initial commit

android-google-play-services/PKGBUILD

@@ -0,0 +1,19 @@
+pkgname=android-google-play-services
+pkgver=r23
+_build=7095000
+pkgrel=3
+pkgdesc='Google Play Services client library and sample code'
+arch=('any')
+url="https://developers.google.com/android/google-play-services/"
+license=('custom')
+options=('!strip')
+source=("http://dl.google.com/android/repository/google_play_services_${_build}_${pkgver}.zip" "source.properties")
+sha1sums=('987520c73e66d58fe3811f542366369ddd79e733'
+          '764a1d373c96c226782b4023da85c3734481f38f')
+
+package() {
+  mkdir -p "${pkgdir}/opt/android-sdk/extras/google/"
+  cp -dpr --no-preserve=ownership "${srcdir}/google-play-services" "${pkgdir}/opt/android-sdk/extras/google/google_play_services"
+  chmod -R ugo+rX "${pkgdir}/opt"
+  install -Dm644 "${srcdir}/source.properties" "${pkgdir}/opt/android-sdk/extras/google/google_play_services/source.properties"
+}

cufflinks/PKGBUILD

@@ -0,0 +1,29 @@
+# Maintainer: Thiago Yukio Kikuchi Oliveira <[email protected]>
+
+pkgname=cufflinks
+pkgver=2.2.1
+pkgrel=1
+pkgdesc="Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.."
+arch=("x86_64")
+url="http://cufflinks.cbcb.umd.edu"
+license=('Artistic')
+depends=('boost' 'eigen3' 'python2' 'samtools' 'perl')
+source=(http://cufflinks.cbcb.umd.edu/downloads/$pkgname-$pkgver.tar.gz)
+md5sums=('9a5ba7a7710cd864932cf205c17851f0')
+
+build() {
+  cd $srcdir/$pkgname-$pkgver
+  # cufflinks use python2 but archlinux uses python3 as default python
+  perl -i -pne '$_ =~ s/python/python2/ if $_ =~ /^#!\/usr/' src/cuffmerge
+
+  export EIGEN_CPPFLAGS="-I/usr/include/eigen3"
+  export LDFLAGS="-L/usr/lib -lboost_system"
+  ./configure --prefix=/usr
+  make
+
+}
+
+package() {
+	  cd "$srcdir/$pkgname-$pkgver"
+	  make DESTDIR="$pkgdir/" install
+}

python2-macs2/PKGBUILD

@@ -0,0 +1,35 @@
+# $Id$
+# Maintainer: Grey Christoforo <grey at christoforo dot net>
+
+pkgbase=python2-macs2
+pkgname=('python2-macs2')
+_pkgname=MACS2
+pkgver=2.1.0.20140616
+pkgrel=1
+pkgdesc="MACS -- Model-based Analysis of ChIP-Seq"
+arch=('i686' 'x86_64')
+url="https://github.com/taoliu/MACS/"
+license=('Artistic')
+depends=('python2-numpy')
+source=(https://pypi.python.org/packages/source/M/${_pkgname}/${_pkgname}-${pkgver}.tar.gz)
+md5sums=('ad105b9ad25bc2eedc78c38d54cf76e8')
+
+prepare() {
+  cp -r "${_pkgname}-${pkgver}" "${_pkgname}-${pkgver}-py2"
+  # change python to python2
+  find "${_pkgname}-${pkgver}-py2" -name '*.py' -type f -exec \
+      sed -i 's|env python|env python2|' {} \;
+}
+
+build() {
+  cd "${srcdir}/${_pkgname}-${pkgver}-py2"
+  python2 setup.py build
+}
+
+package_python2-macs2() {
+  depends=('python2-numpy')
+
+  cd "${srcdir}/${_pkgname}-${pkgver}-py2"
+  python2 setup.py install --root="${pkgdir}"
+  install -Dm644 "COPYING" "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
+}

rsem/PKGBUILD

@@ -0,0 +1,32 @@
+# Maintainer: Grey Christoforo <grey at christoforo dot net>
+
+pkgname=rsem
+_pkgname=RSEM
+pkgver=1.2.19
+pkgrel=1
+pkgdesc="accurate quantification of gene and isoform expression from RNA-Seq data"
+arch=('i686' 'x86_64')
+url="http://deweylab.biostat.wisc.edu/rsem/"
+install=${pkgname}.install
+license=GNU
+depends=('perl' 'r')
+optdepends=('bowtie2')
+source=(https://github.com/bli25wisc/${_pkgname}/archive/v${pkgver}.tar.gz)
+md5sums=('69667ee47337617847dc97da2765fd08')
+
+build() {
+   cd "${srcdir}/${_pkgname}-${pkgver}"
+   make
+}
+
+package() {
+   cd "${srcdir}/${_pkgname}-${pkgver}"
+   mkdir -p "${pkgdir}/usr/bin/${pkgname}"
+   mv `find . -maxdepth 1 -type f -perm -u+x` "${pkgdir}/usr/bin/${pkgname}/."
+   mv WHAT_IS_NEW "${pkgdir}/usr/bin/${pkgname}/."
+
+   mkdir -p "$pkgdir/etc/profile.d"
+   echo "export PATH=/usr/bin/${pkgname}:"'$PATH' > "$pkgdir/etc/profile.d/${pkgname}.sh"
+}
+
+# vim:set ts=2 sw=2 et:

rsem/rsem.install

@@ -0,0 +1,7 @@
+post_install() {
+   echo
+   echo "To use rsem, log out and log back in, or run"
+   echo "source /etc/profile"
+   echo "To enable it immediately"
+   echo
+}

ruby-daemons/PKGBUILD

@@ -0,0 +1,24 @@
+# Generated by gem2arch (https://github.com/anatol/gem2arch)
+# Maintainer: Anatol Pomozov <[email protected]>
+# Contributor: eagletmt <[email protected]>
+
+_gemname=daemons
+pkgname=ruby-$_gemname
+pkgver=1.1.9
+pkgrel=1
+pkgdesc='A toolkit to create and control daemons in different ways'
+arch=(any)
+url='http://daemons.rubyforge.org'
+license=(MIT)
+depends=(ruby)
+options=(!emptydirs)
+source=(https://rubygems.org/downloads/$_gemname-$pkgver.gem)
+noextract=($_gemname-$pkgver.gem)
+sha1sums=('e73ba58fe9e948f7edc5017f91f53b8f0a955a37')
+
+package() {
+  local _gemdir="$(ruby -e'puts Gem.default_dir')"
+  gem install --ignore-dependencies --no-user-install -i "$pkgdir/$_gemdir" -n "$pkgdir/usr/bin" $_gemname-$pkgver.gem
+  rm "$pkgdir/$_gemdir/cache/$_gemname-$pkgver.gem"
+  install -D -m644 "$pkgdir/$_gemdir/gems/$_gemname-$pkgver/LICENSE" "$pkgdir/usr/share/licenses/$pkgname/LICENSE"
+}

ruby-diff-lcs/PKGBUILD

@@ -0,0 +1,26 @@
+# Generated by gem2arch (https://github.com/anatol/gem2arch)
+# Maintainer: Sirat18 <[email protected]>
+# Contributor: Anatol Pomozov <[email protected]>
+# Contributor: Alfredo Palhares <[email protected]>
+# Contributor: mtorromeo
+
+_gemname=diff-lcs
+pkgname=ruby-$_gemname
+pkgver=1.2.5
+pkgrel=3
+pkgdesc='Diff::LCS computes the difference between two Enumerable sequences using the McIlroy-Hunt longest common subsequence (LCS) algorithm'
+arch=(any)
+url='https://github.com/halostatue/diff-lcs'
+license=(MIT 'Perl Artistic v2' 'GNU GPL v2')
+depends=(ruby)
+options=(!emptydirs)
+source=(https://rubygems.org/downloads/$_gemname-$pkgver.gem)
+noextract=($_gemname-$pkgver.gem)
+sha1sums=('5f71a45f13780701f3a42297adc0269d0799e1d5')
+
+package() {
+  local _gemdir="$(ruby -e'puts Gem.default_dir')"
+  gem install --ignore-dependencies --no-user-install -i "$pkgdir/$_gemdir" -n "$pkgdir/usr/bin" $_gemname-$pkgver.gem
+  rm "$pkgdir/$_gemdir/cache/$_gemname-$pkgver.gem"
+  install -D -m644 "$pkgdir/$_gemdir/gems/$_gemname-$pkgver/License.rdoc" "$pkgdir/usr/share/licenses/$pkgname/License.rdoc"
+}

ruby-eventmachine/PKGBUILD

@@ -0,0 +1,23 @@
+# Generated by gem2arch (https://github.com/anatol/gem2arch)
+# Maintainer: 
+
+_gemname=eventmachine
+pkgname=ruby-$_gemname
+pkgver=1.0.7
+pkgrel=1
+pkgdesc='Ruby/EventMachine library'
+arch=(i686 x86_64)
+url='http://rubyeventmachine.com'
+license=(Ruby GPL)
+depends=(ruby)
+options=(!emptydirs)
+source=(https://rubygems.org/downloads/$_gemname-$pkgver.gem)
+noextract=($_gemname-$pkgver.gem)
+sha1sums=('4e6fe81a3e424e8d6f53d4774364fa0d47da27fb')
+
+package() {
+  local _gemdir="$(ruby -e'puts Gem.default_dir')"
+  gem install --ignore-dependencies --no-user-install -i "$pkgdir/$_gemdir" -n "$pkgdir/usr/bin" $_gemname-$pkgver.gem
+  rm "$pkgdir/$_gemdir/cache/$_gemname-$pkgver.gem"
+  install -D -m644 "$pkgdir/$_gemdir/gems/$_gemname-$pkgver/LICENSE" "$pkgdir/usr/share/licenses/$pkgname/LICENSE"
+}

ruby-grit/PKGBUILD

@@ -0,0 +1,23 @@
+# Generated by gem2arch (https://github.com/anatol/gem2arch)
+# Maintainer: Anatol Pomozov <[email protected]>
+
+_gemname=grit
+pkgname=ruby-$_gemname
+pkgver=2.5.0
+pkgrel=1
+pkgdesc='Ruby Git bindings.'
+arch=(any)
+url='http://github.com/mojombo/grit'
+license=(MIT)
+depends=(ruby ruby-posix-spawn ruby-mime-types-1 ruby-diff-lcs)
+options=(!emptydirs)
+source=(https://rubygems.org/downloads/$_gemname-$pkgver.gem)
+noextract=($_gemname-$pkgver.gem)
+sha1sums=('0581087581cd522a697616b835b4d57f90a90ca6')
+
+package() {
+  local _gemdir="$(ruby -e'puts Gem.default_dir')"
+  gem install --ignore-dependencies --no-user-install -i "$pkgdir/$_gemdir" -n "$pkgdir/usr/bin" $_gemname-$pkgver.gem
+  rm "$pkgdir/$_gemdir/cache/$_gemname-$pkgver.gem"
+  install -D -m644 "$pkgdir/$_gemdir/gems/$_gemname-$pkgver/LICENSE" "$pkgdir/usr/share/licenses/$pkgname/LICENSE"
+}

ruby-nokogiri/PKGBUILD

@@ -0,0 +1,28 @@
+# Generated by gem2arch (https://github.com/anatol/gem2arch)
+# Maintainer: Anatol Pomozov <[email protected]>
+# Contributor: eagletmt <[email protected]>
+
+_gemname=nokogiri
+pkgname="ruby-${_gemname}"
+pkgver=1.6.6.2
+pkgrel=1
+pkgdesc='HTML, XML, SAX, and Reader parser'
+arch=('any')
+url='http://nokogiri.org'
+license=('MIT')
+depends=('libxml2' 'libxslt' 'ruby' 'ruby-mini_portile')
+options=('!emptydirs')
+source=("https://rubygems.org/downloads/${_gemname}-${pkgver}.gem")
+noextract=("${_gemname}-${pkgver}.gem")
+sha512sums=('bb0422878e690648ab154c7d1ab0bd4fd9ec0875b2f0be0292ba9cb5541ea33b770794a7ba411e603a06472af4f9a3337ec8ff5d74debd826fc63f1d3ab1d5f1')
+
+package() {
+	local _gemdir="$(ruby -e'puts Gem.default_dir')"
+	# TODO: in the future releases of nokogiri we can use -- --use-system-libraries
+	# see https://github.com/sparklemotion/nokogiri/blob/master/ext/nokogiri/extconf.rb
+	NOKOGIRI_USE_SYSTEM_LIBRARIES=1 gem install --ignore-dependencies --no-user-install -i "${pkgdir}/${_gemdir}" -n "${pkgdir}/usr/bin" "${_gemname}-${pkgver}.gem"
+	rm "${pkgdir}/${_gemdir}/cache/${_gemname}-${pkgver}.gem"
+
+	rm -rf "${pkgdir}/${_gemdir}/gems/${_gemname}-${pkgver}/ports"
+	rm -rf "${pkgdir}/${_gemdir}/gems/${_gemname}-${pkgver}/ext"
+}

ruby-rack-protection/PKGBUILD

@@ -0,0 +1,24 @@
+# Generated by gem2arch (https://github.com/anatol/gem2arch)
+# Maintainer: Anatol Pomozov <[email protected]>
+# Contributor: Alexsandr Pavlov <kidoz at mail dot ru>
+
+_gemname=rack-protection
+pkgname=ruby-$_gemname
+pkgver=1.5.3
+pkgrel=1
+pkgdesc='You should use protection!'
+arch=(any)
+url='https://github.com/rkh/rack-protection'
+license=(MIT)
+depends=(ruby ruby-rack)
+options=(!emptydirs)
+source=(https://rubygems.org/downloads/$_gemname-$pkgver.gem)
+noextract=($_gemname-$pkgver.gem)
+sha1sums=('1c28529c1d7376c61faed80f3d3297905a14c2b3')
+
+package() {
+  local _gemdir="$(ruby -e'puts Gem.default_dir')"
+  gem install --ignore-dependencies --no-user-install -i "$pkgdir/$_gemdir" -n "$pkgdir/usr/bin" $_gemname-$pkgver.gem
+  rm "$pkgdir/$_gemdir/cache/$_gemname-$pkgver.gem"
+  install -D -m644 "$pkgdir/$_gemdir/gems/$_gemname-$pkgver/License" "$pkgdir/usr/share/licenses/$pkgname/License"
+}

ruby-rack-ssl/PKGBUILD

@@ -0,0 +1,23 @@
+# Generated by gem2arch (https://github.com/anatol/gem2arch)
+# Maintainer: Anatol Pomozov <[email protected]>
+
+_gemname=rack-ssl
+pkgname=ruby-$_gemname
+pkgver=1.4.1
+pkgrel=1
+pkgdesc='Force SSL/TLS in your app.'
+arch=(any)
+url='https://github.com/josh/rack-ssl'
+license=(MIT)
+depends=(ruby ruby-rack)
+options=(!emptydirs)
+source=(https://rubygems.org/downloads/$_gemname-$pkgver.gem)
+noextract=($_gemname-$pkgver.gem)
+sha1sums=('87f2fb53c6882436b8d522288993d658dc7025ce')
+
+package() {
+  local _gemdir="$(ruby -e'puts Gem.default_dir')"
+  gem install --ignore-dependencies --no-user-install -i "$pkgdir/$_gemdir" -n "$pkgdir/usr/bin" $_gemname-$pkgver.gem
+  rm "$pkgdir/$_gemdir/cache/$_gemname-$pkgver.gem"
+  install -D -m644 "$pkgdir/$_gemdir/gems/$_gemname-$pkgver/LICENSE" "$pkgdir/usr/share/licenses/$pkgname/LICENSE"
+}

ruby-sinatra/PKGBUILD

@@ -0,0 +1,23 @@
+# Generated by gem2arch (https://github.com/anatol/gem2arch)
+# Maintainer: Anatol Pomozov <[email protected]>
+
+_gemname=sinatra
+pkgname=ruby-$_gemname
+pkgver=1.4.5
+pkgrel=1
+pkgdesc='Classy web-development dressed in a DSL'
+arch=(any)
+url='http://www.sinatrarb.com/'
+license=(MIT)
+depends=(ruby ruby-rack ruby-tilt-1 ruby-rack-protection)
+options=(!emptydirs)
+source=(https://rubygems.org/downloads/$_gemname-$pkgver.gem)
+noextract=($_gemname-$pkgver.gem)
+sha1sums=('97e695f50c078ea57424dd8a48424269e6afdacb')
+
+package() {
+  local _gemdir="$(ruby -e'puts Gem.default_dir')"
+  gem install --ignore-dependencies --no-user-install -i "$pkgdir/$_gemdir" -n "$pkgdir/usr/bin" $_gemname-$pkgver.gem
+  rm "$pkgdir/$_gemdir/cache/$_gemname-$pkgver.gem"
+  install -D -m644 "$pkgdir/$_gemdir/gems/$_gemname-$pkgver/LICENSE" "$pkgdir/usr/share/licenses/$pkgname/LICENSE"
+}

ruby-thin/PKGBUILD

@@ -0,0 +1,24 @@
+# Generated by gem2arch (https://github.com/anatol/gem2arch)
+# Maintainer: Anatol Pomozov <[email protected]>
+
+_gemname=thin
+pkgname=ruby-$_gemname
+pkgver=1.6.3
+pkgrel=1
+pkgdesc='A thin and fast web server'
+arch=(i686 x86_64)
+url='http://code.macournoyer.com/thin/'
+license=(Ruby)
+depends=(ruby ruby-rack ruby-eventmachine ruby-daemons)
+options=(!emptydirs)
+source=(https://rubygems.org/downloads/$_gemname-$pkgver.gem)
+noextract=($_gemname-$pkgver.gem)
+sha1sums=('ad99e77149b922c3f067b0140438c044d24115f1')
+
+package() {
+  local _gemdir="$(ruby -e'puts Gem.default_dir')"
+  gem install --ignore-dependencies --no-user-install -i "$pkgdir/$_gemdir" -n "$pkgdir/usr/bin" $_gemname-$pkgver.gem
+  rm "$pkgdir/$_gemdir/cache/$_gemname-$pkgver.gem"
+
+  rm -rf "$pkgdir/$_gemdir/gems/$_gemname-$pkgver/ext"
+}

ruby-tilt-1/PKGBUILD

@@ -0,0 +1,25 @@
+# Generated by gem2arch (https://github.com/anatol/gem2arch)
+# Maintainer: Anatol Pomozov <[email protected]>
+
+_gemname=tilt
+pkgname=ruby-$_gemname-1
+pkgver=1.4.1
+pkgrel=1
+pkgdesc='Generic interface to multiple Ruby template engines'
+arch=(any)
+url='https://github.com/rtomayko/tilt/'
+license=(MIT)
+depends=(ruby)
+options=(!emptydirs)
+source=(https://rubygems.org/downloads/$_gemname-$pkgver.gem)
+noextract=($_gemname-$pkgver.gem)
+sha1sums=('a63b374ab06aeb6f567bd24e61434e386cce0811')
+
+package() {
+  local _gemdir="$(ruby -e'puts Gem.default_dir')"
+  gem install --ignore-dependencies --no-user-install -i "$pkgdir/$_gemdir" -n "$pkgdir/usr/bin" $_gemname-$pkgver.gem
+  rm "$pkgdir/$_gemdir/cache/$_gemname-$pkgver.gem"
+  install -D -m644 "$pkgdir/$_gemdir/gems/$_gemname-$pkgver/COPYING" "$pkgdir/usr/share/licenses/$pkgname/COPYING"
+
+  rm -rf "$pkgdir/usr/bin/"
+}