ScientificOSX
These are the steps I took recently to setup a new MacbookPro (Catalina OSX 10.15.7) for scientific/bioinformatics use.
Step 1, base software:
Log in to App Store with login. Xcode and other needed items are autodownloaded by homebrew via the App Store.
Install homebrew, update
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"
brew analytics off
brew update && brew upgrade
brew config
Extras
#update bash
bash --version
brew install bash
#The newer version of bash is located at /usr/local/bin/bash:
ls -l /usr/local/bin/bash
cat /etc/shells
# If not in /etc/shells, append it:
sudo -i
echo /usr/local/bin/bash >> /etc/shells
#Set default shell to /usr/local/bin/bash, run the following chsh command
chsh -s /usr/local/bin/bash
#should have changed to latests
bash --version
Create
touch ~/.bash_profile
# to edit use nano
nano ~/.bash_profile
Include this in ~/.bash_profile & save.
export PATH=/usr/local/bin:/usr/local/sbin:$PATH
alias rc='source ~/.bash_profile'
alias man='_() { echo $1; man -M $(brew --prefix)/opt/coreutils/libexec/gnuman $1 1>/dev/null 2>&1; if [ "$?" -eq 0 ]; then man -M $(brew --prefix)/opt/coreutils/libexec/gnuman $1; else man $1; fi }; _'
source ~/.bash_profile
Xquartz
brew install --cask xquartz
JAVA
brew tap AdoptOpenJDK/openjdk
brew install --cask adoptopenjdk11
R and R studio:
Install latest R: https://cran.r-project.org/bin/macosx/ RStudio: https://www.rstudio.com/products/rstudio/download/#download
Multiple versions of R
Blindly using the binary installer (*.pkg) version available through CRAN will remove the current version of the r framework (including your package libraries).
Thus, prior to installing the new version of R is trick OSX into forgetting that R is already installed on your system by using pkgutil.
https://rud.is/rswitch/guide/index.html
pkgutil --pkgs #shows what is installed
#updated for catalina, and I installed 4.0 first then 3.6 and the below code worked great.
#Make sure you copy over the RSwitch.App to your applications folder and run it.
sudo pkgutil --forget org.R-project.R.fw.pkg
sudo pkgutil --forget org.r-project.x86_64.tcltk
sudo pkgutil --forget org.R-project.R.GUI.pkg
Base Needs
brew install hdf5 git freetype
brew install cmake automake fontconfig jpeg libtiff libpng libffi doxygen
brew install glib libcaca libconfig libtasn1 libtool libunistring zlib icu4c
brew install tmux
Python and Libs
management of different python versions
There are a number of tools available that enable the installation and management of different python versions.
pyenv is one tool to do this.
brew install pyenv
echo 'eval "$(pyenv init -)"' >> ~/.bash_profile
source ~/.bash_profile
pyenv install --list
#see list for latest
#pyenv install 3.9.1 # 3.9 does not support Numpy
pyenv install 3.8.7
pyenv install 2.7.18
#set globally which python
pyenv global 3.8.7
pyenv version
#update pip
pip install --upgrade pip
virtual python environments
To have different python projects with different dependencies and versions of python; environments help isolate them.
to create python virtual environments using pipenv:
brew install pipenv
mkdir MyPyTest
cd MyPyTest
pipenv --python 3.8
#to install packages use pipenv within the environment
pipenv install ipykernel
Note: Jupyter Notebooks are able to work with virtual environments so that you are able to run the notebooks for a project in the correct project environment.
#change myenv to a name
python3 -m ipykernel install --user --name myenv --display-name "Python (myenv)"
Python Packages
jupyter notebook can be invoked which will automatically open a window in your browser.
pip3 install notebook
ip3 install h5py
pip3 install umap-learn
Extra installs
Install latest gfortran https://github.com/fxcoudert/gfortran-for-macOS/releases
R packages
Note if you have multiple R environments, you may want to do this for each.
#update Rprofile by adding the line below and saving
nano ~/.Rprofile.site
# local({options(repos = BiocManager::repositories())})
install.packages(c('devtools', 'BiocManager', 'remotes'), dependencies=TRUE, ask = FALSE)
install.packages('XML', repos = 'http://www.omegahat.net/R')
BiocManager::install(c('org.Hs.eg.db', 'org.Mm.eg.db', 'HSMMSingleCell', 'monocle', 'DelayedMatrixStats', 'DESeq2', 'genefilter'), dependencies=TRUE, ask = FALSE)
BiocManager::install("DropletUtils")
BiocManager::install("SingleR")
BiocManager::install("MAST")
BiocManager::install("scDblFinder")
BiocManager::install("ExperimentHub")
BiocManager::install("ComplexHeatmap")
BiocManager::install("celldex")
BiocManager::install("clusterProfiler")
devtools::install_github('VPetukhov/ggrastr')
remotes::install_github("juba/rmdformats")
devtools::install_github(repo = 'bimberlabinternal/cellmembrane', dependencies = TRUE)
cask software
brew cask install cyberduck
brew cask install mendeley
brew cask install TexStudio
brew cask install docker