shiny-electron-ngsAnalysis

Electron-Shiny standalone app to bring DNA sequencing data analysis to the point of your mouse-clicks!

prerequisites

Internet connection
macOS 10.13 (High Sierra) and higher
R 4.1.1 (https://cran.r-project.org/bin/macosx/)
Python 3.7.7 (https://www.python.org/downloads/release/python-377/)
XQuartz latest (https://www.xquartz.org/)

you may use the links above to download appropriate versions; double click the .pkg file and follow the on screen instructions to install. XQuartz .pkg is inside the .dmg file.

install pyhton virtual environment

open terminal window

click top menu's Go button and choose utilities
inside utilities double-click Terminal
it will open up a Terminal window

check python version

paste this line below in the terminal prompt and press enter
python --version

this will give you the following result
Python 2.7.16

this is the mac's system python
but we will use python3 and that's why we installed Python 3.7.7, now we will check if the installation was fine

copy and paste the following command in your terminal prompt and press enter
python3 --version

if everything okay, you will have the following result
Python 3.7.7

install virtual environment

Now paste the following command in your terminal prompt and press enter
pip3 install virtualenv

this will install virtual environment and you can confirm the installation by pasting the following command
virtualenv

this will produce the following
usage: virtualenv [--version] [--with-traceback] [-v | -q] ...

and the system will exit with error message
virtualenv: error: the following arguments are required: dest

================================================================

install xz (for macOS 10.13)

The xz library in macOS 10.13 is not compatible with samtools-1.13, which is the ngsAnalyser version.
So, if your macOS is 10.13, you need to install newer xz library.

If you don't have Homebrew installed in your mac already, copy and paste the following command in the terminal prompt, same like you did with virtualenv - Homebrew installation may take few minutes

(following is a single command from ruby upto null, don't miss)
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)" 2> /dev/null

now use Homebrew to install xz, copy and paste the following command in terminal and press enter
brew install xz

===============================================================

install ngsAnalyser

Download the following file from here
(https://ifu.cib.csic.es/index.php/s/T7tZ88CwCbY5ECB)
ngsAnalyser-1.1.4.dmg
double click the file and copy the app file to your Applications folder.

now you can simply double-click the app icon and it should open a new window on your desktop.

in case you are missing Command Line Tools

After successfully completeing all the previous steps, you double-click the ngsAnayser app

ngsAnalyser window opens and then gets blurry and nothing works.
You can confirm it by clicking the refresh or quit button, there is no response.
This is becuase your mac is missing Command Line Tools!

The solution is to install Xcode and compile gcc from there.

However, if you run the ngsAnalyser with the shell executable, it will run in the terminal.
This will directly offer you the prompt to install gcc.

Just right click on ngsAnalyser, navigate to Show Package Contents
and inside Contents folder, there is a folder named MacOS
inside MacOS, you have the ngsAnalyser shell executable.

Double-click it and it will open the app window as well as a terminal window
In absence of gcc, the app fails when trying to install minipython

Now you will see a auto-prompt asking gcc is missing.
Heat the install button and just wait for the installation to finish.

Relaunch ngsAnalyser, it should be ready at your service!

Persistent issues

If you face any further obstackle in running ngsAnalyser,
please start an issue by going to the issues section above.

Thanks for using ngsAnalyser!

copyright

DNA Replication and Genome Integrity Lab, CIB-CSIC
(https://www.cib.csic.es/research/cellular-and-molecular-biology/dna-replication-and-genome-integrity)