[MAINTAIN] java related packages polishment
starsareintherose opened this issue · 13 comments
List of Pacakges
- aliview
- artemis
- bbmap
- beast
- beast2
- canu
- #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-runtimeandjava-enviromentinstead 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
@Kiri2002 if you want, you can choose to maintain mesquite, it's an excellent start for your bioarchlinux tour.
- tempest: can't exec beast-dev/Tempest#3
tempest now merge into beast 93554af
- spread3: build error phylogeography/SpreaD3#43 and version issue phylogeography/SpreaD3#39
- spread: can't compile and no version phylogeography/spread#208
considering there is no source code here, don't build from source
trimmomatic: bump java version of ant usadellab/Trimmomatic#36
open-delta: can't be built, AtlasOfLivingAustralia/open-delta#259
solved: aliview: compile error AliView/AliView#118
- 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
- Artemis 1850076 need more fix for shell script
- Also see sanger-pathogens/Artemis#344
pre-build binary can't work also, therefore, build from source
@BioArchLinux/bioarchlinux-group anyone can help me solve these java problems?
solved fasqc: s-andrews/FastQC#115
Only one (mesquite) remains as single issue (134).