Install BII Singapore NGS pipeline

Download latest ZIP file here
Dimitar Kenanov, Vithiagaran Gunalan, Sebastian Maurer-Stroh

Zip file contents:
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1) Workshop_Flu directory - Overall Pipeline directory
Within this are 3 directories: bin, lib, FLU_DATA and 2 files: install.sh and rakudo-pkg-Ubuntu18.04_2019.03.1-01_amd64.deb
Do not alter the "bin" or "lib" directories, this will cause the pipeline to fail. In the event that you mess things up, re-unzip from the zipfile in the USB stick (move your data elsewhere first).
FLU_DATA contains data as well as references for mapping, etc. Files whose names start with "PROJCONF" or "CURRENTVAC" in this directory are also ESSENTIAL to the running of the pipeline.
install.sh is an installation script for the pipeline.
rakudo-pkg-Ubuntu18.04_2019.03.1-01_amd64.deb - Perl6 installation file - leave exactly where it is.

2) README.txt - this readme file you're reading now.

NOTES:
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The install.sh script inside the Workshop_Flu directory will install perl6 on Ubuntu, as well as all the programs required, as the commands below illustrate.
Run the pipeline with run_fluAB.pl  (where  is the appropriate .conf file for your data, see below)

INSTALLATION COMMANDS 
=========================
Note: these are specific to Ubuntu 18.04 in Windows Subsystem for Linux. Will be sligtly different for other installs.

###### INSTALL PERL6

1. Install perl6:
		sudo dpkg -i rakudo-pkg-Ubuntu18.04_2019.03.1-01_amd64.deb (enter sudo password when prompted)
2. Update apt-get
		sudo apt update
3. Install 'execstack' package. Needed for perl6.
		sudo apt-get install execstack
4. Patch perl6 to work on win10
		/opt/rakudo-pkg/bin/fix_windows10
5. Check if perl6 works
		/opt/rakudo-pkg/bin/perl6 --version	
	Expected output: This is Rakudo version ...
	
###### INSTALL OTHER PROGRAMS

1. Install required programs:
		sudo apt-get -y install bwa bedtools samtools default-jre varscan seqtk ncbi-blast+ fastqc trimmomatic
		
###### MY NGS MODULES and Scripts

1. Copy and unzip the archive: WSHOP_FLU_2019.zip.
2. Modify PATH and add PERL6LIB environment variables
	a) change to directory Workshop_Flu:
		cd Workshop_Flu
	b) get current working dir
		pwd
	c) copy the result from 'pwd' - to do this, select with mouse in terminal, and Ctrl-c to copy.
	d) add PERL6LIB environment variable
		export PERL6LIB=/lib
		(to paste the path you copied from earlier, right-click in the terminal)
	e) modify PATH environment variable
		export PATH=$PATH:/bin
3. Modify the file appropriate config file in directory FLU_DATA
	a) There are 4 configuration files provided:
		- FLUAB_VACCREFMIX_SE.conf  -- single-end NGS
		- FLUAB_VACCREFMIX_PE.conf  -- paired-end NGS
		- FLUAB_VACCREFMIX_SE_QUASI.conf  -- single-end NGS, also gives variants
		- FLUAB_VACCREFMIX_PE_QUASI.conf  -- paired-end NGS, also gives variants
	b) change to directory Workshop_Flu:
		cd FLU_DATA
	c) get current working dir
		pwd
	d) copy the result from 'pwd'
	e) modify the file with nano
		nano FLUAB_VACCREFMIX_PE.conf (and do this for the other 3)
	f) Go to section 'COMMON_DATA' and modify the lines  VRM_INDEX and BTGEN to the following:
		VRM_INDEX=/FLU_DATA/
		BTGEN=/FLU_DATA/
	To exit nano, press Ctrl+o,  press 'Enter' when asked about the file name to be used, then ctrl-x to exit.
	g) Setting up config files
		Navigate to FLU_DATA directory, ensure data you want to run is there as well
		Make a new sample file:
			nano samp.txt
		Assuming your filenames are ABC_12345_L001_S2_R1_001.fastq and  ABC_12345_L001_S2_R2_001.fastq, type the following:
			ABC_12345	ABC12345
		Do this for each file or pair of files you have - one sample per line.
		Ctrl-c, enter, ctrl-x to get out of the nano editor.
	h) Use the config.pl script to modify the config files and create symlinks for the pipeline:
			config.pl –s samp.txt –d `pwd` -c FLUAB_VACCREFMIX_PE.conf
		**remember to choose the correct .conf file for the sample/s you are running. PE and SE samples have to be run separately.
	i) Run the pipeline
			run_fluAB.pl FLUAB_VACCREFMIX_PE.conf

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