Project

This is the main repository for the HackBio'2020 Virtual Internship Experience.

Main goal of the project is write small scripts in different languages with the next output in sdout - name, e-mail, used_language, biostack, slack_username. Next step is to make csv file with rows corresponding to the person and columns to the values (as name, e-mail, etc) in bash, using sdout from scripts.

For neat-looking documentation check out site

Table of content

• Getting Started
  • Prerequisites
  • Running the tests
    • Check if dependencies are satisfied
    • Installing missing dependencies
  • Installing
• Flowchart
• Usage
• Versioning
• For participants
  • Goals (Stage 0):
  • Language check
  • I am not a coder, what should I choose?
  • Unified template for output
  • Generate a new table of content

Getting Started

Prerequisites

• Julia language
• Octave
• Python language
• GCC and G++ compilers. Available via standard package managers
• R language
• Nodejs for javascript
• Linux (awk command must be recognisable in shell)

Running the tests

Check if dependencies are satisfied

Script for tests (tests.sh) is included in the repo. You can run it with the following command:

wget https://github.com/Team-Rosalind/team-rosalind-project/blob/master/tests.sh && sh tests.sh

The above command will download only the target script and check if all required software is already installed.

Installing missing dependencies

<<<<<<< Updated upstream

Ubuntu

=======

Ubuntu

Stashed changes

sudo apt-get update && sudo apt-get install python octave julia gcc g++ r nodejs npm

Please note, that Ubuntu-based installation hasn't been checked yet. Command based on Google search results. If you have any problems please report an issue and try official instruction dor every package as stated on official sites

Arch-based distributions

sudo pacman -Su && sudo pacman -S python octave julia gcc nodejs npm

Installing

The main goal of the project is create a bash script that will clone the repo and produce a csv file with the participants' personal information. For this goal no installation is required, however check if all dependencies are satisfied.

Flowchart

TO-DO

Usage

Please download the following script csv-producer.sh. Downloading and running the script can be done from a terminal with the following command:

wget https://github.com/Team-Rosalind/team-rosalind-project/blob/master/csv-producer.sh && sh csv-producer.sh 

Script is intended to work only in Linux-based systems

Versioning

• README.md -> v 1.7
• csv-producer -> v 2.0
• stage_0_Anu.C v 1.1
• stage_0_Suritra.cpp -> v 1.0
• stage_0_Vika.m -> v 1.0
• stage_0_dolu.js -> v 1.1
• stage_0_harinath.C -> v 1.0
• stage_0_hildred.py -> v 1.1
• stage_0_pavlo.jl -> v 1.0
• stage_0_rajvi.jl -> v 1.0
• stage_0_rupa.py -> v 1.0
• stage_0_shirine.R -> v 1.0
• Stage_0_Ife.R -> v 1.0
• Stage_0_Leye.py -> v 1.1
• Stage_0_siddhant.py -> v 1.3
• Stage_0_Busayo.py -> v 1.1

For participants

Goals (Stage 0):

• Make this documentation neat and nice. (Novice Friendly)
• Complete task 2 (multiple languages)
• Make a simple bash script for git commit

Language check

• Python
• Julia
• C++
• R
• Java
• MATLAB
• Javascript
• C

Note: The checklist has 8 languages right now. The minimum required amount is 7. If it is not satisfied, please choose unchecked languages from a list.

I am not a coder, what should I choose?

Everyone began from something (: Actually the language in this task doesn't matter, as the script is very simple. You can search smth similar to "write hello world script in language_of_interest ".

If all of the languages are checked, and the requirements (about programming language variety) are satisfied, you are free to choose whatever language you like. A good start is to become more familiar with R or Python. Both of these languages are extremely popular within the bioinformatics community. See templates for "Hello world script" for R and Python.

Unified template for output

Human text is an excellent example of unstructured data. Desired fields (for this task) can be printed out in many different ways. Therefore I propose a unified template for your script output:

NAME: *Your full name*
E-MAIL: *Your e-mail* 
USED LANGUAGE: *Name of used scripted language. All letters are capital*
BIOSTACK: *Name of biostack you chose. The only first letter is capital* 
SLACK USERNAME: @+*username*

An example:

NAME: Pavlo Hrab
E-MAIL: pavlo.hrab@lnu.edu.ua
USED LANGUAGE: JULIA
BIOSTACK: Genomics
SLACK USERNAME: @pavlo 

After you get the desired output, please name your file stage_0_slack-username
An example: stage_0_pavlo.jl

Generate a new table of content

The table of content was generated here Please if you do any updates to file itself, update a table of content as well