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
- First download Ubuntu from ubuntu.com (the alternate version)
- Place the ISO image in this folder
- Modify the create.sh to fit to your ISO image name
- Run:
sudo bash create.sh
- 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
.
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
In Virtualbox select the virtualmachine that was created using the custom ISO.
- Make sure the VM is currently not running.
- Open the settings screen with CTRL+S
- Click 'Storage' and Add a new disk to the SATA controller.
- In the question popup, select 'Create new disk'
- 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
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
This repository is based on previous (drafts) work on: https://github.com/wyleung/nebulae
2013-2014 (c) Wai Yi Leung - SASC - Leiden University Medical Centre