 2015 17:50
question.? So for the CDS. We disabled them and we made our own CDS.
now we have to bring it back?
Deepak
@deepakunni3
Nov 03 2015 17:51
No No.
We changed gff3_config.properties to ignore CDS lines from a GFF3 file
Aditi
@tayala
Nov 03 2015 17:51
yes
Deepak
@deepakunni3
Nov 03 2015 17:51
and we loaded CDS sequences separately
Aditi
@tayala
Nov 03 2015 17:51
yes
Deepak
@deepakunni3
Nov 03 2015 17:52
this time the only thing that has changed is the CDS sequences itself. Instead of computing them ourselves, we are going to download it from NCBI and ENSEMBL and just load them as-is
the only extra step would be to prepare the FASTA headers of the CDS sequences to be compatible with the CDS sequence loader that we made
Aditi
@tayala
Nov 03 2015 17:53
got it
Aditi
@tayala
Nov 03 2015 19:34
i think george is down?
Deepak
@deepakunni3
Nov 03 2015 20:04
no, its not. You won’t be able to do a direct login
but you can login to genomes and then ssh george-i
Aditi
@tayala
Nov 03 2015 20:06
I did a git clone and deployed the web app. When I go to the web app (or just george.missouri.edu) it times out
Deepak
@deepakunni3
Nov 03 2015 20:11
oh right. You can’t visit george.missouri.edu from an outside network
Didn
Didn’t think of that
Aditi
@tayala
Nov 03 2015 20:13
:worried: ok
Deepak
@deepakunni3
Nov 03 2015 20:13
you didn’t get access to a VPN?
Aditi
@tayala
Nov 03 2015 20:14
nope i am using the server through kilgore
Deepak
@deepakunni3
Nov 03 2015 20:16
thats odd. employees generally can use the VPN :confused:
Aditi
@tayala
Nov 03 2015 20:16
i am not an employee
I am a consultant with a contract
Deepak
@deepakunni3
Nov 03 2015 20:17
oh, okay. So I guess the rules are different.
well, colin is working on a solution such that you can access george.missouri.edu via genomes.
Aditi
@tayala
Nov 03 2015 20:21
oh yeyy! okie. Do you know where the NCBI CDS file is
Deepak
@deepakunni3
Nov 03 2015 20:25
hunting ...
The file with CDS for Bos taurus:
ftp://ftp.ncbi.nlm.nih.gov/genomes/Bos_taurus/RNA/rna.fa.gz
Aditi
@tayala
Nov 03 2015 20:27
thanx
Deepak
@deepakunni3
Nov 03 2015 20:27
similar folder structure would apply for any organism
welcome! :)
Aditi
@tayala
Nov 03 2015 22:28
I think thats mRNA transcript file
not CDS
Deepak
@deepakunni3
Nov 03 2015 22:31
uh oh!
lemme look around.
Deepak
@deepakunni3
Nov 03 2015 22:40
hey, I doubt NCBI provides CDS in a file. That is so weird.
Ensembl does provide it in a neat file:
ftp://ftp.ensembl.org/pub/release-82/fasta/bos_taurus/cds/
Aditi
@tayala
Nov 03 2015 22:41
yes i found that one
Deepak
@deepakunni3
Nov 03 2015 22:42
okay, I’ll look around. I assumed since Ensembl provided it, NCBI would too.
Aditi
@tayala
Nov 03 2015 22:44
i didnt think NCBI did because I remember I was trying to check the parsed CDS and I was never able to check against NCBI . Just always against OGS
Deepak
@deepakunni3
Nov 03 2015 22:44
oh, right.