Dockerfile upgrade

[alexiswl]

Issues Fixed

• Installs bedtools for [bed_read] Parse error reading "...slice.bam.gridss.target.bed" at line 1498 : end (5095) must not be less than start (18446744073709546616) #449
• Installs samtools for Docker image doesn't support gridss_extract_overlapping_fragments script #457
• Installs R 4.0 and StructuralVariantAnnotation bumped from 1.2.0 to 1.6.0 for Docker image doesn't support gridss_extract_overlapping_fragments script #457
• Added instructions and dockerfile for creating 'target' folder for release create_release.sh fails on alinux2, recommend using docker to build docker file requirements #458

Breakdown by Commit

Dockerfile Upgrade: (968fa87)

• Upgraded ubuntu from bionic (18) to focal (20)
• Removed aarnet soures, causing issues in R4.0 upgrade
• Used instructions on https://linuxize.com/post/how-to-install-r-on-ubuntu-20-04/ for installing R 4.0
• Re-structured apt-installations in list format
• Install Biobase as it's a dependency of NMF.
• Install NMF after everything else

Building Gridss Update (73cc8d4)

• Created dockerfile for building a container / environment for creating the target directory.
• Added Readme to building said container.

[d-cameron]

Docker is still missing some of the more annoying to install VIRUSBreakend dependencies (RepeatMasker, kraken2, e-Utilities, dustmaster)