These are the steps I took recently to setup a new MacbookPro for scientific/bioinformatics use.
/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
brew analytics off
brew update && brew upgrade
brew config
brew tap brewsci/bio
brew tap brewsci/science
brew tap brewsci/num
brew install tcl-tk
echo 'export PATH="/usr/local/opt/tcl-tk/bin:$PATH"' >> ~/.bash_profile.
brew install libgit2
brew instal fftw
brew install libomp
brew install proj
brew cask install xquartz #may ask for password
brew install Caskroom/cask/mactex
For some reason I hit problems installing R packages like kableExtra which require xml2 to be installed....
brew install libxml2
R CMD INSTALL --configure-vars='INCLUDE_DIR=/usr/local/opt/libxml2/include/libxml2 LIB_DIR=/usr/local/opt/libxml2/lib/' xml2_1.2.0.tar.gz
But if this does not work (didnt for me) as mojave has a different version already installed...
sudo installer -pkg /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg -target /
Install R studio: https://www.rstudio.com/products/rstudio/download/#download
Using 'brew cask install rstudio' also works but the last time I did that, there was a problem with the version on brew, so just get the latest from above link.
To setup SSH keys for easy fast connection between Rstudio and Github: https://happygitwithr.com/ssh-keys.html
At some point I hit an error "ector memory exhausted (limit reached?)"...
nano ~/.Renviron
#copy these two lines over then save and quit.
PATH="/usr/local/clang6/bin:${PATH}"
R_MAX_VSIZE=100Gb
brew cask install docker
brew cask install docker
brew install python
brew install python@2
pip install --upgrade distribute
pip install --upgrade pip
pip install Cython
brew install libtiff libjpeg webp little-cms2
pip install Pillow
brew install imagemagick --with-fftw --with-librsvg --with-x11
brew install graphviz --with-librsvg
brew install cairo
brew install py2cairo # this will ask you to download xquartz and install it
brew install qt pyqt5
pip install scipy
pip install numpy
brew install matplotlib --with-cairo --with-tex
pip install pandas
pip install nltk
pip install sympy
pip install q
pip install snakeviz
brew install zmq
pip install ipython[all]
pip install html5lib cssselect pyquery lxml BeautifulSoup
pip install Flask Django tornado
pip install rdflib SPARQLWrapper
pip install networkx
pip install git+git://github.com/scikit-learn/scikit-learn.git
pip install git+git://github.com/statsmodels/statsmodels.git
pip install umap-learn
If you have a current R environment that you use and like, it can help to transfer the libraries to a new computer.
For convenience, I have the installed_packages.rds stored in /data path.
#in the old computer:
tmp = installed.packages()
installedpackages = as.vector(tmp[is.na(tmp[,"Priority"]), 1])
saveRDS(installedpackages, file="./installed_packages.rds")
#in the new computer:
install.packages("BiocManager")
installedpackages <- readRDS("./installed_packages.rds")
BiocManager::install(installedpackages)
#some packages may not install this way, either they are not on CRAN or Bioconductor or there was a problem. Google each to install. :)
The original source is: https://cole-trapnell-lab.github.io/monocle-release/monocle3/#what-s-new-in-monocle-3
source("http://bioconductor.org/biocLite.R")
biocLite()
biocLite("monocle")
devtools::install_github("cole-trapnell-lab/DDRTree", ref="simple-ppt-like")
devtools::install_github("cole-trapnell-lab/L1-graph")
# if everything above is installed, this is not needed as other packages like Seurat also require these
#install.packages("reticulate")
#library(reticulate)
#py_install('umap-learn', pip = T, pip_ignore_installed = T) # Ensure the latest version of UMAP is installed
#py_install("louvain")
devtools::install_github("cole-trapnell-lab/monocle-release", ref="monocle3_alpha")
But for this to work, rgdal and sf packages and their dependencies also need to be installed.
From https://www.kyngchaos.com/software/frameworks/ download and install the OSX GDAL framework. I downloaded the 'GDAL_Complete-2.4.dmg'. Also see https://stat.ethz.ch/pipermail/r-sig-mac/2017-June/012429.html if stuck.
The whole point of this is to install https://github.com/r-spatial/sf which depends on gdal and etc.
Install gdal
brew install gdal
install.packages("sf", configure.args=c('--with-gdal-config=/Library/Frameworks/GDAL.framework/Programs/gdal-config',
'--with-proj-include=/Library/Frameworks/PROJ.framework/Headers',
'--with-proj-lib=/Library/Frameworks/PROJ.framework/unix/lib'))
install.packages('rgdal', type = "source", configure.args=c(
'--with-gdal-config=/Library/Frameworks/GDAL.framework/Programs/gdal-config',
'--with-proj-include=/Library/Frameworks/PROJ.framework/Headers',
'--with-proj-lib=/Library/Frameworks/PROJ.framework/unix/lib'))
Now this should run without any errors.
devtools::install_github("cole-trapnell-lab/monocle-release", ref="monocle3_alpha")
Next, several additional dependencies need to be installed that are tricky also:
For sanity reinstall cairo with brew to the latest.
brew reinstall cairo
Then, add the three lines to nano ~/.R/Makevars below and save close and restart R.
CAIRO_CFLAGS = /usr/local/include
CAIRO_LIBS = /usr/local/opt/cairo
PKG_CONFIG_PATH=/usr/local/lib/pkgconfig
now installing Cairo in R should work, followed by ggraster.
install.packages("Cairo")
devtools::install_github('VPetukhov/ggrastr')
- Atom to edit anything. From txt to markdown. https://atom.io/
- Box sync. Setup as directed. https://ohsu.account.box.com/login
- Evernote. https://evernote.com/
- Mendeley. https://www.mendeley.com/
- Latex Editor, TexStudio. https://www.texstudio.org/
- VLC: https://www.videolan.org/vlc/download-macosx.html
- Mozilla Firefox: https://www.mozilla.org
Halfstar Itunes: defaults write com.apple.iTunes allow-half-stars -bool TRUE