diff --git a/scripts/README.md b/scripts/README.md index 37f9f05..782e847 100644 --- a/scripts/README.md +++ b/scripts/README.md @@ -19,6 +19,8 @@ $ apt-get install moreutils ``` +
+ ## In case of non-unique FASTA IDs -> make them unique ### 🏷 one possible way as follows: ``` @@ -30,6 +32,9 @@ $ awk '/^>/ {$0=$0".Seq"++count[$0]}1' $INP | sponge $INP $ awk '/^>/ {$0=$0"_Seq"++count[$0]}1' input.fasta > output.fasta ``` +
+ + ## 📓 Shiny script: MIR_loci_overlaps.R ``` @@ -104,6 +109,9 @@ Options: inpfn.fasta - input file (fasta format) ``` +
+
+ # 📝 Useful links and code lines ## :wrench: convert line breaks from DOS to Unix format (dos2unix) and vice versa (unix2dos) @@ -182,11 +190,11 @@ $ rm ../output/alias.txt ## :clipboard: Obtaining materials from the GitHub -i) use wget to pull down the ```raw``` file +- use wget to pull down the ```raw``` file ``` $ wget https://raw.githubusercontent.com/username/reponame/path/to/file ``` -ii) use git clone to pull the complete repository (prerequisites: user with ```sudo``` privileges) +- use git clone to pull the complete repository (prerequisites: user with ```sudo``` privileges) ``` $ sudo apt update $ sudo apt install git @@ -194,7 +202,7 @@ $ git clone https://github.com/username/reponame.git ``` ## :clipboard: Install Perl on Ubuntu-like Linux OS -i) Install Perl on Ubuntu-like Linux OS (prerequisites: user with ```sudo``` privileges) +- Install Perl on Ubuntu-like Linux OS (prerequisites: user with ```sudo``` privileges) ``` $ sudo apt update $ sudo apt-get install perl @@ -203,9 +211,9 @@ $ perl -v ``` More details for installing Perl can be found at [perl.org](www.perl.org/get.html#unix_like) -ii) Use [CPAN](www.cpan.org) (‘Comprehensive Perl Archive Network’) to install Perl modules +- Use [CPAN](www.cpan.org) (‘Comprehensive Perl Archive Network’) to install Perl modules -iii) Install different version of Perl +- Install different version of Perl ``` $ sudo cpan App::perlbrew $ perlbrew init @@ -229,15 +237,15 @@ $ perlbrew off # (or perlbrew switch-off) ## :clipboard: Install R on Ubuntu-like Linux OS Install R on Ubuntu-like Linux OS (prerequisites: user with sudo privileges) with add-apt-repository (adapt values in the square brackets and delete the brackets) -i) Import the repository public key +- Import the repository public key ``` $ apt-key adv --keyserver [from this location or server] --recv-keys [retrieve key(s)] ``` -ii) Add the CRAN repository to your system sources’ list +- Add the CRAN repository to your system sources’ list ``` $ sudo add-apt-repository ‘deb https://cloud.r-project.org/bin/linux/ubuntu [type appropriate selection from https://cloud.r-project.org/bin/linux/ubuntu/]’ ``` -iii) Install the complete R system +- Install the complete R system ``` $ sudo apt-get update $ sudo apt install r-base @@ -253,6 +261,7 @@ Installing pip for Python 3 and Python2 on Ubuntu-like OS (prerequisites: user w # 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 @@ -276,6 +285,8 @@ Described at [How to Install and Use the Linux Bash Shell on Windows 10](https:/ [Wine](https://www.winehq.org/) +
+
## :notebook_with_decorative_cover: Shiny and R Markdown @@ -285,6 +296,8 @@ Described at [How to Install and Use the Linux Bash Shell on Windows 10](https:/ [R Markdown introduction](https://rmarkdown.rstudio.com/lesson-1.html) +
+ ## :green_book: FAIR data [The FAIR Guiding Principles for scientific data management and stewardship](https://www.nature.com/articles/sdata201618)