Swapnil Doijad, VEO Group Dry Lab Manager, is reading code

Bioinformatics access

Swapnil Doijad, VEO Group Dry Lab Manager, is reading code
Image: Sybille Huck
  • What is Draco?

    The Draco server has been online since June 2021

    At the moment, the Draco server has a capacity of 197 TBs (shared with other users of other group)

    The server consists of the following components

    • 8 standard compute nodes
      • 48 CPU cores (2x Intel Xeon 6248R 24 Core 3.0 GHz)
      • 384GB of RAM
    • 1 visualization node (“Remote Workstation” via NiceDCV)
      • 40 CPU cores (2x Intel Xeon 6240R 20 Core 3.1 GHz)
      • 768GB of RAM
      • 1 NVIDIA Quadro RTX 5000
      • 3.2TB NVMe local scratch storage
    • 4 hybrid CPU-GPU nodes
      • 128 CPU cores (2x AMD Epyc 7702 64 Core 2.0 GHz)
      • 1TB of memory
      • 2 NVIDIA Tesla V100 GPUs 32GB RAM
    • 1 NVIDIA 4 GPU node
      • 128 CPU cores (2x AMD EPYC 7662 64 core 2.0 GHz)
      • 512GB of RAM
      • NVIDIA HGX A100 4-GPU 40GB SXM4 GPUs
      • 6.4 TB on-premises scratch storage
    • BeeGFS file system  with a storage capacity of approx.  66 TB  for the user directories (/home)
    • Infiniband Interconnect (EDR 100Gb/s)

    Details of each node can be found hereExternal link

  • How do I get access to Draco?

    To become a VEO group member, you need to forward your URZ ID requesting to be added to the group to swapnil.doijad@uni-jena.de   and bas.dutilh@uni-jena.de

    Once you are added to the VEO group, you will get access to the DRACO server and bioinformatics page.

  • I want to access Draco and /or work from home. How do I connect to VPN?

    The Draco server and other university internet facilities are only available through a secure VPN. To use the VPN on your computer, you need to download the VPN client ( https://www.uni-jena.de/vpn-windows-apple-mobile de ). 

    Follow the instructions for the setup https://wiki.uni-jena.de/pages/viewpage.action?pageId=36504687External link . You need your URZ ID and password to access this page. 

  • How can I use the tools or databases that are installed on Draco?

    For the convenience of the VEO bioinformaticians, many useful tools and databases are already installed and maintained (details: VEO tools and databasesExternal link ). These tools and databases are updated if you notify Swapnil, the Bioinformatics Lab Manager. If you think the tool or database can be useful for other VEO members and not installed at the Draco, you can also write your request in  VEO tools and databaseExternal link

    Preferentially tools are installed in the conda environmen t ; if not they can be called from the path where binary or scripts are located. 

    For example, if you want to use prokkaExternal link 

    step-1: log in to the Draco server from your computer terminal. The terminal will prompt you for the password; fill in the password, and you are ready to go.

    ssh ab12xyz@login2.draco.uni-jena.de

    step-2: source the conda base environment 

    source /home/groups/VEO/tools/anaconda3/etc/profile.d/conda.sh

    step-3: activate tool specific

    conda activate prokka

    step-4: access the tool

    prokka -h

    Tools in binary format or those that need to be called by the script can be called through the path 

    For example, if you want to use 

    step-1: log in to the Draco server from your computer terminal. The terminal will prompt you for the password; fill in the password, and you are ready to go.

    ssh ab12xyz@login2.draco.uni-jena.de

    step-2:  directly call the tool

    for python script

    python3.6 /home/groups/VEO/tools/other/tool.py

    for binary

    /home/groups/VEO/tools/other/blast

    step-3:  access the tool

    python3.6 /home/groups/VEO/tools/other/tool.py -h

    /home/groups/VEO/tools/other/blast -h

    If the tool is not functioning as expected, please update  VEO tools and databasesExternal link

  • Whats the default path for tools and databases on Draco server?

    By default, the tools are installed at

    tools in the conda environment

    /home/groups/VEO/tools/andaconda3

    scripts and binaries

    /home/groups/VEO/tools/tool_name

    /home/groups/VEO/tools/other/tool_name

  • How can I use scripts that have already been created?

    Some users may find it useful to run scripts preconstructed. These scripts are listed in google sheetExternal link

    The scripts are located at /home/groups/VEO/scripts_for_users/

    you can run the script, for eg for prokka, as...

    step-1: log in to the Draco server from your computer terminal. The terminal will prompt you for the password; fill in the password, and you are ready to go.

    ssh ab12xyz@login2.draco.uni-jena.de

    step-2:

    bash /home/groups/VEO/scripts_for_users/008_annotation.sh