igv: Add package (#202)

* igv: Add package

* igv: Update PKGBUILD

* igv: Update lilac.yaml

BioArchLinux/igv/PKGBUILD

@@ -0,0 +1,64 @@
+# Maintainer: Kiri <kiri@vern.cc>
+# Contributor: Decrypted Epsilon <decrypted.epsilon@gmail.com>
+# Contributor: Stefan Husmann <stefan-husmann@t-online.de>
+# Contributor:  Piotr Balwierz <parseByHuman(surname at email_service_of_google)>
+# Co-maintainer: Rhinoceros <https://aur.archlinux.org/account/rhinoceros>
+
+pkgname=igv
+pkgver=2.17.3
+pkgrel=2
+pkgdesc="High-performance visualization tool for interactive exploration of large, integrated genomic datasets. From Broad Institute. \
+        https://doi.org/10.1093/bioinformatics/btac830"
+arch=('any')
+url="https://igv.org"
+license=('MIT')
+makedepends=('gendesk' 'gradle' 'java-environment=17')
+depends=('java-runtime>=17' 'sh')
+source=("${pkgname}-${pkgver}.tar.gz::https://github.com/igvteam/igv/archive/v${pkgver}.tar.gz")
+sha256sums=('81ab0164014612ff37eea6c7673072fb38ba65b527c05c1197f605c3e9cf3c39')
+
+prepare() {
+    # generate /usr/bin entry
+    cat <<'EOF' > igv
+#!/usr/bin/sh
+export PATH=/usr/lib/jvm/java-11-openjdk/bin/:$PATH
+exec /usr/share/igv/igv.sh
+EOF
+
+    cat <<'EOF' > igvtools
+#!/usr/bin/sh
+export PATH=/usr/lib/jvm/java-11-openjdk/bin/:$PATH
+exec /usr/share/igv/igvtools
+EOF
+
+    # generate desktop entry
+    gendesk -f -n --pkgname "igv" \
+        --pkgdesc "Integrative Genomics Viewer" \
+        --exec="igv" \
+        --icon="/usr/share/icons/${pkgname}.ico" \
+        --name="IGV" \
+        --categories="Science"
+}
+
+build() {
+    export PATH=/usr/lib/jvm/java-17-openjdk/bin/:$PATH
+    cd ${srcdir}/${pkgname}-${pkgver}
+    gradle createDist
+}
+
+package() {
+    cd ${srcdir}
+    install -Dm755 igv ${pkgdir}/usr/bin/igv
+    install -Dm755 igvtools ${pkgdir}/usr/bin/igvtools
+    install -Dm644 ${pkgname}.desktop ${pkgdir}/usr/share/applications/${pkgname}.desktop
+    cd ${srcdir}/${pkgname}-${pkgver}
+    install -Dm644 license.txt ${pkgdir}/usr/share/licenses/${pkgname}/LICENSE
+    install -Dm644 resources/IGV_64.ico ${pkgdir}/usr/share/icons/${pkgname}.ico
+    cd ${srcdir}/${pkgname}-${pkgver}/build/IGV-dist
+    install -Dm755 igv.sh ${pkgdir}/usr/share/${pkgname}/igv.sh
+    install -Dm755 igvtools ${pkgdir}/usr/share/${pkgname}/igvtools
+    install -Dm644 igv.args ${pkgdir}/usr/share/${pkgname}/igv.args
+    install -Dm644 lib/*jar -t ${pkgdir}/usr/share/java/${pkgname}
+    install -Dm644 lib/genomes/* -t ${pkgdir}/usr/share/${pkgname}/lib/genomes
+    ln -sr ${pkgdir}/usr/share/java/${pkgname}/* ${pkgdir}/usr/share/${pkgname}/lib
+}

BioArchLinux/igv/lilac.yaml

@@ -0,0 +1,13 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: kiri2002
+  email: kiri@vern.cc
+pre_build_script: |
+  update_pkgver_and_pkgrel(_G.newver)
+post_build_script: |
+  git_pkgbuild_commit()
+update_on:
+  - source: github
+    github: igvteam/igv
+    use_latest_tag: true
+    prefix: 'v'