A collection of useful commands and keyboard shortcuts for Mac OSX and Linux. Mostly for my own reference but might also be useful for others :)
command-shift-3 : full screen
command-shift-4 : selectable area
command-shift-4 then space : single window
option-shift-dash
control-click then select Open
command-shift-G
ssh servername.uzh.ch then enter password (you can also set up automatic password with ssh keygen)
ssh -X servername.uzh.ch if using GUI applications (then just launch apps as usual — requires XQuartz on Mac OSX)
run R command .libPaths()
cat /etc/*-release, uname -a
nproc, lscpu
free, top, df -H
cat /proc/meminfo, cat /proc/cpuinfo
sysctl hw.ncpu hw.physicalcpu hw.logicalcpu
ls -alh : list files — including hidden files and directories (-a), long format details (-l), and human readable file sizes (-h)
ls -t : sort by date modified
du -ahc --max-depth=1
file <filename> : for example to check which type of compressed file
wc -l <filename> : stands for word count, number of lines
ln -s <target> <name> : creates a symbolic/soft link called name pointing to the file target
export PATH=~/new_directory:$PATH (paste in .bash_profile or .bashrc file; note order of terms matters — first has highest priority)
option + click to place cursor anywhere on a line
ctrl + \
Use this to terminate a process that is not responding to the standard ctrl + c command — this tends to happen with R sessions.
wget http://address.of.file/filename.tar.gz : download .tar.gz source archive (run in /home/username/src folder to save it there)
tar xfvz filename.tar.gz : uncompress .tar.gz source archive (run in home/username/src)
cd filename : go to uncompressed source directory
./configure --prefix=$HOME : run configure script (performs installation checks and creates Makefile)
- IMPORTANT: include the option
--prefix=$HOMEto install the program in your home directory instead of the default Linux binary directories
make : run Makefile (compiles the program and creates executables)
make install : run install part of Makefile (copies executables into directories)
tar -xfvz : uncompress .tar.gz files
tar -xjf : uncompress bzipped files
tar -czf : create a zipped tar file
switch user to admin account: su Admin (assuming account name is "Admin"), then enter password
then can enter commands as superuser with sudo <command>
GNU screen is useful when working on a server, since programs running in a screen session will continue to run even if the server connection is interrupted.
screen or screen -S <name> : create new screen session (with optional name)
screen -x or screen -r <name> : attach to running screen session (with optional name)
exit : close session
screen -ls : list running screen sessions
screen -d -r : force detach and reattach a screen if connection drops out
full list of screen commands: http://aperiodic.net/screen/quick_reference
GNU parallel lets you parallelize commands from the shell. This can be useful to greatly speed up runtime if you are running shell command-line utilities multiple times, and have a system with multiple processors.
Here is an example of how to run GNU parallel.
parallel -j 24 fastq-dump --split-files -O FASTQ -- SRA/*.sra
The option -j 24 sets the maximum number of processors; the rest of the command after this runs once on each processor; and any arguments after the double dashes -- are expanded out (here it is a list of SRA files, so each processor gets one SRA file).
git init to create local repository in a folder
manually create README.md, .gitignore, and LICENSE files
git remote add origin https://github.com/user/repository-name.git (paste repository address from GitHub)
git add . to add new files
git add . (if no new files can skip this and go straight to commit)
or git add -A . to include file deletions
git commit -am "commit message" to commit (-a includes file deletions)
git push -u origin master to push to GitHub
git pull origin (merges into local repository)
git reset --soft HEAD^ : Use this to undo the previous commit if it hasn't been pushed to GitHub yet, for example if you have added the wrong files or want to change the commit message.
Enter these commands in an R session to create output in both HTML and standard markdown (.md) format. The standard markdown file is useful as it can be viewed directly in a GitHub repository (GitHub cannot automatically render Rmarkdown .Rmd files). With the option variant="markdown_strict", line breaks entered as single backslash characters render correctly on GitHub.
library("rmarkdown")
rmarkdown::render("filename.Rmd", output_format="html_document")
rmarkdown::render("filename.Rmd", output_format="md_document", output_options=list(variant="markdown_strict"))
To run IPython Notebook: Open Terminal, go to working directory using cd, then type ipython notebook. IPython Notebook should then open in the default browser (Chrome or Firefox).