Bio-Linux 8 on iPlant Atmosphere

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Tony Travis

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Apr 23, 2015, 11:38:14 AM4/23/15
to cloudb...@googlegroups.com
Hi,

I've created a Bio-Linux 8 instance on iPlant Atmosphere:

https://atmo.iplantcollaborative.org

ID396a5744-87c2-4d3f-ad40-75134482f5ee

I worked around a problem of insufficient space on their default 10GB VM
system volume by mounting /usr on a 20GB partition of an attached volume
instead (I've asked them about getting a 20GB system volume):

> # login to instance
> ajt@beluga:~$ ssh ajtr...@128.196.64.133
>
> # list available block devices
> ajtravis@vm64-133:~$ lsblk
> NAME MAJ:MIN RM SIZE RO TYPE MOUNTPOINT
> vda 253:0 0 9.4G 0 disk /
> vdb 253:16 0 60G 0 disk
> vdc 253:32 0 120G 0 disk
>
> # partition attached volume /dev/vdc
> parted /dev/vdc
> unit MiB
> mklabel msdos
> mkpart primary 1 20GB
> mkpart primary 20GB -0
>
> lsblk
> NAME MAJ:MIN RM SIZE RO TYPE MOUNTPOINT
> vda 253:0 0 9.4G 0 disk /
> vdb 253:16 0 60G 0 disk
> vdc 253:32 0 120G 0 disk
> ├─vdc1 253:33 0 18.6G 0 part
> └─vdc2 253:34 0 101.4G 0 part
>
>
> # create filesystems
> mkfs -t ext4 /dev/vdc1
> mkfs -t ext4 /dev/vdc2
>
> # move /usr onto attached volume
> mount /dev/vdc1 /mnt
> rsync -axHP /usr/ /mnt/
> mv -i /usr /usr.old
> mkdir /usr
> mount /dev/vdc1 /usr
>
> # update /etc/fstab
> vim /etc/fstab
> ...
> /dev/sda1 / ext3 defaults 0 0
> /dev/vdc1 /usr ext4 defaults 0 0
> ...
>
> # reboot to make sure /usr on attached volume is available at boot
> reboot -f
>
> # login again and do Bio-Linux 8 upgrade
> wget -q http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh
>

This is the disk usage after installation:

> ajtravis@vm64-133:~$ df -hT -t ext3 -t ext4
> Filesystem Type Size Used Avail Use% Mounted on
> /dev/vda ext3 9.3G 3.8G 5.1G 43% /
> /dev/vdc1 ext4 19G 8.9G 8.6G 52% /usr

I can access my Bio-Linux 8 instance via "x2go", which is my preferred
method, but I can't get their web-browser RealVNC client to connect: It
complains that their licence has expired

I going to use this Bio-Linux 8 instance to try out iPlant Atmosphere
with a view to maybe using it for teaching a Bio-Linux course at UoA.

Anyone else using iPlant Atmosphere (based on OpenStack)?

Bye,

Tony.
Screenshot from 2015-04-23 14:24:28.png

Brad Chapman

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Apr 23, 2015, 8:41:38 PM4/23/15
to Tony Travis, cloudb...@googlegroups.com

Tony;
Nice work. I've only played with iPlant a little to help debug someone's
problem there but it's great to have this available there. Thanks for
doing that,
Brad
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Tony Travis

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Jul 22, 2015, 7:28:15 AM7/22/15
to Brad Chapman, cloudb...@googlegroups.com, Bio-Linux technical discussion
On 24/04/15 01:41, Brad Chapman wrote:
> Tony;
> Nice work. I've only played with iPlant a little to help debug someone's
> problem there but it's great to have this available there. Thanks for
> doing that,
> Brad
> [...]

Hi, Brad.

The iPlant Collaborative have now created a Bio-Linux 8 image for me
with a 20GB root filesystem.

Their base image was installed from the NEBC/EOS .iso but, by default,
you can't login by SSH...

I've created a new image from the base image called "Bio-Linux-8-debug"
that you can login by SSH/x2go.

Please let anyone who might be interested know that "Bio-Linux-8-debug"
is now available on iPlant Atmosphere:

http://www.iplantcollaborative.org/ci/atmosphere

My "Bio-Linux-8-debug" image is:

https://atmo.iplantcollaborative.org/application/images/1134

Thanks,

Tony.
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