Arvados

Hi Albert, we have recently (in the past couple of days) merged some substantial improvements to the Docker containers. Could you download the latest containers and try again?

trying again now...

# Ubuntu 14.04.2 laptop

sudo add-apt-repository ppa:docker-maint/testing
sudo apt-get update
sudo apt-get install docker.io

docker --version
sudo groupadd docker
sudo gpasswd -a ${USER} docker
sudo service docker restart

\curl -sSL get.arvados.org | bash

echo "nameserver 172.17.42.1" | sudo resolvconf -a wlan0.inet
sudo resolvconf -u

# Open browser with website
http://workbench.dev.arvados

I get a fiddlesticks error on the home page. Not if I click on 'Dashboard' though. If I try to create a new project 'foo' and then upload data:

http://workbench.dev.arvados/collections?collection%5Bmanifest_text%5D=&collection%5Bname%5D=New+collection&collection%5Bowner_uuid%5D=xxxxx-j7d0g-uanjb7ne0338td5&options%5Bensure_unique_name%5D=true&redirect_to_anchor=Upload

I get a fiddlesticks error:

An error occurred when Workbench sent a request to the Arvados API server. Try reloading this page. If the problem is temporary, your request might go through next time. If that doesn't work, the information below can help system administrators track down the problem.

API request URL
https://api.dev.arvados/arvados/v1/collections
API response
{
  ":errors":[
    "Unparseable response from API server" 
  ]
}

If you suspect this is a bug, you can help us fix it by sending us a problem report:

If I try again and create a new 'bar' project, I get an "Unparseable..." error box. I try again with 'yolo', I can now go to the Upload menu, I get a bottom page 'Internal server error', I click 'Reload' and can get to the upload menu and choose a file.

I then can choose 2 smallish fastq.gz files, then click on 'Start' and successfully upload them.

All in all, most menus require to click "Refresh" a couple of times to get working, but it is now functional.

Next step, add a simple biobox pipeline...

I'm glad you're making progress!

There's a startup time of 10-15 seconds for the API server, you may be trying to load workbench (which is a separate application from the API server) before it has come up. However, once the API server is running, you shouldn't be seeing any more error pages. I'm not sure why you would see "Unparseable response from API server".

Also, some of the pages that are supposed to auto-refresh but currently do not. This is being worked on, you can watch bug #4752.

Thanks!

Hi Albert,

We've merged several fixes to our docker containers (specifically, bug #4752 has been closed).

Could you try again with the latest set of Docker images and let us know how that goes? The documentation at http://doc.arvados.org/install/pre-built-docker.html has also been updated to reflect the new, much improved Docker images.

Thanks,
Ward.