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Mac_install.md

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Welcome to installation protocol for Mac OS

System prerequisites

  • 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

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.

Installing miRge3.0

First install miRge dependenceis

python3.7 -m pip install --user cutadapt==2.7 reportlab==3.5.42 biopython==1.77  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  -i  https://test.pypi.org/simple/  mirge==0.1.54

Install additional C-libraries based tools

Install Bowtie

  • wget -O bowtie-1.2.3-macos-x86_64.zip https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.2.3/bowtie-1.2.3-macos-x86_64.zip/download
  • unzip bowtie-1.2.3-macos-x86_64.zip
  • cd bowtie-1.2.3-macos-x86_64
  • pwd
    • /Users/loaneruser/Software/bowtie-1.2.3-macos-x86_64
  • Add this bowtie binaries to .bash_profile as shown below:
export PATH=$PATH:"/Users/loaneruser/Software/bowtie-1.2.3-macos-x86_64/"
  • After that type source ~/.bash_profile on the command line -Or- simply, close the terminal.

Install Samtools

brew install samtools

Install RNA Fold

sudo ./configure 
sudo make 
sudo make install

Downloading FASTQ files from NCBI:

  • 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.

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/.

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-1.2.3-macos-x86_64/bowtie /usr/local/bin/bowtie
sudo ln -s /Users/loaneruser/Software/bowtie-1.2.3-macos-x86_64/bowtie-build /usr/local/bin/bowtie-build
sudo ln -s /Users/loaneruser/Software/bowtie-1.2.3-macos-x86_64/bowtie-inspect /usr/local/bin/bowtie-inspect