Tools, dependencies and course data
List of Bioinformatic Tools used
Conda environment file
A conda environment.yml file to build the course environment and install all tools into it can be found inside the biosec_course.tar.gz file that can be found here.
Untar the file in your home directory using
course_user> tar -xzvf biosec_course.tar.gz
The environment files can be foudn in biosec_course/misc/install_files.
Create the course environment with the following commands:
course_user> conda env create -f environment.yaml
course_user> conda env create -f environment.busco.yaml
course_user> conda env create -f environment.artic.yaml
course_user> install.sh
course_user> basta.sh
Course VM account
Account details to login/unlock the screen are
login: course_user
passwd: course_user
Course data
All course data will be provided with the VirtualBox image. However, a zipped version of the course data and directory structure can be found here inside the nbiosec_course.tar.gz file.
Dependencies
Developer tools
Linux and MACOS users will need developer tools installed.
Ubuntu users will need to install build-essentials
course_user> sudo apt-get install build-essential
MACOS users will need to install XCode available from the App Store and install command-line tools on the terminal using
course_user> sudo sudo xcode-select --install
Conda / Mamba
The tutorial provides a primer for package managers Conda & Mamba, i.e., a conda implementation will have to be installed
Miniconda installation
Several implementations of Conda exist, e.g., Anaconda and Miniconda, which differ only in the amount of pre-installed tools and packages. As the name implies, Miniconda is a light-weight implementation of Anaconda and is much quicker to install.
To install Miniconda, go to the miniconda download page here to get the latest version of the miniconda installer. Here, we assume you would like to install Miniconda3 Linux 64-bit which will work for most linux computers. First, download the installer using the wget command:
course_user> wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
--2022-11-14 12:22:06-- https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
Resolving repo.anaconda.com (repo.anaconda.com)... 2606:4700::6810:8203, 2606:4700::6810:8303, 104.16.130.3, ...
Connecting to repo.anaconda.com (repo.anaconda.com)|2606:4700::6810:8203|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 76607678 (73M) [application/x-sh]
Saving to: 'Miniconda3-latest-Linux-x86_64.sh’
Miniconda3-latest-Linux-x86_64.sh 100%[=======================================================================================================>] 73.06M 3.02MB/s in 23s
2022-11-14 12:22:29 (3.15 MB/s) - 'Miniconda3-latest-Linux-x86_64.sh’ saved [76607678/76607678]
The output above should be very close to what you will see when downloading the installer. You can check that the file was downloaded using the ll command:
course_user> ll
drwxrwxrwt 19 root root 20480 Nov 14 12:22 ./
drwxr-xr-x 21 root root 4096 Nov 4 10:41 ../
-rw-rw-r-- 1 course_user course_user 76607678 May 17 06:01 Miniconda3-latest-Linux-x86_64.sh
Next, we will need to run the installer on the command line simply by typing the name and pressing Enter. The installer will then guide you through the installation process.
course_user> Miniconda3-latest-Linux-x86_64.sh
Welcome to Miniconda3 py39_4.12.0
In order to continue the installation process, please review the license
agreement.
Please, press ENTER to continue
>>>
When you come to the License Agreement you will have to press Space several times until you are at the end of the agreement. When asked if you agree (and in case you do) type yes and press enter
Do you accept the license terms? [yes|no]
[no] >>> yes
When you’re asked about the installation path just go with the default unless you know what you’re doing, i.e., simply press Enter which will start the installtion. When asked if you want to run conda init type yes and press Enter again. Now conda should be ready to use.
If you now type conda –version you should see the conda version printed to the command-line
course_user> conda --version
conda 4.14.4
Conda can now be used on your system.