These are chat archives for nextflow-io/nextflow

4th
May 2015
Andrew Stewart
@andrewcstewart
May 04 2015 19:48
Hey @pditommaso Im having that network problem reaching nextflow.io (and downloads) from inside our network. Ive got our nextwork engineer taking a look at it, but Im wondering if there's any chance I could grab a copy of nextflow somehow else?
(looking for the most recent version, and the self-installer isn't working within network due to the above problem)
Andrew Stewart
@andrewcstewart
May 04 2015 19:56
Actually I can try to compile from github I suppose
Im going to do some tests to see if this is just something to do with reaching any site hosted on S3 or specific to nextflow.io
If whoever on your side setup the website is willing / interested in discussing the issue though I can loop in our network engineer too - its possible that others might be experiencing this problem.
Paolo Di Tommaso
@pditommaso
May 04 2015 19:59
you can download from here
but that is just the launcher script, it still try to download a from nextflow.io/S3
I'm definitively interested to figure out what the problem is
but on my side there's nothing more than a name server + S3 storage
I should take in consideration to change name server
gosh!
Amazon acquired ClusterK !
Paolo Di Tommaso
@pditommaso
May 04 2015 20:17
@andrewcstewart Could you please try to open S3 domain directly
Andrew Stewart
@andrewcstewart
May 04 2015 20:54
yes1 sec
(Sorry was onphone call)
whoa re:clusterK
Amazon ElasticClusterService ?
well..ECSistaken
Paolo Di Tommaso
@pditommaso
May 04 2015 20:55
:)
Andrew Stewart
@andrewcstewart
May 04 2015 20:56
yea..no good on that direct link
Paolo Di Tommaso
@pditommaso
May 04 2015 20:56
So I can't see how I can help on my side
that's just S3 storage
Andrew Stewart
@andrewcstewart
May 04 2015 20:57
Im going to test creating my own static site real quick
my IT guy just has some questions about something IP related... im an idiot when it comes to networking so I can't properly translate
Paolo Di Tommaso
@pditommaso
May 04 2015 21:01
what's the question?
Andrew Stewart
@andrewcstewart
May 04 2015 21:12
ill see if he can jump on the mailing list
Michael L Heuer
@heuermh
May 04 2015 21:35
is there any support for killing a process after a certain amount of time in nextflow? I can think of various different ways (gnu timeout, slurm job control, etc.) but I believe they would all return non-zero return codes, which would stop the entire nextflow job
Andrew Stewart
@andrewcstewart
May 04 2015 21:36
you set the error handler directive to permissable
Paolo Di Tommaso
@pditommaso
May 04 2015 21:36
@heuermh Using slurm?
Andrew Stewart
@andrewcstewart
May 04 2015 21:36
isnt there also a time directive though?
Paolo Di Tommaso
@pditommaso
May 04 2015 21:36
yep
but it only works with a grid engine
Michael L Heuer
@heuermh
May 04 2015 21:37
yeah currently on slurm
@andrewcstewart what's that?
Michael L Heuer
@heuermh
May 04 2015 21:38
D'oh!
Andrew Stewart
@andrewcstewart
May 04 2015 21:38
beat me too it. im having to look up documentation on my phone lol
Paolo Di Tommaso
@pditommaso
May 04 2015 21:40
@andrewcstewart you may use mobile hotspot ;)
@heuermh but do you need to fail silently, isn't it ?
Andrew Stewart
@andrewcstewart
May 04 2015 21:41
@pditommaso my guy wants to know if its possible to know the range of IP addresses that have beenallocated tothat domain.. or is it completely dynamic?
Paolo Di Tommaso
@pditommaso
May 04 2015 21:41
@andrewcstewart no clue, I can't manage that
@andrewcstewart that is managed by the name maintainer
Michael L Heuer
@heuermh
May 04 2015 21:42
Apparently I have missed that entire page of documentation! Many of those directives look useful.
Paolo Di Tommaso
@pditommaso
May 04 2015 21:43
good!
I didn't waste my time writing it ! :)
Andrew Stewart
@andrewcstewart
May 04 2015 21:48
huh.. I tried setting up a static html file on our own S3 hosted site
and it works
Paolo Di Tommaso
@pditommaso
May 04 2015 21:50
well, maybe the problem is that nextflow is hosted in a different region
I mean "eu-west-1"
but it makes no sense you cannot open it
Michael L Heuer
@heuermh
May 04 2015 21:52
so if we set the time directive on this particular process we would like it to continue on timeout rather than fail. looks like we need to set errorStrategy 'ignore' and we're good
Paolo Di Tommaso
@pditommaso
May 04 2015 21:52
yep
@andrewcstewart do you use any proxy ?
Andrew Stewart
@andrewcstewart
May 04 2015 21:54
nope
but Im about to setup a SOCKS4 proxy reverse SSH tunnel through an EC2 instance so I can at least get the download :D
*reverse proxy
Paolo Di Tommaso
@pditommaso
May 04 2015 21:56
can't you open this either ?
Andrew Stewart
@andrewcstewart
May 04 2015 21:57
nah
Paolo Di Tommaso
@pditommaso
May 04 2015 21:58
ok, that's bad
Andrew Stewart
@andrewcstewart
May 04 2015 21:58
That wouldn't help anyway though unless I modified the loader script to fetch from the direct URL
Paolo Di Tommaso
@pditommaso
May 04 2015 21:58
I'm going to share a dropbox folder with you
Andrew Stewart
@andrewcstewart
May 04 2015 22:04
Thanks
copy the nextflow file on your PATH
and .nextflow folder in your $HOME
Andrew Stewart
@andrewcstewart
May 04 2015 22:08
will grab in a bit, gotta run to a meeting
Paolo Di Tommaso
@pditommaso
May 04 2015 22:08
no pb
Paolo Di Tommaso
@pditommaso
May 04 2015 22:38
@andrewcstewart The funny thing is the "veracyte inc" appears in the nextflow website logs .. (?)
Andrew Stewart
@andrewcstewart
May 04 2015 22:39
hmm
we figured out can access over wifi haha
(but unfortunately the servers are on ethernet)
(well.. fortunatley)
btw .. this news about ClusterK has convinced me to check out Cirrus more closely
looks like all you do is start up their AMI?