[MAINTAIN] java related packages polishment

[starsareintherose]

List of Pacakges

• aliview
• artemis
• bbmap
• beast
• beast2
• canu
• cytoscape #101
• emboss
• fastqc
• figtree
• gatk
• insight-toolkit
• jane
• libsbml
• mcscanx
• mesquite
• morphoj
• open-delta
• phyde
• phylip
• pibuss
• phylonet
• picard
• sequencematrix
• spread3
• spread
• tempest
• tracer
• treemap
• trimmomatic

Description

These packages need to be checked the following points

• use java-runtime and java-enviroment instead of jdk, jre, etc.
• confirm the java version and limit the enviroment in PKGBUILD
• check if they can be compiled from the source code [may be difficult, considering some software use quite low version java-enviroment]
• check if PKGBUILD style can be auto updated

[starsareintherose]

• mesquite: fix pom.xml download error MesquiteProject/MesquiteCore#104 Compile error MesquiteProject/MesquiteCore#105

@Kiri2002 if you want, you can choose to maintain mesquite, it's an excellent start for your bioarchlinux tour.

[starsareintherose]

- tempest: can't exec beast-dev/Tempest#3

tempest now merge into beast 93554af

[starsareintherose]

- spread3: build error phylogeography/SpreaD3#43 and version issue phylogeography/SpreaD3#39

[starsareintherose]

- spread: can't compile and no version phylogeography/spread#208

considering there is no source code here, don't build from source

[starsareintherose]

trimmomatic: bump java version of ant usadellab/Trimmomatic#36

[starsareintherose]

open-delta: can't be built, AtlasOfLivingAustralia/open-delta#259

[starsareintherose]

solved: aliview: compile error AliView/AliView#118

[starsareintherose]

Artemis: sanger-pathogens/Artemis#340

[starsareintherose]

- gatk: lfs issue, similar to broadinstitute/gatk#4687 , but also consider PKGBUILD working with git LFS https://bbs.archlinux.org/viewtopic.php?id=250669

fixed f27e196

[starsareintherose]

- Artemis 1850076 need more fix for shell script

• Also see I try to build, but exec fail sanger-pathogens/Artemis#344

pre-build binary can't work also, therefore, build from source

[starsareintherose]

@BioArchLinux/bioarchlinux-group anyone can help me solve these java problems?