knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
Time to allow: ETA ~20 min
This vignette purposes is to show users how to setup their computers for RADseq genomic analysis inside R. It targets users of my packages or workshops.
The vignette as an Installation problems
section, browse through it if your experiencing
installation issues.
The vignette is also usefull if your:
grur
and it's dependencies or simulations with strataG
. rmetasim
XGBoost
LightGBM
randomForestSRC
ranger
missRanger
pcaMethods
I'm currently merging information also found in this tutorial
Warning: package management software Homebrew and/or MacPorts : My experience with these packages is that at some point they will be unreliable with genomic software installation. It might do the trick for some software, but eventually you will loose a lot of time trying to figure out what's your problem.
Make sure you have administrator and root user access to your computer how.
Make sure it's installed...if not, follow instructions. Although the prompt message may be a bit confusing, just click install.
```{bash eval=FALSE} xcode-select --install
In the finder using keyboard shorcut `cmd+shift+g` go to: `/Library/Developer/CommandLineTools/Packages/` and double click on `macOS_SDK_headers_for_macOS_10.14.pkg` to install. **Notes:** * If command line tools is already installed you'll get this message `xcode-select: error: command line tools are already installed, use "Software Update" to install updates` * to test if you have a compiler, you can also type: `make` in the terminal * `./configure`: configure everything before installation * `make`: connect libraries and the source before make install ([doc](http://www.gnu.org/software/make/manual/make.html)) * `make install`: use to build (compile) source code to create binary files and install the application on our system as configured using `./configure`, usually in `/usr/local/bin`. * [Reading](https://thoughtbot.com/blog/the-magic-behind-configure-make-make-install): to understand the basic steps to install software with the terminal (*configure*, *make* and *sudo make install* steps) * for more *curl* option type `curl -h` ## Compiler Apple can't ship GNU [Compiler](http://en.wikipedia.org/wiki/Compiler) Collection (GCC) with OpenMP enabled, similar story with [Clang](http://en.wikipedia.org/wiki/Clang) the other compiler used in macOS. Consequently, both need to be updateed manually if you want to run software that ues parallel computing (like stacks). The command below fro both GCC and Clang will: * change directory to your downloads * download the compiler's binaries * uncompress and move folders (`bin`, `include`, `lib`, `libexec` and `share`) of the compiler on your computer `/usr/local` directory. * remove the downloaded file * check the version of gcc ### Update GCC Choose the binary version number based on your OS and change the version accordingly [link](http://hpc.sourceforge.net). **Catalina** [gcc-9.2-bin.tar.gz](http://prdownloads.sourceforge.net/hpc/gcc-9.2-bin.tar.gz) **Mojave** [gcc-8.3.tar.gz](http://prdownloads.sourceforge.net/hpc/gcc-8.3-bin.tar.gz) ```{bash eval=FALSE} #In Terminal cd Downloads sudo tar -zxvf gcc-9.2-bin.tar.gz -C /usr/local --strip-components=2
```{bash eval=FALSE} sudo rm gcc-9.2-bin.tar.gz gcc -v
### Update Clang We want [clang](https://en.wikipedia.org/wiki/Clang) compiler with OpenMP enabled. ```{bash eval=FALSE} #In browser http://releases.llvm.org/9.0.0/clang+llvm-9.0.0-x86_64-darwin-apple.tar.xz #In Terminal cd Downloads sudo tar -xzvf clang+llvm-9.0.0-x86_64-darwin-apple.tar.xz -C/usr/local --strip-components=1
```{bash eval=FALSE} sudo rm clang+llvm-9.0.0-x86_64-darwin-apple.tar.xz clang -v
## PATH The shell start up script and PATH to programs** To make things a little easier to talk to your computer, each time you open the *Terminal* a [shell start up scripts](http://en.wikipedia.org/wiki/Bash_(Unix_shell)) tells your computer where to look for programs. The path for your programs can be modified in your shell start up script. When your computer is searching for programs, it looks into these [path](http://en.wikipedia.org/wiki/PATH_(variable)): ```{bash eval=FALSE} $PATH
The output should look like this:
/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin
.
But sometimes, it will also say: No such file or directory
(no worries, see below).
Use the pwd
command to know exactly where you are!
The name of the shell startup file differs across platforms. Depending on OS it is called ~/.bash_profile and sometimes ~/.profile. Filename beginning with a dot "." are reserved for the system and are invisible in the mac Finder.
Find your shell start up script with the following command:
```{bash eval=FALSE} ls -al ~ | grep profile
If this returns nothing (blank), you don't have a shell start up script. Create one with this command ```{bash eval=FALSE} sudo touch $HOME/.bash_profile
To modify, you can use BBEdit to open or make and modify hidden items (using the option Show hidden items on the open file screen). With Linux, use Vi!
Copy/paste the line below in your .bash_profile
file:
```{bash eval=FALSE}
PATH="$PATH:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin"
After modifying your shell start up script always run the command `source ~/.bash_profile` to reload it. ## Useful tools Below are useful but not essential software you will like to have on your mac. ### [wget](https://www.gnu.org/software/wget/) utility This software is similar to curl that is already on your Mac, it's also good to have it. This will help you save a lot of time in the future. **Option 1: trouble-free install** ```{bash eval=FALSE} cd ~/Downloads curl -O https://raw.githubusercontent.com/rudix-mac/packages/master/10.12/wget-1.18-0.pkg # Go in your Downloads folder double-click on the wget file and follow the instructions
Option 2: from source
Install gnutls dependency
```{bash eval=FALSE}
cd ~/Downloads curl -O http://www.gnupg.org/ftp/gcrypt/gnutls/v3.5/gnutls-3.5.18.tar.xz tar -zxvf gnutls-3.5.18.tar.xz cd gnutls-3.5.18 ./configure --with-included-libtasn1 --without-p11-kit
make
make sudo make install
Now the wget part... First look for the *.tar.gz* file with the latest release (currently: wget2-1.99.2.tar.gz) in this [folder](<http://ftp.gnu.org/gnu/wget/), Modify (if you need to), Copy & Paste the commands below (one line at a time): ```{bash eval=FALSE} cd ~/Downloads # change the '-x.xx.tar.gz' number below with the latest release version. curl -O http://ftp.gnu.org/gnu/wget/wget2-1.99.2.tar.gz tar -zxvf wget2-1.99.2.tar.gz cd wget2-1.99.2 ./configure make sudo make install # will prompt you to enter your password cd .. # goes up to the enclosing directory wget --help # to test installation!
Note:
To remove a folder and downloaded packages use the sudo rm -R
command,
but be very careful with this command because the content is deleted FOREVER,
it doesn't go in the trash...
Delete the wget folder and package using sudo rm -R wget*
.
This is TextWrangler replacement and is a free text editor that will help you save time. Once
installed, go in the Apple Menu bar -> BBEdit -> Install Command Line
This is a Python installer tool that I highly recommend. To install or upgrade pip, securely download get-pip.py.
Run this from you Terminal:
```{bash eval=FALSE} cd ~/Downloads sudo python get-pip.py
```{bash eval=FALSE} pip install -U pip # to upgrade
```{bash eval=FALSE} sudo rm -R ~/Downloads/get-pip.py # to remove the downloaded file
# Linux Make sure you have GCC and CLANG with OpenMP enabled. Several flavors available, check for the proper [link](http://releases.llvm.org/download.html) # Install [R](https://cran.r-project.org) To install R v3.6.3 **"Holding the Windsock"** released on 2020-02-29 download the installer and follow the instructions ```{bash eval=FALSE} # for macOS cd Downloads curl -O https://cran.r-project.org/bin/macosx/el-capitan/base/R-3.6.3.pkg
To remove R completely from macOS ```{bash eval=FALSE} sudo rm -rf /Library/Frameworks/R.framework /Applications/R.app \ /usr/bin/R /usr/bin/Rscript
# Rstudio To download RStudio, check this [link](https://www.rstudio.com/products/rstudio/download/#download) and download the installer for your OS. # Installing Libraries Below is how I setup most of my computers after a clean macOS install. 1. Start with **devtools** and **tidyverse** ```r if (!require("devtools")) install.packages("devtools") # to install install.packages("tidyverse")
install.packages("gsl")
If the console print this: Do you want to install from sources the package which needs compilation? (Yes/no/cancel)
. Always aswer no unless of course you know what you are doing.
devtools::install_github("thierrygosselin/grur") devtools::install_github("thierrygosselin/assigner")
For some packages you might have to compile from source and
the use of different compiler is sometimes very useful.
You need to tell R how to use the compilers.
This might change from one package
to another. Nothing is simple, you know this by now...
All this is done through R's Makevars file located in ~/.R/Makevars
.
To modify or create the file, the fastest way is to use the package usethis (it's installed automatically with devtools
):
usethis::edit_r_makevars()
Makevars content required: ```{bash eval=FALSE} CC=/usr/local/bin/gcc CXX=/usr/local/bin/g++ FC=/usr/local/bin/gfortran F77=/usr/local/bin/gfortran PKG_LIBS = -fopenmp -lgomp PKG_CFLAGS= -O3 -Wall -pipe -pedantic -std=gnu99 -fopenmp PKG_CXXFLAGS=-fopenmp -std=c++11 CFLAGS= -O3 -Wall -pipe -pedantic -std=gnu99 -fopenmp SHLIB_OPENMP_CFLAGS = -fopenmp SHLIB_OPENMP_CXXFLAGS = -fopenmp SHLIB_OPENMP_FCFLAGS = -fopenmp SHLIB_OPENMP_FFLAGS = -fopenmp
FLIBS=-L/usr/local/lib/gcc/x86_64-apple-darwin19/9.2.0/finclude CFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion CXXFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
# Installation problems {#Installation_problems} Sometimes you'll get warnings while installing dependencies required for *x* package. ```r #Warning: cannot remove prior installation of package ‘stringi’
To solve this problem, delete manually the problematic package in the installation folder (on mac: /Library/Frameworks/R.framework/Resources/library
) or in the Terminal
:
```{bash eval=FALSE} sudo rm -R /Library/Frameworks/R.framework/Resources/library/package_name
* Using the latest version of R, RStudio and packages is recommended. If your heart start pounding just at the thought of having to install a new R version, you should have a look at [packrat](https://www.rstudio.com/resources/webinars/managing-package-dependencies-in-r-with-packrat/). * Look at the output in R console when you get an error message. If it's related to one's of the packages dependencies, try installing it separately before attempting to reinstall the problematic package. ## Error saying "https" not supported or disabled in libcurl ### Installing [OpenSSL](www.openssl.org) Required if GCC compiler is used (TLS backend is then used). Not required if clang is used (securetransport backend is used). ```{bash eval=FALSE} #In browser https://www.openssl.org/source/openssl-1.1.1.tar.gz #In Terminal cd Downloads curl -O https://www.openssl.org/source/openssl-1.1.1.tar.gz tar -zxvf openssl-1.1.1.tar.gz cd openssl-1.1.1 ./config make -j12 #change with your number of CPU make test #long sudo make install cd .. sudo rm -R openssl*
Check for the latest release of curl ```{bash eval=FALSE}
https://curl.haxx.se/download/curl-7.69.0.tar.gz
cd Downloads tar -zxvf curl-7.69.0.tar.gz cd curl-7.69.0
The next step depends on the compulier used With **gcc**: ```{bash eval=FALSE} ./configure --with-ssl # to enable https via OpenSSL and using GCC
Note: with macOS 10.15 this give me an error configure: error: OpenSSL libs and/or directories were not found where specified!
If this is the case, use clang: ```{bash eval=FALSE} CC="/usr/local/bin/clang" ./configure --without-ssl --with-darwinssl # to install via clang
```{bash eval=FALSE} make -j12 #change with your number of CPU sudo make install cd .. sudo rm -R curl*
If you have an install problem, the problem might be very computer-specific.
e.g. if the problem is related to strataG
, copula
and/or gsl
, try
installing libgsl0-dev
in the Terminal (very easy now with the latest RStudio release!):
```{bash eval=FALSE} sudo apt-get install libgsl0-dev
## Error saying: `Error: vector memory exhausted (limit reached)` {#Renviron} Check that you have a file called `~/.Renviron`: ```r file.exists("~/.Renviron")
If you dont have the file:
```{bash eval=FALSE}
cd ~ touch .Renviron sudo nano .Renviron
Add this to your `.Renviron` file located in `~/.Renviron`: ```{bash eval=FALSE} R_MAX_VSIZE = 100Gb
Use BBEdit or other software that allows you to see hidden files starting with a dot
string.h
, math.h
or any other .h
vroom
rmetasim
An example during vroom
installation:
```{bash vroom problem, eval=FALSE} clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/progress/include" -I/usr/local/include -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -fPIC -Wall -g -O2 -c gen.cc -o gen.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/progress/include" -I/usr/local/include -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -fPIC -Wall -g -O2 -c index_collection.cc -o index_collection.o /usr/local/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/progress/include" -I/usr/local/include -fPIC -I/usr/local/include -c localtime.c -o localtime.o localtime.c:42:10: fatal error: 'string.h' file not found
^~~~~~~~~~
**With macOS:** * version 10.14, do this: ```{bash solution, eval=FALSE} sudo installer -pkg \ /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg \ -target /
.Makevars
configuration.setMaxGlobalSize
Its a problem with a previous version of pbmcapply
and it's interaction with
future
.
Solution:
RStudio > Session > Restart R
)Note: if your heart start pounding just at the thought of having to update everything on your computer you should definitely have a look at packrat: it's very easy to use.
.DynamicClusterCall
If you have a PC and you're getting this error or closely related error: ```{bash, eval=FALSE}
**Solution:** Use `parallel.core = 1` in the function generating the error. ## Error during install when numerous of packages are updated: ```{bash, eval=FALSE} # Error in get0(oNam, envir = ns) : # lazy-load database '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/callr/R/callr.rdb' is corrupt # In addition: Warning message: # In get0(oNam, envir = ns) : internal error -3 in R_decompress1
Solution:
dyn.load
Here is an example below:
```{bash, eval=FALSE}
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/home/rstudio/R/x86_64-pc-linux-gnu-library/3.6/units/libs/units.so':
libudunits2.so.0: cannot open shared object file: No such file or directory
Calls:
**Solution:** 1. In R, check the output of this command that look for the [environment variables](https://stat.ethz.ch/R-manual/R-devel/library/base/html/EnvVar.html): ```r Sys.getenv("LD_LIBRARY_PATH") # [1]""
Note that if the output is not empty, like in the example above, write down the output.
/usr/local/lib/
to the output above:When it's empty:
# in R: Sys.setenv(LD_LIBRARY_PATH="/usr/local/lib/") # For Linux you could use: /usr/local/lib/:/usr/lib64
When it's not, add at the end, separated by :
Sys.setenv(LD_LIBRARY_PATH="/usr/local/lib64/R/lib::/lib:/usr/local/lib64:/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.amzn2.0.1.x86_64/jre/lib/amd64/server:/usr/local/lib/:/usr/lib64")
Long-term solution:
Instead of using Sys.setenv
each time you have a similar problem,
you could add the environment variables LD_LIBRARY_PATH
to your .Renviron file
. This is discussed in another problem above.
C stacks usage
Error: C stack usage 7971092 is too close to the limit
So far, I haven't found the cure to this computer-specific problem.
Potential solutions:
rmetasim
Download the latest github release of Allan Strand's rmetasim ```{bash eval=FALSE} cd ~/Downloads wget --no-check-certificate https://github.com/stranda/rmetasim/archive/master.zip curl -O https://github.com/stranda/rmetasim/archive/master.zip unzip master.zip
### Modify the number of loci: MAXLOCI If you want to use more loci during your simulations (default is 10001), you need to modify rmetasim before compiling. With a text editor, modify the `const.h` file in the `src` folder: `rmetasim-master/src/const.h`. Navigate to **lane 33** and change the integer to the desired maximum number of loci. Or do this in the Terminal: ```{bash eval=FALSE} sed -i -e 's/#define MAXLOCI 10001/#define MAXLOCI 20000/g' rmetasim-master/src/const.h
rmetasim requires these Makevars (~/.R/Makevars
file) specifications.
If you have other lines, comment (#) before compiling rmetasim
:
usethis::edit_r_makevars()
With most OS (including macOS 10.14):
```{bash eval=FALSE} CC=/usr/local/bin/clang CC=/usr/local/bin/clang CXX=/usr/local/bin/clang++ CXX1X=/usr/local/bin/clang++ CXX11=/usr/local/bin/clang++ FLIBS=-L/usr/local/lib CFLAGS=-I/usr/local/include LDFLAGS=-L/usr/local/lib CPPFLAGS=-I/usr/local/include SHLIB_OPENMP_CFLAGS= -fopenmp SHLIB_OPENMP_FCFLAGS= -fopenmp SHLIB_OPENMP_FFLAGS= -fopenmp SHLIB_OPENMP_CXXFLAGS= -fopenmp
**macOS 10.15** This latest os requires extra lines: ```{bash eval=FALSE} CC=/usr/local/bin/clang CC=/usr/local/bin/clang CXX=/usr/local/bin/clang++ CXX1X=/usr/local/bin/clang++ FLIBS=-L/usr/local/lib LDFLAGS=-L/usr/local/lib SHLIB_OPENMP_CFLAGS= -fopenmp SHLIB_OPENMP_FCFLAGS= -fopenmp SHLIB_OPENMP_FFLAGS= -fopenmp SHLIB_OPENMP_CXXFLAGS= -fopenmp CFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk CCFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk CXXFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk CPPFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
```{bash eval=FALSE} R CMD INSTALL "rmetasim-master" # Terminal command sudo rm -R rmetasim* # to remove the folders no longer required
## `XGBoost` ### Download the github version ```{bash eval=FALSE} # terminal cd Downloads git clone --recursive https://github.com/dmlc/xgboost cd xgboost
If you're getting this error: "https" not supported or disabled in libcurl
, extra steps are required,
check the installation problems section to install
OpenSSL
and curl
and enabling https
with --with-ssl
option.
Modify in a text editor the configure
file inside the xgboost/R-package
folder:
```{bash eval=FALSE}
ac_pkg_openmp=no
ac_pkg_openmp=yes
### Makevars configuration `XGBoost` requires these Makevars specifications. If you have other lines, comment (#) before compiling: ```r usethis::edit_r_makevars()
```{bash eval=FALSE} CC=/usr/local/bin/gcc CXX=/usr/local/bin/g++ CXX11=/usr/local/bin/g++ CXX14=/usr/local/bin/g++ CXX17=/usr/local/bin/g++ SHLIB_OPENMP_CFLAGS= -fopenmp SHLIB_OPENMP_FCFLAGS= -fopenmp SHLIB_OPENMP_FFLAGS= -fopenmp SHLIB_OPENMP_CXXFLAGS= -fopenmp CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe LDFLAGS=-L/usr/local/lib -Wl,-rpath,/usr/local/lib CPPFLAGS=-I/usr/local/include -I/usr/local/include
### Compile ```{bash eval=FALSE} sudo R CMD INSTALL R-package
You should see a time difference between both runs
require(xgboost) x <- matrix(rnorm(100*10000), 10000, 100) y <- x %*% rnorm(100) + rnorm(1000) system.time({bst = xgboost(data = x, label = y, nthread = 1, nround = 100, verbose = FALSE)}) system.time({bst = xgboost(data = x, label = y, nthread = 4, nround = 100, verbose = FALSE)})
LightGBM
LightGBM
requires an OpenMP-enabled compiler. Currently, it doesn't work well with
clang, so make sure you have updated your GCC compiler (instructions above).
Additionally, LightGBM
requires CMake
```{bash eval=FALSE}
https://cmake.org/files/v3.12/cmake-3.12.2-Darwin-x86_64.dmg
To add CMake to the PATH: ```{bash eval=FALSE} PATH="/Applications/CMake.app/Contents/bin":"$PATH" # Or, to install symlinks to '/usr/local/bin', run: sudo "/Applications/CMake.app/Contents/bin/cmake-gui" --install # Or, to install symlinks to another directory, run: sudo "/Applications/CMake.app/Contents/bin/cmake-gui" --install=/path/to/bin #Then, run the following commands to install LightGBM:
```{bash eval=FALSE} cd Downloads git clone --recursive https://github.com/Microsoft/LightGBM cd LightGBM Rscript build_r.R
## `randomForestSRC` [randomForestSRC](http://web.ccs.miami.edu/~hishwaran/ishwaran.html) requires the GCC OpenMP-enabled compiler to run in parallel. See instructions above if not already done. ### Makevars configuration Check that the lines below **are not** commented in your `~/.R/Makevars` file: ```r usethis::edit_r_makevars()
```{bash eval=FALSE} CC=/usr/local/bin/gcc CXX=/usr/local/bin/g++ CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe PKG_CFLAGS= -O3 -Wall -pipe -pedantic -std=gnu99 -fopenmp PKG_CXXFLAGS=-fopenmp -std=c++11 FC=/usr/local/bin/gfortran F77=/usr/local/bin/gfortran LDFLAGS=-L/usr/local/lib PKG_LIBS = "-liconv"
### Download and install From the Terminal run these steps to download and compile randomForestSRC: ```{bash eval=FALSE} cd ~/Downloads curl -O https://cran.r-project.org/src/contrib/randomForestSRC_2.9.3.tar.gz tar -zxvf randomForestSRC_2.9.3.tar.gz cd randomForestSRC
Make sure you have autoconf installed: ```{bash eval=FALSE}
cd ~/Downloads autoconf
Should output: `autoconf: error: no input file`, if not, install following the [steps here](#useful). ```{bash eval=FALSE} # in Terminal cd ~/Downloads/randomForestSRC autoconf cd ~/Downloads R CMD INSTALL --preclean --clean randomForestSRC
You want to make sure that this line is printed during execution of the previous command:
checking whether OpenMP will work in a package... yes
or checking for /usr/local/bin/gcc option to support OpenMP... -fopenmp
ranger
ranger is easy to install.
install.packages("ranger")
missRanger
missRanger is also very easy to install.
install.packages("missRanger")
miceRanger
miceRanger easy to install.
install.packages("miceRanger")
pcaMethods
To install pcaMethods, from bioconductor:
BiocManager::install("pcaMethods")
fastsimcoal2
To install fastsimcoal2 v.2.6.0.3, to use in
grur::simulate_rad
:
```{bash Linux, eval=FALSE} wget http://cmpg.unibe.ch/software/fastsimcoal2/downloads/fsc26_linux64.zip unzip fsc26_linux64.zip sudo mv fsc26_linux64/fsc26 /usr/local/bin/fsc26 # will ask for your computer password
### MacOS ```{bash macOS, eval=FALSE} cd ~/Downloads curl -O http://cmpg.unibe.ch/software/fastsimcoal2/downloads/fsc26_mac64.zip unzip fsc26_mac64.zip sudo mv fsc26_mac64/fsc26 /usr/local/bin/fsc26 # will ask for your computer password
```{bash chunk common to both OS, eval=FALSE} sudo chmod 777 /usr/local/bin/fsc26 fsc26 ````
Re-start R and the software fastsimcoal2 will automatically be in your PATH...
To see the path of the installation, in the Terminal
:
```{bash, eval=FALSE}
which fsc26
If that doesn't work, do: ```{bash, eval=FALSE} source ~/.bash_profile
Remove the files in the folder: ```{bash, eval=FALSE} sudo rm -R ~/Downloads/fsc26_mac64*
## `COLONY` To install [COLONY 30/07/2018, V2.0.6.5](https://www.zsl.org/science/software/colony): ### MacOS The old openmpi version (openmpi-1.6.5) is required, saddly. ```{bash macOS openmpi-1.6.5, eval=FALSE} cd ~/Downloads curl -O https://download.open-mpi.org/release/open-mpi/v1.6/openmpi-1.6.5.tar.gz tar -zxvf openmpi-1.6.5.tar.gz cd openmpi-1.6.5 export TMPDIR=/tmp ./configure F77=gfortran #--prefix=/usr/local -openmp # no longer work for some reason make -j 12 sudo make install sudo rm -R ~/Downloads/openmpi*
To download COLONY, follow instructions on Jinliang Wang ZSL website. The file you need to
uncompress is named: colony2.mac_.20180730.zip
.
To download COLONY, follow instructions on Jinliang Wang ZSL website. The file you need to
uncompress is named: colony2.linux_.20180730.zip
.
Several options are available depending on the compiler you have installed.
macOS Catalina comes with Github, a Version Control System
(VCS), pre-installed. However, the install is in /usr/bin/git
which can make it difficult for beginners to update. To change this, run these
commands:
```{bash eval=FALSE} cd ~/Downloads wget http://ftp.gnu.org/gnu/autoconf/autoconf-latest.tar.gz curl -O http://ftp.gnu.org/gnu/autoconf/autoconf-latest.tar.gz tar -xvzf autoconf-latest.tar.gz cd autoconf-2.69 ./configure make sudo make install cd .. sudo rm -R ~/Downloads/autoconf-*
2. Install Github ```{bash eval=FALSE} git --version # show current git version installed which git # returns where is git on your computer cd ~/Downloads git clone https://github.com/git/git # install the latest Git cd git make configure ./configure make -j12 sudo make install cd .. sudo rm -R ~/Downloads/git/ # remove git folder source ~/.bash_profile # reload startup script git --version # confirmed the version you just installed which git # returns /usr/local/bin
In System Preferences choose Keyboard -> Shortcuts
. From the left panel, choose
Services. In the right panel, under Files and Folders, choose New
Terminal at Folder and/or New Terminal Tab at Folder. Now you can right-click
your track pad or mouse on a folder and choose Services -> New Terminal at
Folder!
knitr::include_graphics("terminal_folder_shortcut.png")
Open the Automator application (it's on all MAC...).
knitr::include_graphics("automator.png")
```{bash eval=FALSE} File -> New (cmd-N) Choose: Services Left panel, choose: Library -> Utilities Middle, choose: Copy to Clipboard and drag it to the right panel Now you want to have: Service receives selected FILES OR FOLDERS in FINDER> You should have something similar to the image below:
```r knitr::include_graphics("copy_path.png")
{bash eval=FALSE}
Save (cmd-S) or File -> Save service as: copy path to clipboard
Go in the Finder, select a folder and right click on it you should see 'copy path to clipboard' at the bottom or in Services.
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