These are chat archives for nextflow-io/nextflow

30th
Jan 2015
Paolo Di Tommaso
@pditommaso
Jan 30 2015 00:06
What are deployment keys? A Bitbucket related feature?
Andrew Stewart
@andrewcstewart
Jan 30 2015 00:41
just ssh keys
Paolo Di Tommaso
@pditommaso
Jan 30 2015 00:42
ah
Andrew Stewart
@andrewcstewart
Jan 30 2015 00:42
but iow it looks like nextflow is using https ?
Paolo Di Tommaso
@pditommaso
Jan 30 2015 00:43
Yes, currently only http/s is supported
Andrew Stewart
@andrewcstewart
Jan 30 2015 00:43
(btw, when I try to run nextflow from the bitbucket repository a 2nd time, it doesn't seem to have pulled subsequent changes)
(possible bug?)
Paolo Di Tommaso
@pditommaso
Jan 30 2015 00:44
to fetch changes from the remote repo after the first run/pull you will need either to run ut by using the -latestoption or use pullcommand
Andrew Stewart
@andrewcstewart
Jan 30 2015 00:44
ahhhhhhhh
thats why you use latest :)
Paolo Di Tommaso
@pditommaso
Jan 30 2015 00:45
:)
you may not want always run the latest version
Andrew Stewart
@andrewcstewart
Jan 30 2015 00:47
maybe. But I (personally) wouldn't mind it as default behavior. I imagine if I wanted to run anything but latest I would use -r
btw, Im currently running nextflow on a star cluster deployment with docker
and it's as cool as it sounds
Paolo Di Tommaso
@pditommaso
Jan 30 2015 00:48
Wow, cool
Andrew Stewart
@andrewcstewart
Jan 30 2015 00:48
My qstat, htop and docker -ps are lighting up like its Christmas
Paolo Di Tommaso
@pditommaso
Jan 30 2015 00:48
A blog post about that would be greatly appreciated
Andrew Stewart
@andrewcstewart
Jan 30 2015 00:48
Yea?
Maybe with some best practices
Paolo Di Tommaso
@pditommaso
Jan 30 2015 00:50
Yes, it's very interesting
I saw some people asking about StarCluster + Docker on their (StarCluster) but without a clear answer
(.. their forum)
Sabarish Subramanian
@sabarish14
Jan 30 2015 16:54
Hi, Can somebody give me a detailed documentation on how to install docker on a HPC and the challenges that need to be faced when installing
Andrew Stewart
@andrewcstewart
Jan 30 2015 20:11
@sabarish14 I don't believe any such documentation yet exists. Not that I've come across at least. It's fairly new territory.
I'd be happy to discuss my own experiences in doing so however
Paolo Di Tommaso
@pditommaso
Jan 30 2015 21:45
@sabarish14 I've blogged about that, but there isn't a detailed description
It requires to install the docker engine in each node of your cluster, also a local docker registry from where pull your images is highly recommended.
Docker installation is not a trivial task, it required an updated linux kernel and root permissions
I would suggest to consult your sysadm
Andrew Stewart
@andrewcstewart
Jan 30 2015 22:38
docker image distribution is also an issue, depending how you're using them
if using public images, no big deal... just specify the image name and Docker will grab them from docker hub
if building from scratch, you'll need to build the docker images on each node in the cluster
or use a registry like @pditommaso mentioned
Hm.. I like StarCluster, but all of this could be put into an Ansible playbook using ElastiCluster