Chapter 2 Prerequisites

2.1 NCGR Workshop Server

Use the following information to connect to the server for this workshop:

  • hostname: inbre.ncgr.org
  • port: 2503

For example, this information can be used to connect to the server using the ssh command as follows:

ssh -p 2503 <username>@inbre.ncgr.org

2.2 Software

You will need to install the following software on your computer.

  • Zoom
    • https://zoom.us/download
    • Install the correct version for your OS. Don’t plan to use the web version, as this does not have enough features.
  • Terminal Emulator
    • Comes with Linux/Mac
    • Windows: MobaXterm
  • Bandage and BLAST+ v2.2.18
    • https://github.com/rrwick/Bandage
    • https://github.com/rrwick/Bandage/wiki/BLAST-searches
    • https://academic.oup.com/bioinformatics/article/31/20/3350/196114
    • Mac Install
      • Go to https://github.com/rrwick/Bandage/releases
      • Scroll down to assets
      • Download the macOS zip file with aarch64 if you have Apple Silicon (M1 or M2 processor)
        • you can check this under the apple menu: About this Mac
      • Otherwise download the macOS zip file with x86-64
      • Double-click to unzip
      • If you have security warnings you can go to the apple menu: System Preferences: Privacy and Security. Choose “Open Anyway” (you might need to scroll down).
      • If you get a “Bandage is damaged and can’t be opened” message, it means your mac has put the file in quarantine. Open a terminal, cd to Downloads, then cd into the unzipped Bandage folder. Type the following then hit enter: xattr -cr Bandage.app
      • If you are still having issues with the “damaged” error, you can download the x86-64 version instead
      • To install blast, go to https://www.ncbi.nlm.nih.gov/books/NBK569861/, click on the ftp link, choose “LATEST”, and download the one ending in dmg
      • Double-click on it and follow the install instructions, using the default location where Bandage should be able to see it.
    • Windows Install
      • Go to https://github.com/rrwick/Bandage/releases
      • Scroll down to assets
      • Download Bandage_Windows_v0_8_1.zip
      • Right-click (or ctrl-click) on the dowloaded file and choose “Extract All”
      • Open up the unzipped Bandage folder and double-click on “Bandage.exe”. If you get a secruity warning, choose “More Info” and “Run Anyway”
      • To install blast, go to https://www.ncbi.nlm.nih.gov/books/NBK52637/ and follow the directions under “Steps” (you will download the file ending in .exe)
      • If you get an error that makeblastdb can’t be found, we need to fix your windows environment paths. In the windows search bar type “environment” and click on “Edit the system environment variables”. Click on “New” and under Variable_name type “BLASTDB”. Under Variable_value type the path to the blast db folder (for example: C:\Users\jm\Downloads\blast-2.2.18+\db\). Restart your computer.

The following software is provided for you on the server.

2.3 Runnning Singularity

Some software on the server will be run with Singularity. Singularity runs software in containers. To run a container, singularity must be given a filepath to the .sif file of the container. For this workshop, all .sif files are located at /home/data/pangenomics-2503/sif/**. For example the following commmand will run the pggb container:

singularity run --no-privs /home/data/pangenomics-2503/sif/pggb.sif

Note the use of the --no-privs flag. This is required to run singularity on our environment but is generally not necessary.

2.4 Data

For this workshop, all data for this workshop is located at /home/data/pangenomics-2503/ on the server.