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
### đˇ 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
```
+
+
+
## đ Shiny script: MIR_loci_overlaps.R
```
@@ -104,6 +109,9 @@ Options:
inpfn.fasta - input file (fasta format)
```
+
+
+
# đ 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) (âComprehensive Perl Archive Networkâ) to install Perl modules
+- Use [CPAN](www.cpan.org) (âComprehensive Perl Archive Networkâ) 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 sourcesâ list
+- Add the CRAN repository to your system sourcesâ list
```
$ sudo add-apt-repository âdeb https://cloud.r-project.org/bin/linux/ubuntu [type appropriate selection from https://cloud.r-project.org/bin/linux/ubuntu/]â
```
-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)