taxondna: replace sequencematrix

BioArchLinux/sequencematrix/PKGBUILD

@@ -1,25 +0,0 @@
-# Maintainer: Malacology <guoyizhang at malacology dot com>
-# Contributor: Malacology <guoyizhang at malacology dot com>
-
-pkgname=sequencematrix
-_pkgname=SequenceMatrix
-pkgver=1.9
-pkgrel=6
-depends=(
-	'java-runtime'
-)
-pkgdesc="Taxonomy-aware DNA sequence processing toolkit"
-arch=('x86_64')
-url="https://github.com/gaurav/taxondna"
-license=('GPL2')
-source=("https://github.com/gaurav/taxondna/releases/download/v${pkgver}/SequenceMatrix-${pkgver}.zip" "$pkgname.desktop")
-sha256sums=('ba46fe8672ded973c835ea0a636c251d28fa2f80ee30a69469a4a7fab204e814'
-            'a0ab58fb1c9611627344cf20e1441b913fae37287d375ace9837763fabd1dd65')
-
-package() {
-    install -dm755 "$pkgdir"/usr/share/{$pkgname,applications}
-    chmod +x ${srcdir}/SequenceMatrix-${pkgver}/SequenceMatrix.jar
-    install -Dm755 ${srcdir}/$pkgname.desktop "${pkgdir}/usr/share/applications/$pkgname.desktop"
-    install -Dm755 ${srcdir}/SequenceMatrix-${pkgver}/SequenceMatrix.jar ${pkgdir}/usr/share/$pkgname/$pkgname.jar
-    mv ${srcdir}/SequenceMatrix-${pkgver}/* ${pkgdir}/usr/share/$pkgname/
-}

BioArchLinux/sequencematrix/lilac.py

@@ -1,10 +0,0 @@
-#!/usr/bin/env python3
-
-from lilaclib import *
-
-def pre_build():
-  update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
-
-def post_build():
-  git_add_files('PKGBUILD')
-  git_commit()

BioArchLinux/sequencematrix/lilac.yaml

@@ -1,8 +0,0 @@
-build_prefix: extra-x86_64
-maintainers:
-  - github: starsareintherose
-    email: kuoi@bioarchlinux.org
-update_on:
-  - source: github
-    github: gaurav/taxondna
-    use_latest_release: true

BioArchLinux/taxondna/PKGBUILD

@@ -0,0 +1,43 @@
+# Maintainer: Malacology <guoyizhang at malacology dot com>
+# Contributor: Malacology <guoyizhang at malacology dot com>
+
+pkgbase=taxondna
+pkgname=('sequencematrix' 'speciesidentifier' 'genbankexplorer')
+pkg0=TaxonDNA
+pkg1=SequenceMatrix
+pkg2=SpeciesIdentifier
+pkg3=GenBankExplorer
+pkgver=1.9
+pkgrel=6
+depends=('java-runtime=11')
+makedepends=('maven')
+pkgdesc="Taxonomy-aware DNA sequence processing toolkit"
+arch=('x86_64')
+url="https://github.com/gaurav/taxondna"
+license=('GPL2')
+source=("$url/archive/refs/tags/v${pkgver}.tar.gz"
+	"${pkg1,,}.desktop"
+	"${pkg2,,}.desktop"
+	"${pkg3,,}.desktop")
+sha256sums=('54d6a2fdf4067e7f89fdeea971c44d5b938e44a495119807f0a9892af919e162'
+            'f9b4e4eae5d8ef90b9dffe16209555773be8b0e111b9a69620b9be76604a73e4'
+            '9ceb29dfe8bab70723a5876745f345e29ca7b37884da4f67b2dbe042cdc46fe3'
+            '0b786535540f3adf3f979fb6af824238b2bd0f8bcb9c5721b0065bb35563e65d')
+build () {
+  cd $pkgbase-$pkgver
+  mvn package
+}
+package_sequencematrix () {
+  install -Dm755 ${srcdir}/$pkgname.desktop "${pkgdir}/usr/share/applications/$pkgname.desktop"
+  install -Dm755 ${srcdir}/$pkgbase-$pkgver/target/$pkg0-$pkgver-$pkg1.jar ${pkgdir}/usr/share/$pkgname/$pkgname.jar
+}
+
+package_speciesidentifier () {
+ install -Dm755 ${srcdir}/$pkgname.desktop "${pkgdir}/usr/share/applications/$pkgname.desktop"
+  install -Dm755 ${srcdir}/$pkgbase-$pkgver/target/$pkg0-$pkgver-$pkg2.jar ${pkgdir}/usr/share/$pkgname/$pkgname.jar
+}
+
+package_genbankexplorer () {
+  install -Dm755 ${srcdir}/$pkgname.desktop "${pkgdir}/usr/share/applications/$pkgname.desktop"
+  install -Dm755 ${srcdir}/$pkgbase-$pkgver/target/$pkg0-$pkgver-$pkg3.jar ${pkgdir}/usr/share/$pkgname/$pkgname.jar
+}

BioArchLinux/taxondna/genbankexplorer.desktop

@@ -0,0 +1,18 @@
+[Desktop Entry]
+Categories=
+Encoding=UTF-8
+Exec=java -jar /usr/share/genbankexplorer/genbankexplorer.jar
+GenericName=
+GenericName[zh]=
+Icon=java11-openjdk
+MimeType=
+Name=GenBankExplorer
+Name[zh]=GenBankExplorer
+ServiceTypes=
+SwallowExec=
+SwallowTitle=
+Terminal=false
+TerminalOptions=
+Type=Application
+X-KDE-SubstituteUID=false
+X-KDE-Username=root

BioArchLinux/taxondna/lilac.yaml

@@ -0,0 +1,15 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: starsareintherose
+    email: kuoi@bioarchlinux.org
+pre_build_script: |
+  update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
+  run_cmd(['updpkgsums'])
+post_build_script: |
+  git_add_files('PKGBUILD')
+  git_commit()
+update_on:
+  - source: github
+    github: gaurav/taxondna
+    use_max_tag: true
+    prefix: 'v'

BioArchLinux/taxondna/sequencematrix.desktop

@@ -4,7 +4,7 @@ Encoding=UTF-8
 Exec=java -jar /usr/share/sequencematrix/sequencematrix.jar
 GenericName=
 GenericName[zh]=
-Icon=java15-openjdk
+Icon=java11-openjdk
 MimeType=
 Name=SequenceMatrix
 Name[zh]=SequenceMatrix

BioArchLinux/taxondna/speciesidentifier.desktop

@@ -0,0 +1,18 @@
+[Desktop Entry]
+Categories=
+Encoding=UTF-8
+Exec=java -jar /usr/share/speciesidentifier/speciesidentifier.jar
+GenericName=
+GenericName[zh]=
+Icon=java11-openjdk
+MimeType=
+Name=SpeciesIdentifier
+Name[zh]=SpeciesIdentifier
+ServiceTypes=
+SwallowExec=
+SwallowTitle=
+Terminal=false
+TerminalOptions=
+Type=Application
+X-KDE-SubstituteUID=false
+X-KDE-Username=root