NIB-SI/_p_stRT

Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato

general information

ISA-tab

linked from https://isa-tools.org/format/specification.html

pISA-tree structure

pISA-tree: Standard project directory tree (ISA-tab compliant)

https://github.com/NIB-SI/pISA

seekr

pISA-tree: Standard project directory tree (ISA-tab compliant)

https://github.com/NIB-SI/seekr

pisaR

R support for pISA-tree

https://github.com/NIB-SI/pisar

FAIRDOMHub

FAIRDOMHub: a repository and collaboration environment for sharing systems biology research

https://fairdomhub.org/

recommended OS

LTS versions of:

https://linuxmint.com/

https://ubuntu.com/

R on linux

install R and pandoc

apt-key adv --keyserver [from this location or server] --recv-keys [retrieve key(s)]
add-apt-repository ‘deb https://cloud.r-project.org/bin/linux/ubuntu [type appropriate selection from https://cloud.r-project.org/bin/linux/ubuntu/]’

apt-get update
apt-get install r-base
apt-get install r-base-dev
apt install build-essential
apt-get install pandoc

invoke R from the command line

R

quit R

q()

help

R --help

install packages/libraries

R -e 'install.packages("rmarkdown", repos="https://cran.rstudio.com/")'

run app, script, ...

R -e "shiny::runApp('./pathToShinyApp/name.R')"
Rscript -e "rmarkdown::render('./pathToScript/scriptName.Rmd')"

Biopython and conda

pip install biopython

biopython.org

docs.conda.io

other packages/libraries

apt-get install dos2unix

apt-get install moreutils

R -e 'install.packages(c("Rcpp", "httpuv"))'

R -e 'install.packages("shiny")'

R -e 'install.packages("devtools", repos="https://cran.rstudio.com/")'

apt-get install libssl-dev libxml2-dev libcurl4-openssl-dev libcurl4-gnutls-dev curl

cheatsheet

command line cheatsheet

linked from www.git-tower.com

relative path

always use relative path

  . represents the current directory

  .. represents the parent directory

ls .. list information about the files one level up,

ls ../.. or ls ../../ list information about the files two levels up, etc

📝 Useful links and code lines

📋 Obtaining materials from the GitHub

• use wget to pull down the raw file

$ wget https://raw.githubusercontent.com/username/reponame/path/to/file

• use git clone to pull the complete repository (prerequisites: user with sudo privileges)

$ sudo apt update
$ sudo apt install git
$ git clone https://github.com/username/reponame.git

📋 Install Perl on Ubuntu-like Linux OS

• Install Perl on Ubuntu-like Linux OS (prerequisites: user with sudo privileges)

$ sudo apt update
$ sudo apt-get install perl
# check version 
$ perl -v

More details for installing Perl can be found at perl.org

• Use CPAN (‘Comprehensive Perl Archive Network’) to install Perl modules

• Install different version of Perl

$ sudo cpan App::perlbrew
$ perlbrew init

# see which versions are available:
$ perlbrew available

# install version 5.X.Y
$ perlbrew install perl-5.X.Y

# list all installed versions
$ perlbrew list

# change Perl for the current shell # (or per your sessions)
$ perlbrew use perl-5.X.Y # (or perlbrew switch perl-5.X.Y)
$ which perl

# revert version to default for the current shell # (or per your sessions)
$ perlbrew off # (or perlbrew switch-off)

📋 pip

Installing pip for Python 3 and Python2 on Ubuntu-like OS (prerequisites: user with sudo privileges)

# Installing pip for Python 3
$ sudo apt update
$ sudo apt install python3-pip

# Installing pip for Python 2
$ sudo apt update 
$ sudo apt install python2
$ curl https://bootstrap.pypa.io/get-pip.py --output get-pip.py
$ sudo python2 get-pip.py