Installation

Docker - biocontainers

For users who prefer docker, can obtain a docker image at Biocontainers

Linux OS

Welcome to installation protocol for Linux OS

Install python3.8 and R

This installation protocol is based on Ubuntu, please use the commands that suit your Linux distribution. For example, apt should be replaced with yum in Fedora/CentOS.

  • Search and start the terminal

  • Follow the commands to update Ubuntu and install python 3.8
    A password will be prompted when you type sudo, use the one you have set during Ubuntu (or your distro) installation.

sudo apt update
sudo apt install software-properties-common
sudo add-apt-repository ppa:deadsnakes/ppa
sudo apt install python3.8
sudo apt install python3-setuptools
sudo apt install python3-pip
sudo apt install r-base

Linux (Ubuntu 18.04) comes with python2.7 installed by default. To use python3.8, creating an alias in .bashrc would do the trick.

Use vim editor if you are familiar using this editor vi .bashrc or open the .bashrc using text editor by gedit .bashrc and add the following line at the bottom of the text.

alias python=python3.8

Save and exit. After that type bash on the command line -Or- simply, close the terminal.

Installing miRge3.0 with conda

conda install -c bioconda mirge3

If you want to use your own environment, please follow the instruction here.

Updating miRge3.0 with conda
conda update mirge3

Installing miRge3.0 with PyPi

First install miRge dependenceis
  • Search and start the terminal, execute the command below:

python3.8 -m pip install --user cutadapt reportlab==3.5.42 biopython==1.78  scikit-learn==0.23.1  hypothesis==5.15.1 pytest==5.4.2  scipy==1.4.1  matplotlib==3.2.1  joblib==0.15.1  pandas==1.0.3 future==0.18.2

If you encounter a WARNING, like below:

WARNING: The script cutadapt is installed in '/home/arun/.local/bin' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.

Then, open a new terminal window or type cd to get to home directory. Add bin folder PATH to the .bashrc, as shown below: Example: export PATH=$PATH:"/home/arun/.local/bin" Remeber to add your path /PATH_TO_USERS/bin.

Install miRge3.0 by this simple command
python3.8 -m pip install --user mirge3
To upgrade miRge3.0
python3.8 -m pip install --user --upgrade  mirge3

Install additional C-libraries based tools

Install Bowtie
  • Search and start the terminal

  • Download bowtie

wget -O bowtie-1.3.0-linux-x86_64.zip https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.3.0/bowtie-1.3.0-linux-x86_64.zip/download
  • unzip bowtie-1.3.0-linux-x86_64.zip

  • cd bowtie-1.3.0-linux-x86_64

  • pwd

    • /home/arun/software/bowtie-1.3.0-linux-x86_64

  • Add these bowtie binaries to .bashrc as shown below:

export PATH=$PATH:"/home/arun/software/bowtie-1.3.0-linux-x86_64"
  • After that type bash on the command line -Or- simply, close the terminal.

Install Samtools
  • Search and start the terminal, execute the below command:
    sudo apt install samtools

Install RNA Fold
  • Search and start the terminal, execute the following commands:

  • wget “https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/ViennaRNA-2.4.16.tar.gz”

  • cd ViennaRNA-2.4.16

sudo ./configure 
sudo make 
sudo make install

GUI requirements

Providing system wide access to miRge3.0, cutadapt, bowtie and bowtie-build, please type or (copy and paste) and submit each of the following commands on the terminal:
NOTE: Make sure to change your path to python bin folder; Replace /home/arun/.local/ with /Path on your computer/.

  • Search and start the terminal, execute the following commands:

sudo ln -s /home/arun/.local/bin/miRge3.0 /usr/local/bin/miRge3.0
sudo ln -s /home/arun/.local/bin/cutadapt /usr/local/bin/cutadapt
sudo ln -s /home/arun/software/bowtie-1.3.0-linux-x86_64/bowtie /usr/local/bin/bowtie
sudo ln -s /home/arun/software/bowtie-1.3.0-linux-x86_64/bowtie-build /usr/local/bin/bowtie-build
sudo ln -s /home/arun/software/bowtie-1.3.0-linux-x86_64/bowtie-inspect /usr/local/bin/bowtie-inspect

Downloading FASTQ files from NCBI:

  • Search and start the terminal, follow the commands below:

  • wget -c https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.10.8/sratoolkit.2.10.8-ubuntu64.tar.gz

  • tar -xvzf sratoolkit.2.10.8-ubuntu64.tar.gz

  • cd sratoolkit.2.10.8-ubuntu64/bin

  • pwd

    • /home/arun/software/sratoolkit.2.10.8-ubuntu64/bin

  • Add to .bashrc

    • cd

    • vi .bashrc or gedit .bashrc and add the following line at the bottom of the page

    • export PATH=$PATH:"/home/arun/software/sratoolkit.2.10.8-ubuntu64/bin"

Save and exit. After that type bash on the command line -Or- simply, close the terminal.

vdb-config
Please follow these instructions for vdb-config here

Downloading FASTQ files, please type the following:
fastq-dump [options] < accession >
Example: fastq-dump SRR772403 SRR772404

Obtaining and installing GUI application

Uninstalling miRge3.0

To uninstall open the terminal and type:

python3.8 -m pip uninstall mirge3

Conda uninstall:

conda remove mirge3

For more details on conda uninstallation process, click here


macOS

Welcome to installation protocol for Mac OS

System prerequisites

  • Search and start the terminal, execute the following commands

  • ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

  • brew update

  • brew install wget

Install python3.7

Please note, any version other than py3.7 causes error in Mac with multiprocessing, issues-1, issues-2.
Download python 3.7.5 from python.org

  • Search and start the terminal, execute the following commands

wget https://www.python.org/ftp/python/3.7.5/python-3.7.5-macosx10.9.pkg
sudo installer -pkg python-3.7.5-macosx10.9.pkg -target /

Mac comes with python2.7 installed by default. To use python3.7, creating an alias in .bash_profile would do the trick
Open a new terminal window. Use vim editor if you are familiar using this editor vi .bash_profile or open the .bash_profile using text editor by open -e .bash_profile and add the following line at the bottom of the text.

alias python=python3.7

Save and exit. After that type source ~/.bash_profile on the command line -Or- simply, close the terminal.

Install R

  • Search and start the terminal, execute the following command

brew install r

Installing miRge3.0 with conda

conda install -c bioconda mirge3

If you want to use your own environment, please follow the instruction here.

Error: Type samtools --version and make sure you don’t encounter any libcrypto.so errors. If you do encounter, simply reinstall samtools with conda as shown below: conda install samtools. If the error still persists, please let us know.

Updating miRge3.0 with conda
conda update mirge3

Installing miRge3.0 with PyPi

First install miRge dependenceis
  • Search and start the terminal, execute the following command

python3.7 -m pip install --user cutadapt reportlab==3.5.42 biopython==1.78  scikit-learn==0.23.1  hypothesis==5.15.1 pytest==5.4.2  scipy==1.4.1  matplotlib==3.2.1  joblib==0.15.1  pandas==1.0.3 future==0.18.2

If you encounter a WARNING, like below:

WARNING: The script cutadapt is installed in '/Users/loaneruser/Library/Python/3.7/bin' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.

Then, open a new terminal window or type cd to get to home directory. Add bin folder PATH to the .bash_profile, as shown below: Example: export PATH=$PATH:"/Users/loaneruser/Library/Python/3.7/bin/" Remeber to add your path /PATH_TO_USERS/Python/3.7/bin.

Install miRge3.0 by this simple command
python3.7 -m pip install --user  mirge3
To upgrade miRge3.0
python3.7 -m pip install --user --upgrade  mirge3

Install additional C-libraries based tools

Install Bowtie
  • Search and start the terminal, execute the following command

  • Download bowtie

wget -O bowtie-1.3.0-macos-x86_64.zip  https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.3.0/bowtie-1.3.0-macos-x86_64.zip/download
  • unzip bowtie-1.3.0-macos-x86_64.zip

  • cd bowtie-1.3.0-macos-x86_64

  • pwd

    • /Users/loaneruser/Software/bowtie-1.3.0-macos-x86_64

  • Add these bowtie binaries to .bash_profile as shown below:

export PATH=$PATH:"/Users/loaneruser/Software/bowtie-1.3.0-macos-x86_64/"
  • After that type source ~/.bash_profile on the command line -Or- simply, close the terminal.

Install Samtools
  • Search and start the terminal, execute the following command
    brew install samtools

Install RNA Fold
  • wget https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/ViennaRNA-2.4.16.tar.gz

  • tar -xvzf ViennaRNA-2.4.16.tar.gz

  • cd ViennaRNA-2.4.16

sudo ./configure 
sudo make 
sudo make install

Downloading FASTQ files from NCBI:

  • Search and start the terminal, execute the following command

  • wget -c https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.10.8/sratoolkit.2.10.8-mac64.tar.gz

  • tar -xvzf sratoolkit.2.10.8-mac64.tar.gz

  • cd sratoolkit.2.10.8-mac64/bin

  • pwd

    • /Users/loaneruser/Software/sratoolkit.2.10.8-mac64/bin

  • Add to .bash_profile

    • cd

    • vi .bash_profile or open -e .bash_profile and add the following line at the bottom of the page

    • export PATH=$PATH:"/Users/loaneruser/Software/sratoolkit.2.10.8-mac64/bin"

Save and exit. After that type source ~/.bash_profile on the command line -Or- simply, close the terminal.

vdb-config
Please follow these instructions for vdb-config here

Downloading FASTQ files, please type the following:
fastq-dump [options] < accession >
Example: fastq-dump SRR772403 SRR772404

GUI requirements

Providing system wide access to miRge3.0, cutadapt, bowtie and bowtie-build, please type or (copy and paste) and submit each of the following commands on the terminal:
NOTE: Make sure to change your path to python bin folder; Replace /Users/loaneruser/Library/ with /Path on your computer/.

  • Search and start the terminal, execute the following command

sudo ln -s /Users/loaneruser/Library/Python/3.7/bin/miRge3.0 /usr/local/bin/miRge3.0
sudo ln -s /Users/loaneruser/Library/Python/3.7/bin/cutadapt /usr/local/bin/cutadapt
sudo ln -s /Users/loaneruser/Software/bowtie-1.3.0-macos-x86_64/bowtie /usr/local/bin/bowtie
sudo ln -s /Users/loaneruser/Software/bowtie-1.3.0-macos-x86_64/bowtie-build /usr/local/bin/bowtie-build
sudo ln -s /Users/loaneruser/Software/bowtie-1.3.0-macos-x86_64/bowtie-inspect /usr/local/bin/bowtie-inspect

Obtaining and installing GUI application

  • Download GUI for OSX

Uninstalling miRge3.0

To uninstall open the terminal and type:

python3.8 -m pip uninstall mirge3

Conda uninstall:

conda remove mirge3

For more details on conda uninstallation process, click here


Windows OS

Welcome to installation protocol for Windows OS

System prerequisites

  • Require Windows 10

  • Require WSL and Ubuntu 18

Install WSL

Please follow one of the following guidlines for installing WSL and Ubuntu 18.04 (recommended Ubuntu distribution)

Install python3.8 and R

  • Search and start Ubuntu _images/Ubuntu.pngUbuntu

  • Follow the commands to update ubuntu and install python 3.8
    A password will be prompted when you type sudo, use the one you have set during Ubuntu installation.

sudo apt update
sudo apt install software-properties-common
sudo add-apt-repository ppa:deadsnakes/ppa
sudo apt install python3.8
sudo apt install python3-setuptools
sudo apt install python3-pip
sudo apt install r-base

Linux (Ubuntu 18.04) comes with python2.7 installed by default. To use python3.8, creating an alias in .bashrc would do the trick

Use vim editor if you are familiar using this editor vi .bashrc or open the .bashrc using text editor by gedit .bashrc and add the following line at the bottom of the text.

alias python=python3.8

Save and exit. After that type bash on the command line -Or- simply, close the terminal.

Installing miRge3.0 with conda

conda install -c bioconda mirge3

If you want to use your own environment, please follow the instruction here.

Updating miRge3.0 with conda
conda update mirge3

Installing miRge3.0 with PyPi

First install miRge dependenceis
  • Search and start Ubuntu, execute the following command

python3.8 -m pip install --user cutadapt reportlab==3.5.42 biopython==1.78  scikit-learn==0.23.1  hypothesis==5.15.1 pytest==5.4.2  scipy==1.4.1  matplotlib==3.2.1  joblib==0.15.1  pandas==1.0.3 future==0.18.2

If you encounter a WARNING, like below:

WARNING: The script cutadapt is installed in '/home/arun/.local/bin' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.

Then, open a new terminal window or type cd to get to home directory. Add bin folder PATH to the .bashrc, as shown below: Example: export PATH=$PATH:"/home/arun/.local/bin" Remeber to add your path /PATH_TO_USERS/bin.

Install miRge3.0 by this simple command
python3.8 -m pip install --user mirge3
To upgrade miRge3.0
python3.8 -m pip install --user --upgrade  mirge3

Install additional C-libraries based tools

Install Bowtie
  • Search and start Ubuntu, execute the following command

  • Download bowtie

wget -O bowtie-1.3.0-linux-x86_64.zip https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.3.0/bowtie-1.3.0-linux-x86_64.zip/download
  • unzip bowtie-1.3.0-linux-x86_64.zip

  • cd bowtie-1.3.0-linux-x86_64.zip

  • pwd

    • /home/arun/software/bowtie-1.3.0-linux-x86_64

  • Add these bowtie binaries to .bashrc as shown below:

export PATH=$PATH:"/home/arun/software/bowtie-1.3.0-linux-x86_64"
  • After that type bash on the command line -Or- simply, close the terminal.

Install Samtools
  • Search and start Ubuntu, execute the following command
    sudo apt install samtools

Install RNA Fold
  • wget “https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/ViennaRNA-2.4.16.tar.gz”

  • cd ViennaRNA-2.4.16

sudo ./configure 
sudo make 
sudo make install

GUI requirements

Providing system wide access to miRge3.0, cutadapt, bowtie and bowtie-build, please type or (copy and paste) and submit each of the following commands on the terminal:
NOTE: Make sure to change your path to python bin folder; Replace /home/arun/.local/ with /Path on your computer/.

  • Search and start Ubuntu, execute the following command

sudo ln -s /home/arun/.local/bin/miRge3.0 /usr/local/bin/miRge3.0
sudo ln -s /home/arun/.local/bin/cutadapt /usr/local/bin/cutadapt
sudo ln -s /home/arun/software/bowtie-1.3.0-linux-x86_64/bowtie /usr/local/bin/bowtie
sudo ln -s /home/arun/software/bowtie-1.3.0-linux-x86_64/bowtie-build /usr/local/bin/bowtie-build
sudo ln -s /home/arun/software/bowtie-1.3.0-linux-x86_64/bowtie-inspect /usr/local/bin/bowtie-inspect

Change Command Prompt Properties

One last thing to avoid an error The directory name is invalid:

  • Type cmd in Windows search box, right-click on Command Prompt and select Open file location. _images/cmd_prompt.png

  • Right-click on Command Prompt and click on Properties. _images/cmd_prop.png

  • Under the Shortcut tab, replace Start in option by changing the value %HOMEDRIVE%%HOMEPATH% to %WINDIR%. Click OK.

    _images/cmd_windir.png

Obtaining and installing GUI application

  • Download GUI for Windows 10

  • Double click miRge3.0.exe to install miRge3.0 windows GUI application. _images/Win_installer_starter.png

  • Click Next to complete miRge3.0 installation _images/Win_installer.png

Uninstalling miRge3.0

  • Step 1: To uninstall open the terminal and type:

python3.8 -m pip uninstall mirge3

Conda uninstall:

conda remove mirge3

For more details on conda uninstallation process, click here

  • Step 2:

    • Search miRge3.0, right click and select uninstall _images/uninstall1.png

    • Under Programs and Features, select miRge3.0 and click Uninstall _images/uninstall2.png

    • Then select Uninstall by clicking Ok. Done. _images/uninstall3.png