vbox

VBoxManage internalcommands sethduuid genomics_course_2018.vdi 
R
VBoxManage modifyhd genomics_course_2018.vdi --resize 60000


wget http://pathogenseq.lshtm.ac.uk/ps_course/genomics_software.tgz
tar -xvf genomics_software.tgz 
sudo bash aliview.install.run 
tar -xvf artemis.tar.gz 
sudo mv artemis /usr/local/src/
tar -xvf emmax-beta-07Mar2010.tar.gz 
sudo mv emmax-beta-07Mar2010/emmax* /usr/local/bin/
tar -xvf FigTree_v1.4.3.tgz 
sudo mv FigTree_v1.4.3/lib/figtree.jar  /usr/local/bin/
sudo mv figtree /usr/local/bin/
unzip gPLINK-2.050.zip 
sudo mv gPLINK2.jar /usr/local/bin/
sudo mv gplink /usr/local/bin/
sudo mv Haploview.jar /usr/local/bin/
sudo mv haploview /usr/local/bin/
sudo mv TempEst_v1.5.1/lib/tempest.jar /usr/local/bin/
sudo mv tempest /usr/local/bin/

conda install tablet  trimmomatic kraken fastqc  bwa minimap2 bowtie2 bowtie samtools  bcftools delly gatk4   velvet perl-velvetoptimiser  htseq  plink  mothur krona  beast beagle-lib tracer mafft raxml 
ktUpdateTaxonomy.sh /home/user/miniconda3/opt/krona/taxonomy

sudo apt install r-base-core libxml2-dev libcurl4-openssl-dev