add seqtk and trim

BioArchLinux/seqtk/PKGBUILD

@@ -0,0 +1,25 @@
+# Maintainer: alienzj <alienchuj@gmail.com>
+
+pkgname=seqtk
+pkgver=1.3
+pkgrel=1
+pkgdesc="Toolkit for processing sequences in FASTA/Q formats"
+arch=('x86_64')
+url="https://github.com/lh3/seqtk"
+license=('MIT')
+makedepends=('zlib' 'make')
+provides=('seqtk')
+conflicts=('seqtk')
+source=("https://github.com/lh3/seqtk/archive/v${pkgver}.tar.gz")
+md5sums=('39a499431a10fe2412925a53ecfbab2b')
+
+build() {
+  cd $srcdir/seqtk-${pkgver}
+  make
+}
+
+package() {
+  cd $srcdir/seqtk-${pkgver}
+  install -Dm755 seqtk $pkgdir/usr/bin/seqtk
+  install -Dm644 LICENSE ${pkgdir}/usr/share/licenses/seqtk/LICENSE
+}

BioArchLinux/seqtk/lilac.py

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

BioArchLinux/seqtk/lilac.yaml

@@ -0,0 +1,9 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: starsareintherose
+    email: starsareintherose@outlook.com
+update_on:
+  - source: github
+    github: lh3/seqtk 
+    use_max_tag: true
+    prefix: 'v'

BioArchLinux/trimmomatic/PKGBUILD

@@ -0,0 +1,23 @@
+# Maintainer: ZJLIN <zjin841126@gmail.com>
+pkgname=trimmomatic
+pkgver=0.39
+pkgrel=1
+pkgdesc='Trimmomatic: A flexible read trimming tool for Illumina NGS data'
+arch=('any')
+url="http://www.usadellab.org/cms/?page=trimmomatic"
+license=('GPL3')
+depends=('java-environment>=6')
+source=("http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-$pkgver.zip"
+        "trimmomatic"
+        )
+md5sums=('271ed9dca91132eee0c960e0ae487bcd'
+         'f48f380f206cb5f85bc25b8cf2c35d99')
+
+package() {
+    mkdir $pkgdir/opt/
+    mv $srcdir/Trimmomatic-$pkgver $srcdir/Trimmomatic
+    cp -r $srcdir/Trimmomatic/ $pkgdir/opt/
+
+    mkdir -p "${pkgdir}/usr/bin/"
+    install $srcdir/trimmomatic $pkgdir/usr/bin
+}

BioArchLinux/trimmomatic/lilac.py

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

BioArchLinux/trimmomatic/lilac.yaml

@@ -0,0 +1,9 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: starsareintherose
+    email: starsareintherose@outlook.com
+update_on:
+  - source: github
+    github: usadellab/Trimmomatic 
+    use_max_tag: true
+    prefix: 'v'

BioArchLinux/trimmomatic/trimmomatic

@@ -0,0 +1,2 @@
+#!/usr/bin/bash
+exec java -jar /opt/Trimmomatic/trimmomatic-0.39.jar "$@"