Allbio Virtual Machine installer

This is just a package to streamline the installation of the virtualmachines and/or cluster machines. ( custom installation disk of Ubuntu 12.04.3 LTS )

This package installs the necessary packages needed for the AllbioTC2 pipeline: https://github.com/ALLBio/allbiotc2

Instructions

1. First download Ubuntu from ubuntu.com (the alternate version)
2. Place the ISO image in this folder
3. Modify the create.sh to fit to your ISO image name
4. Run: sudo bash create.sh
5. The new branded ISO image will be ready in a few minutes.

To modify the bootscript and installation of other packages after first boot, check the file conf/firstboot.sh and conf/postinstall.sh.

Changing initial root password and initial user (+passwd)

In conf/preseed.cfg, the root user and its credentials can set in the following subsection:

d-i passwd/root-password-crypted $6$I8WJedWU$UkRom...Uyoj1

You can use the following to get an encrypted version of your password:

$ python -c "import crypt, getpass, pwd; print crypt.crypt('somepassword', '\$6\$I8WJedWU\$')"

Next to this section, you will find the setup for the first user of the system.

In this distribution the root password is allbioroot and the allbio user is allbio

Notes on creating addtional hard drive (Virtualbox specific)

In Virtualbox select the virtualmachine that was created using the custom ISO.

1. Make sure the VM is currently not running.
2. Open the settings screen with CTRL+S
3. Click 'Storage' and Add a new disk to the SATA controller.
4. In the question popup, select 'Create new disk'
5. Go through the virtual disk creation wizard.

After the disk creation, startup the VM and login as root.

Issue blkid on the commandline to see whether a new disk is added. The disk without a LABEL and TYPE is the new disk. (in any case /dev/sda is never the new disk since this is the OS disk)

$ fdisk /dev/sdb

Command (m for help): n
Partition type:
   p   primary (0 primary, 0 extended, 4 free)
   e   extended
Select (default p): p
Partition number (1-4, default 1): 1
First sector (2048-209715199, default 2048): 
Using default value 2048
Last sector, +sectors or +size{K,M,G} (2048-209715199, default 209715199): 
Using default value 209715199

Press w and return to write the changes to disk.

All what is left is to format the disk

$ sudo mkfs.ext4 /dev/sdb1

And give it a label, note that the label should have a _storage suffix in order to make it work with the automount procedure (see below):

$ e2label /dev/sdb1 mygenome_storage

Mounting additional disks in the VM

A automount script is provided in /data; called mountall.sh which does the drive mounting under the /data directory and creates mountpoints for each allbio data diskdrive (download from our website or created as described above)

Just issue the following command:

allbio@machine:/data $ ./mountall.sh

Fork

This repository is based on previous (drafts) work on: https://github.com/wyleung/nebulae

Copyright

2013-2014 (c) Wai Yi Leung - SASC - Leiden University Medical Centre