install.txt

1st	Install BWA.

git clone https://github.com/lh3/bwa.git
cd bwa; make

-->Done,ready to bwa index and bwa mem

2nd Install GATK

Install git lfs (large files): 
	
	git lfs install followed by a git lfs pull from the root 		directory.


git clone https://github.com/broadinstitute/gatk.git

	cd gatk;
	  ./gradlew bundle;
	  ./gradlew bundle

Run cd gatk/  then ./gatk or java -jar /build/libs/gatk"""".jar
or if in gatk-4.0... just java -jar gatk""""".jar

3rd Install Samtools

git clone https://github.com/samtools/samtools.git

autoheader            # Build config.h.in (this may generate a warning about # AC_CONFIG_SUBDIRS - please ignore it).


autoconf -Wno-syntax  # Generate the configure script
./configure           # Needed for choosing optional functionality
make
make install

4th Install HTSLIB

git clone https://github.com/samtools/htslib.git

autoheader     # If using configure, generate the header template...
autoconf       # ...and configure script (or use autoreconf to do both)
./configure    # Optional but recommended, for choosing extra functionality
make
make install

5th Install BCF TOOLS

http://www.htslib.org/download/

KEEP all the same version of samtools,htslibs and bcftools.


6th Install PICARD tools.

    git clone https://github.com/broadinstitute/picard.git
    cd picard/
	    ./gradlew shadowJar
	    java -jar build/libs/picard.jar
	    ./gradlew jar
	    ./gradlew clean



7th Install VEP + $HOME./vep/directory will be created where PLUGINS + Reference files will be stored.

git clone https://github.com/Ensembl/ensembl-vep.git
cd ensembl-vep
perl INSTALL.pl