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[MAINTAIN] java related packages polishment #85

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starsareintherose opened this issue Nov 1, 2022 · 13 comments · Fixed by #106
Closed
34 tasks done

[MAINTAIN] java related packages polishment #85

starsareintherose opened this issue Nov 1, 2022 · 13 comments · Fixed by #106
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maintain Maintain problems about server and packages upstream upstream bug

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starsareintherose commented Nov 1, 2022 •
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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 starsareintherose added the maintain Maintain problems about server and packages label Nov 1, 2022
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starsareintherose commented Nov 30, 2022 •
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@Kiri2002 if you want, you can choose to maintain mesquite, it's an excellent start for your bioarchlinux tour.

@starsareintherose starsareintherose mentioned this issue Dec 1, 2022
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starsareintherose commented Dec 1, 2022 •
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- tempest: can't exec beast-dev/Tempest#3

tempest now merge into beast 93554af

@starsareintherose starsareintherose added the upstream upstream bug label Dec 1, 2022
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starsareintherose commented Dec 1, 2022 •
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- spread3: build error phylogeography/SpreaD3#43 and version issue phylogeography/SpreaD3#39

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starsareintherose commented Dec 1, 2022 •
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- spread: can't compile and no version phylogeography/spread#208

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

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starsareintherose commented Dec 1, 2022 •
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trimmomatic: bump java version of ant usadellab/Trimmomatic#36

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starsareintherose commented Dec 2, 2022 •
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open-delta: can't be built, AtlasOfLivingAustralia/open-delta#259

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starsareintherose commented Dec 2, 2022 •
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solved: aliview: compile error AliView/AliView#118

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starsareintherose commented Dec 2, 2022 •
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Artemis: sanger-pathogens/Artemis#340

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starsareintherose commented Dec 2, 2022 •
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- 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

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starsareintherose commented Dec 3, 2022 •
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- Artemis 1850076 need more fix for shell script

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

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

@kbipinkumar kbipinkumar mentioned this issue Dec 18, 2022
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starsareintherose commented Mar 7, 2023 •
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solved fasqc: s-andrews/FastQC#115

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Only one (mesquite) remains as single issue (134).

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SnpEff PKGBUILD rewritten to compile from source kbipinkumar/Packages_sub
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