• Markdown of Git's wiki : https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet
• linux cheatseet : http://sites.tufts.edu/cbi/files/2013/01/linux_cheat_sheet.pdf
• linux manual : http://www.bioinformatics.babraham.ac.uk/training/Introduction%20to%20unix.pdf
• Install .deb files

.deb files are installed using the dpkg command. So use the following command:

sudo dpkg -i GP6.deb
-i tells dpkg to install
If it gives you errors about other packages/dependencies, run the following to fix it:

sudo apt-get install -f
-f tells apt-get to fix missing dependencies

• accessing a node : do a qrsh -l hostname=nodeX or ssh nodeX in the master
• sizes : of the files and folders du -bsh * (files and folders) du -ah (files and the total)

Package Circos plots in R

• https://cran.r-project.org/web/packages/RCircos/index.html

Hive Plots

http://www.hiveplot.com/ (3 way comparison)

• CircosVCF website : http://legolas.ariel.ac.il/~tools/CircosVCF/
• http://www.ariel.ac.il/research/fbl/software (readme)

documentation website circosplots :

http://www.ariel.ac.il/research/fbl/software

• circos tabe viewer website : http://mkweb.bcgsc.ca/tableviewer/

• ways to do a circos plot : https://medium.com/@Marianattestad/a-treatise-on-making-circos-plots-from-genomic-data-7ff496849e0

• pages inside pages in gitwiki : However the MediaWiki syntax Link Text works for me, even for Markdown wiki pages. test : sdtout de cutadapt (sortie 1). for automation, juste copy the whole thing and paste it and click on it to create the page with the same name (dont forget to copy the name of the page to paste it

• Update gcc to the lastest of ubuntu : sudo apt-get update &&
  sudo apt-get install build-essential software-properties-common -y &&
  sudo add-apt-repository ppa:ubuntu-toolchain-r/test -y &&
  sudo apt-get update &&
  sudo apt-get install gcc-snapshot -y &&
  sudo apt-get update &&
  sudo apt-get install gcc-6 g++-6 -y &&
  sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-6 60 --slave /usr/bin/g++ g++ /usr/bin/g++-6 &&
  -sudo apt-get install gcc-4.8 g++-4.8 -y &&
  -sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.8 60 --slave /usr/bin/g++ g++ /usr/bin/g++-4.8; +# Already installed gcc-5 as part of build-essential; I didn't need this line.. +# sudo apt-get install gcc-5 g++-5 -y &&
  +sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-5 60 --slave /usr/bin/g++ g++ /usr/bin/g++-5;

• install a software : https://ubuntuforums.org/showthread.php?t=1521129 and give its the rights and paste it in the folder hosting all the software to make it launchable from anywhere in th machine :

step 1: chmod +x /path/to/profit

step 2: sudo cp /path/to/profit /usr/local/bin/

step 3: profit

• install vt : Packages for dpkg-based Linux distributions (Debian / Ubuntu) are: zlib1g-dev libbz2-dev liblzma-dev they must already be present be if not to install them, do this for each one : sudo apt-get update sudo apt-get install zlib1g-dev then check the wiki of vt to install it (https://genome.sph.umich.edu/wiki/Vt#Peek)

-Rdirect Stderr ad stdout in a txt file : yourcommand &>filename

Fast working :

• from the working node to the /home :

rsync -arv ./* /home/adiouf/adiouf_div/

• from the /home to the project directory :

rsync -arv /home/adiouf/adiouf_div/* /data3/projects/SV/SV_2018/adiouf_div/

• rename with a prefix all files in a folder :

for f in *; do mv "$f" r900_"$f"; done

• redirects both stdout and stderr to filenamee :

yourcommand &>filename 

and to append to that same file :

anothercommand &>>filename

• empty a file

echo -n "" > file