# Maintainer: Jens Staal <staal1978@gmail.com>

pkgname=meta-ugene-external_tools
pkgver=20181009
pkgrel=2
pkgdesc='Metapackage for External Tools in the UGENE bioinformatics suite'
arch=('any')
license=('none')

depends=(
  'ugene-bin'
  'java-runtime>=8'
  'bedtools'
  'blast+'
  'bowtie'
  'bowtie2'
  'bwa'
  #cap3
  'clustal-omega'
  'clustalw'
  'mafft'
  'tcoffee'
  'mrbayes'
  'phyml-git'
  'kraken'
  #Conduct GO
  #mdseqpos
  #conservation plot
  #peak2gene
  #MACS
  #CEAS
  'cufflinks-bin' #source-based cufflinks does not build
  'samtools'
  'tophat'
  'python'
  'python2'
  'perl'
  'vcftools'
  'vcfanno-bin'
  'snpeff'
  'fastqc'
  'python-cutadapt'
  'hmmer'
  'hmmer2'
  'primer3'
)

#commented out deps are not yet in AUR
replaces=('ugene-external-tools')
url="http://ugene.net/external.html"