The analysis requires R, python3, Cellranger, bamtofastq, GATK, VCFtools, IQtree and BEAST2
Required software can be installed independently, but we suggest the conda package manager. Cellranger and bamtofastq are not available through the conda package manager and need to be installed separately.
To install the conda package manager, either follow the instructions bellow or, for more information, instructions on the conda website.
To download miniconda (minimal installation of conda), open your terminal and type the following:
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
This will download the miniconda into your current directory. Now type:
bash Miniconda3-latest-Linux-x86_64.sh
and follow the installation instructions in your terminal. This will install conda into your computer. To verify that conda is installed, open new terminal window (or type exec bash) and type:
conda --help
You can now install required software by typing:
conda install r-base gatk4 vcftools iqtree beast2
There is no need to install python3 as it is a part of the conda installation.
Cellranger is a proprietary software and its not available through the conda manager.
Visit the Cellranger homepage and fill in required information. You will be provided with a download link and detailed installation instructions.
Download provided link with curl or wget. You will download a compressed archive cellranger-5.0.1.tar.gz (or a newer version). To unpack this archive, type:
tar -xzvf cellranger-5.0.1.tar.gz
This will unpack the archive in your current directory. Personally, You can now remove cellranger-5.0.1.tar.gz by typing:
rm cellranger-5.0.1.tar.gz
Now open .bashrc or .profile in your favourite editor and add export PATH=~/cellranger-5.0.1:$PATH or type:
echo 'export PATH=~/cellranger-5.0.1:$PATH' >> .bashrc
Restart your terminal by typing exec bash and type:
cellranger --help
to verify the installation.
To install bamtofastq visit the project github page or follow these instructions:
To download bamtofastq, type:
wget -O bamtofastq https://github.com/10XGenomics/bamtofastq/releases/download/v1.3.5/bamtofastq_linux
Now you need to add execute (x) permission to bamtofastq:
chmod +x bamtofastq
Finally, add bamtofastq to your PATH like you did with Cellranger:
echo 'export PATH=~/cellranger-5.0.1:$PATH' >> .bashrc
Restart your terminal (exec bash) and type:
bamtofastq --help
to verify the installation.