Installation¶
miRge-build is developed and tested on Linux environment.
Dependencies¶
- miRge-build installation requires
python 3.8 or newer - Bowtie v1.2.3 - please pick one based on your OS.
- After downloading Bowtie, extract it (
unzip bowtie-1.2.3-linux-x86_64.zip), - Change directory to bowtie
cd bowtie-1.2.3-linux-x86_64and typepwdto get full path of the directory (pwd: present working directory). - Add that path to the environment PATH:
export PATH=$PATH:"pwd <path> ". - Example:
export PATH=$PATH:"/home/user/software/bowtie-1.2.3-linux-x86_64"
- Example:
- Add that path to the environment PATH:
- After downloading Bowtie, extract it (
- Requires scipy for enabling novel miRNA analysis
python3.8 -m pip install --user scipy==1.4.1 - Requires scikit-learn for enabling novel miRNA analysis
python3.8 -m pip install scikit-learn==0.23.1 - Requires biopython for parsing all input FASTA files
python3.8 -m pip install biopython==1.77
Quick installation¶
The easiest way to install miRge-build is to use pip3 on the command line:
If you have root previlages, then install miRge-build as follows:
sudo python3.8 -m pip install miRge-build
if you have only user previlages:
python3.8 -m pip install --user miRge-build
This will download the software from PyPI (the Python packaging
index), and
install the miRge-build binary into $HOME/.local/bin. If an old version of
miRge-build exists on your system, the --upgrade parameter is required in order
to install a newer version. You can then run the program like this:
~/.local/bin/miRge-build --help
If you want to avoid typing the full path, add the directory
$HOME/.local/bin to your $PATH environment variable.
Installation with conda¶
Yet to be implemented