<?xml version="1.0"?><!--*- mode: nxml; indent-tabs-mode: nil -*-->
<!DOCTYPE moduleset SYSTEM "moduleset.dtd">
<?xml-stylesheet type="text/xsl" href="moduleset.xsl"?>
<!--
     Syntax reference:
     http://developer.gnome.org/jhbuild/unstable/moduleset-syntax.html.en
 -->
<moduleset>
  <repository type="bzr" name="oisin" default="yes"
              href="bzr+http://fg.oisin.rc-harwell.ac.uk/bzr/"
              trunk-template="series-70/%(module)s"
              branches-template="series-70/%(module)s/"/>
  <repository type="tarball" name="ccp4-tarballs"
              href="ftp://ftp.ccp4.ac.uk/opensource/"/>
  <repository type="tarball" name="files"
              href="http://devtools.fg.oisin.rc-harwell.ac.uk/files/"/>
  <repository type="tarball" name="sf"
              href="http://downloads.sourceforge.net/"/>
  <repository type="tarball" name="github-zip" href="https://github.com/"/>

  <custom id="ccp4-base" install_to="* ./">
    <branch/>
  </custom>

  <autotools id="mmdb">
    <branch/>
  </autotools>

  <autotools id="mmdb2">
    <branch/>
  </autotools>

  <autotools id="libccp4" autogenargs="--datadir=${prefix}/lib/data">
    <branch/>
    <dependencies>
      <dep package="ccp4-base"/>
      <dep package="mmdb2"/>
    </dependencies>
  </autotools>

  <autotools id="ccif" autogenargs="--with-ccp4">
    <branch/>
    <dependencies>
      <dep package="libccp4"/>
    </dependencies>
    <after>
      <dep package="libgnurx"/> <!-- may be needed on Windows only -->
    </after>
  </autotools>

  <autotools id="ssm" autogenargs="--enable-ccp4">
    <branch/>
    <dependencies>
      <dep package="mmdb2"/>
      <dep package="libccp4"/>
    </dependencies>
  </autotools>

  <cmake id="gesamt" cmakeargs="-DUSE_CCP4=1">
    <branch/>
    <dependencies>
      <dep package="mmdb2"/>
      <dep package="libccp4"/>
    </dependencies>
  </cmake>

  <autotools id="ccp4srs">
    <branch/>
    <dependencies>
      <dep package="mmdb2"/>
      <dep package="zlib"/>
      <dep package="ccp4srs-data"/>
    </dependencies>
  </autotools>

  <custom id="ccp4srs-data"
          install_to="* share/ccp4srs/">
    <branch repo="ccp4-tarballs" version="20150205"
            module="ccp4srs-data-${version}.tar.gz"/>
  </custom>

  <cmake id="qtlibs">
    <branch/>
    <dependencies>
    </dependencies>
  </cmake>

  <!-- special case, building pisa without qtpisa -->
  <cmake id="pisa-no-qt" cmakeargs="-DUSE_QT=OFF">
    <branch module="pisa"/>
    <dependencies>
      <dep package="mmdb2"/>
      <dep package="ssm"/>
      <dep package="libccp4"/>
      <dep package="ccp4srs"/>
      <dep package="ccp4srs-data"/>
    </dependencies>
  </cmake>

  <cmake id="pisa">
    <branch/>
    <dependencies>
      <dep package="mmdb2"/>
      <dep package="ssm"/>
      <dep package="libccp4"/>
      <dep package="ccp4srs"/>
      <dep package="ccp4srs-data"/>
      <dep package="qtlibs"/>
    </dependencies>
  </cmake>

  <cmake id="refmac">
    <branch branch="5.8" checkoutdir="refmac5.8"/>
    <dependencies>
      <dep package="libccp4"/>
      <dep package="lapack"/>
      <dep package="fftw2"/>
    </dependencies>
  </cmake>

  <custom id="monomers"
      install_to="* lib/data/monomers/">
    <branch/>
    <!--
    <branch repo="refmac_experimental" version="5.38"
            module="refmac_dictionary_v${version}.tar.gz"
            checkoutdir="refmac_dictionary_v${version}"/>
    -->
  </custom>

  <cmake id="ccp4-progs">
    <branch/>
    <dependencies>
      <dep package="libccp4"/>
      <dep package="ccif"/>
      <dep package="mmdb2"/>
    </dependencies>
  </cmake>

  <custom id="examples"
          install_to="* examples/">
    <branch light="yes"/> <!-- whole repo is big, 280MB -->
  </custom>

  <custom id="documentation"
          install="./installer.sh ${dest}">
    <branch/>
  </custom>

  <custom id="ccp4-lib-data" install_to="* lib/data/">
    <branch repo="files" module="ccp4-lib-data-6.5.0.tar.gz"
            size="15269420" version="6.5.0"/>
  </custom>

  <custom id="test-sys">
    <branch/>
  </custom>

  <cmake id="ccp4i">
    <branch/>
  </cmake>

  <custom id="imosflm" install_to="* share/ccp4i/imosflm/">
    <branch/>
  </custom>

  <cmake id="hklfile">
    <branch/>
    <dependencies>
      <dep package="libccp4"/>
      <dep package="clipper"/>
    </dependencies>
  </cmake>

  <cmake id="viewhkl">
    <branch/>
    <dependencies>
      <dep package="mmdb2"/>
      <dep package="libccp4"/>
      <dep package="clipper"/>
      <dep package="qtlibs"/>
      <dep package="hklfile"/>
    </dependencies>
  </cmake>

  <cmake id="qtrview">
    <branch/>
    <dependencies>
      <dep package="qtlibs"/>
    </dependencies>
  </cmake>

  <cmake id="jsrview">
    <branch/>
    <dependencies>
      <dep package="qtlibs"/>
    </dependencies>
  </cmake>

  <cmake id="setup">
    <branch/>
    <dependencies>
      <dep package="qtlibs"/>
    </dependencies>
  </cmake>

  <custom id="mrbump"
          install_to="bin/* bin/, data share/mrbump/, include share/mrbump/">
    <branch light="yes"/>
    <suggests>
      <dep package="hmmer"/>
      <dep package="mafft"/>
      <dep package="clustalw2"/>
    </suggests>
  </custom>

  <cmake id="dssp">
    <branch/>
    <dependencies>
      <dep package="boost"/>
    </dependencies>
  </cmake>

  <cmake id="xssp">
    <branch repo="github-zip"
        module="cmbi/xssp/releases/download/${version}/xssp-${version}.tar.gz"
        version="2.2.7" size="236575">
      <patch file="xssp.patch" strip="0" />
    </branch>
    <dependencies>
      <dep package="boost"/>
    </dependencies>
  </cmake>

  <cmake id="tgutils">
    <branch/>
    <dependencies>
      <dep package="clipper"/>
    </dependencies>
  </cmake>

  <cmake id="dimple">
    <branch/>
    <dependencies>
      <dep package="clipper"/>
      <dep package="mmdb2"/>
    </dependencies>
  </cmake>

  <custom id="ample"
          install_to="bin/ample.py bin/, * share/ample/">
    <branch/>
    <suggests>
      <dep package="theseus"/>
      <dep package="spicker"/>
    </suggests>
  </custom>

  <autotools id="swig" autogenargs="--bindir=${prefix}/devbin --without-pcre --disable-ccache --without-ocaml">
    <branch repo="sf" module="swig/swig-${version}.tar.gz"
            version="3.0.6" size="5911929"/>
  </autotools>

  <cmake id="ccp4mg">
    <branch branch="ccp4"/>
    <dependencies>
      <dep package="clipper"/>
      <dep package="hklfile"/>
      <dep package="ssm"/>
      <dep package="mmdb2"/>
      <dep package="libccp4"/>
      <dep package="ccp4srs"/>
      <dep package="pyqt4"/>
      <dep package="rdkit"/>
      <!-- below are runtime dependencies, kind of optional -->
      <dep package="suds"/>
      <dep package="lxml"/>
      <dep package="matplotlib"/>
      <dep package="pixie"/>
    </dependencies>
  </cmake>

  <cmake id="ccp4i2">
    <branch/>
    <dependencies>
    <dep package="psutil"/>
    </dependencies>
  </cmake>

  <custom id="jligand"
          build="make" clean="make clean"
          install_to="JLigand.jar bin/, jligand bin/">
    <branch/>
  </custom>

  <cmake id="molrep">
    <branch/>
    <dependencies>
      <dep package="libccp4"/>
    </dependencies>
  </cmake>

  <cmake id="sfcheck">
    <branch/>
    <dependencies>
      <dep package="libccp4"/>
    </dependencies>
  </cmake>

  <cmake id="procheck">
    <branch/>
    <dependencies>
      <dep package="libccp4"/>
    </dependencies>
  </cmake>

  <cmake id="scala">
    <branch/>
    <dependencies>
      <dep package="libccp4"/>
      <dep package="lapack"/>
    </dependencies>
  </cmake>

  <cmake id="dm21">
    <branch/>
    <dependencies>
      <dep package="libccp4"/>
      <dep package="ccif"/>
    </dependencies>
  </cmake>

  <cmake id="ccp4-deprecated">
    <branch/>
    <dependencies>
      <dep package="libccp4"/>
      <dep package="ccif"/>
      <dep package="lapack"/>
    </dependencies>
  </cmake>

  <cmake id="edstats">
    <branch/>
    <dependencies>
      <dep package="libccp4"/>
    </dependencies>
  </cmake>

  <autotools id="mosflm" skip-autogen="never"
             autogenargs="--with-ccp4-prefix=${prefix}"
             supports-non-srcdir-builds="no" makeargs="-j1 clean all">
  <branch/>
    <dependencies>
      <dep package="libccp4"/>
      <dep package="xdl-view"/>
    </dependencies>
  </autotools>

  <!-- requires libxt-dev/libXt-devel -->
  <autotools id="xdl-view" autogen-sh="src/configure">
    <branch/>
  </autotools>

  <cmake id="hklview">
    <branch/>
    <dependencies>
      <dep package="libccp4"/>
      <dep package="xdl-view"/>
    </dependencies>
  </cmake>

  <autotools id="jwc-c">
    <branch/>
    <dependencies>
      <dep package="libccp4"/>
    </dependencies>
  </autotools>

  <autotools id="jwc-f">
    <dependencies>
      <dep package="jwc-c"/>
      <dep package="libccp4"/>
    </dependencies>
    <branch/>
  </autotools>

  <cmake id="rotgen">
    <branch/>
    <dependencies>
      <dep package="jwc-f"/>
      <dep package="xdl-view"/>
    </dependencies>
  </cmake>

  <custom id="balbes-pipeline" install_to="README.USAGE BALBES/, Package/* BALBES/">
    <branch/>
  </custom>

  <custom id="balbesdb" install_to="Package/* BALBES/">
    <branch/>
  </custom>

  <autotools id="dl-laue">
    <branch branch="laue/trunk"/>
  </autotools>

  <custom id="ccp4dispatchers"
          install_to="releaseme/* libexec/">
    <branch/>
  </custom>

  <custom id="devtools"> <!-- only for use in bundling script -->
    <branch/>
  </custom>

  <cmake id="ccp4-core"> <!-- not used anymore -->
    <branch branch="old-trunk" light="yes"/>
  </cmake>

  <autotools id="clipper" autogen-sh="configure"
      autogenargs="--enable-ccp4 --enable-mmdb --enable-cif --enable-minimol">
    <branch/>
    <dependencies>
      <dep package="mmdb2"/>
      <dep package="libccp4"/>
      <dep package="fftw2"/>
    </dependencies>
  </autotools>

  <cmake id="clipper-python">
    <branch branch="trunk"/>
    <dependencies>
      <dep package="libccp4"/>
      <dep package="clipper"/>
    </dependencies>
  </cmake>

  <cmake id="ccp4srs-python">
    <branch branch="trunk"/>
    <dependencies>
      <dep package="ccp4srs"/>
    </dependencies>
  </cmake>

  <!-- cctbx w/ phaser (phaser can be build only as cctbx subdirectory) -->
  <custom id="cctbx-phaser"
          configure="sh ${srcdir}/autogen.sh ${prefix} ${libdir}"
          build="${}" install="${}" clean="${}"
          supports-non-srcdir-builds="yes">
    <branch repo="files" version="2015-12-22"
            module="cctbx-phaser-dials-${version}.tar.gz">
      <patch file="cctbx-autogen.patch" strip="0" />
      <patch file="cctbx-no-unroll.patch" strip="0" />
      <patch file="cctbx-ldflags.patch" strip="0" />
      <patch file="cctbx-ann-mingw.patch" strip="0" />
      <patch file="cctbx-icc.patch" strip="0" />
      <patch file="cctbx-system-boost.patch" strip="0" />
    </branch>
    <dependencies>
      <dep package="boost"/>
      <dep package="hdf5"/>
    </dependencies>
  </custom>

  <repository type="tarball" name="pre_ftp"
              href="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/"/>
  <cmake id="pointless">
    <branch light="yes"/>
    <dependencies>
      <dep package="clipper"/>
      <dep package="libccp4"/>
      <dep package="cctbx-phaser"/>
    </dependencies>
  </cmake>

  <cmake id="aimless">
    <branch/>
    <dependencies>
      <dep package="clipper"/>
      <dep package="libccp4"/>
      <dep package="cctbx-phaser"/>
    </dependencies>
  </cmake>

  <cmake id="feckless">
    <branch/>
    <dependencies>
      <dep package="clipper"/>
      <dep package="libccp4"/>
      <dep package="cctbx-phaser"/>
    </dependencies>
  </cmake>

  <cmake id="clipper-progs">
    <branch/>
    <dependencies>
      <dep package="clipper"/>
      <dep package="libccp4"/>
    </dependencies>
  </cmake>

  <autotools id="cprodrg">
    <branch/>
    <dependencies>
      <dep package="zlib"/>
      <dep package="libccp4"/>
    </dependencies>
  </autotools>

  <cmake id="prosmart">
    <branch/>
  </cmake>

  <custom id="restraint-valid">
    <branch/>
  </custom>

  <cmake id="acedrg">
    <branch light="yes"/>
    <dependencies>
       <dep package="rdkit"/>
    </dependencies>
  </cmake>

  <cmake id="libg">
    <branch/>
  </cmake>

  <cmake id="privateer">
    <branch/>
    <dependencies>
      <dep package="clipper"/>
      <dep package="ccp4srs"/>
    </dependencies>
  </cmake>

  <autotools id="rapper">
    <branch repo="files" module="rapper_ccp4-1.0a.tar.bz2"
            size="11337826" version="1.0a"/>
    <dependencies>
      <dep package="libxml2"/>
      <dep package="gc"/>
    </dependencies>
  </autotools>

  <autotools id="diff-image">
    <branch/>
    <dependencies>
      <dep package="libjpeg"/>
    </dependencies>
    <after>
      <dep package="tcltk84"/>
    </after>
  </autotools>

  <autotools id="ccp4mapwish">
    <branch/>
    <dependencies>
      <dep package="libccp4"/>
    </dependencies>
    <after>
      <!-- it requires Tcl, but on Windows Tcl must be installed manually -->
      <dep package="tcltk84"/>
    </after>
  </autotools>

  <cmake id="crank" cmakeargs="-DCMAKE_BUILD_TYPE=None">
    <branch/>
    <dependencies>
      <dep package="libccp4"/>
      <dep package="clipper"/>
      <dep package="lapack"/>
    </dependencies>
  </cmake>

  <cmake id="crank2">
    <branch/>
    <dependencies>
      <dep package="crank"/>
      <!--<dep package="jsrview"/>-->
    </dependencies>
  </cmake>

  <cmake id="blend">
    <branch/>
    <dependencies>
      <dep package="clipper"/>
      <dep package="cctbx-phaser"/>
    </dependencies>
  </cmake>

  <cmake id="chooch">
    <branch/>
    <dependencies>
      <dep package="gsl"/>
      <dep package="plplot"/>
    </dependencies>
  </cmake>

  <cmake id="spicker">
    <branch/>
  </cmake>

  <cmake id="prelyscar">
    <branch/>
  </cmake>

  <repository type="tarball" name="theseus3d"
              href="http://www.theseus3d.org/src/"/>
  <cmake id="theseus">
    <branch repo="theseus3d" module="theseus_${version}.tar.gz" version="3.3.0"
            size="22548124" checkoutdir="theseus_${version}">
      <patch file="theseus.patch" strip="0" />
    </branch>
    <dependencies>
      <dep package="gsl"/>
    </dependencies>
  </cmake>

  <!-- Unix-only (relies on shell-scripting inside system() call) -->
  <!-- <repository type="tarball" name="pdb-extract"
              href="http://sw-tools.pdb.org/apps/PDB_EXTRACT/"/> -->
  <custom id="pdb-extract" build="make" clean="make clean"
                           install_to="bin/* bin/">
    <!-- <branch module="pdb-extract-v3.11-prod-src.tar.gz" repo="pdb-extract"
               version="3.11"/> - original tarball doesn't compile of-of-box
    -->
    <branch/>
  </custom>

  <repository type="tarball" name="hmmer"
              href="http://selab.janelia.org/software/"/>
  <autotools id="hmmer" autogenargs="--bindir=${prefix}/libexec --enable-sse">
    <branch repo="hmmer" module="hmmer3/3.1b1/hmmer-3.1b1.tar.gz"
            version="3.1b1" size="5778584"/>
  </autotools>

  <repository type="tarball" name="clustal"
              href="http://www.clustal.org/download/current/"/>
  <autotools id="clustalw2" autogenargs="--bindir=${prefix}/libexec">
    <branch repo="clustal" module="clustalw-2.1.tar.gz"
            version="2.1" size="350761">
      <patch file="clustalw2-time.patch" strip="0" />
      <patch file="clustalw2-string.patch" strip="0" />
    </branch>
  </autotools>

  <repository type="tarball" name="mafft"
              href="http://mafft.cbrc.jp/alignment/software/"/>
  <!-- to override CC and CFLAGS in Makefile we either call make with "-e"
        or do "sed -i 's/^C/#C/' core/Makefile in configure"
       s/^rm.*\./true/ is needed because BINDIR is the same as  LIBDIR
  -->
  <custom id="mafft"
      configure="sed -i.bak 's/^rm.*ln -s.*[.]/true/' core/Makefile"
      build="${} -e -C core -j1 clean all"
      install="make -C core install PREFIX=${dest} LIBDIR=${dest}/libexec BINDIR=${dest}/libexec"
      clean="make -C core clean">
    <branch repo="mafft" module="mafft-${version}-without-extensions-src.tgz"
            checkoutdir="mafft-${version}-without-extensions"
            version="7.182" size="389045"/>
  </custom>

<!--
install intltool libfontconfig1-dev libxrender-dev
(libxinerama-dev)
(glut.m4 wants libxmu-dev)
-->
  <repository type="tarball" name="mrc_coot"
              href="http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/"/>
  <custom id="coot-reference-structures"
          install_to="* share/coot/reference-structures/">
    <branch repo="mrc_coot" module="dependencies/reference-structures.tar.gz"
            version="0" size="6728787"/>
  </custom>
  <autotools id="guile-gui">
    <branch repo="mrc_coot" module="dependencies/guile-gui-0.3.tar.gz"
            version="0.3" size="68535"/>
    <dependencies>
      <dep package="guile-gtk"/>
    </dependencies>
  </autotools>

  <!-- not really needed, nor working -->
  <autotools id="greg">
    <branch repo="mrc_coot" module="dependencies/greg-2.0.0-pe.tar.gz"
            version="2.0.0" size="453770"/>
    <dependencies>
      <dep package="guile"/>
    </dependencies>
  </autotools>

  <autotools id="coot" autogen-sh="configure"
             autogenargs="--with-enhanced-ligand-tools --with-guile --with-python --with-pygtk --with-goocanvas-prefix=${prefix} --with-guile-gtk --includedir=${prefix}/include/coot RDKIT_CXXFLAGS=-I${prefix}/include/rdkit RDKIT_LIBS='-lDescriptors -lSubgraphs -lPartialCharges -lForceFieldHelpers -lForceField -lMolChemicalFeatures -lSubstructMatch -lOptimizer -lDepictor -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7' COOT_BUILD_INFO_STRING='CCP4, Oxfordshire'">
    <branch repo="mrc_coot"
            module="source/releases/coot-${version}.tar.gz"
            checkoutdir="coot-${version}" size="15772937" version="0.8.2">
      <patch file="coot-coot-in.patch" strip="0" />
      <patch file="coot-syminfo.patch" strip="0" />
      <patch file="coot-main-title.patch" strip="0"/>
      <patch file="coot-unfog-bitmap.patch" strip="0"/>
      <patch file="coot-rdkit-interface.patch" strip="1"/>
    </branch>
    <dependencies>
      <dep package="ssm"/>
      <!-- dep package="ccp4srs"/> coot w/ SRS crashes.
                       When ready, add -with-ccp4srs-prefix=${prefix}  -->
      <dep package="mmdb2"/>
      <dep package="clipper"/>
      <dep package="monomers"/>
      <dep package="coot-reference-structures"/>
      <dep package="curl"/>
      <dep package="gsl"/>
      <dep package="goocanvas"/>
      <dep package="libgnomecanvas"/>
      <dep package="pygtk"/>
      <dep package="librsvg"/>
      <dep package="gtkglext"/>
      <dep package="guile"/>
      <dep package="guile-gui"/>
      <dep package="guile-lib"/>
      <dep package="freeglut"/>
      <dep package="libglade"/>
      <dep package="rdkit"/>
      <dep package="sqlite3"/>
    </dependencies>
  </autotools>

  <!-- non-crystallographic dependencies -->

  <custom id="tcltk84" configure="true" install="${srcdir}/build.sh ${dest}"
          clean="rm -rf build/" supports-non-srcdir-builds="yes">
    <branch repo="files" module="tcltk++_${version}.tar.gz"
            version="8.4.20.3" size="17833192">
      <patch file="tcltk84-configure.patch" strip="0" />
    </branch>
  </custom>

  <repository type="tarball" name="cmake" href="http://www.cmake.org/files/"/>
  <autotools id="cmake"
             autogen-template="%(srcdir)s/bootstrap --prefix=%(prefix)s">
    <branch module="v3.1/cmake-${version}.tar.gz"
            repo="cmake" version="3.1.3" size="5959549">
    </branch>
  </autotools>

  <repository type="tarball" name="pkgconf"
               href="http://rabbit.dereferenced.org/~nenolod/distfiles/"/>
  <autotools id="pkgconf" autogenargs="--bindir=${prefix}/devbin">
    <branch repo="pkgconf" module="pkgconf-${version}.tar.gz"
            version="0.9.6" size="98886"/>
  </autotools>

  <repository type="tarball" name="nixos" href="http://nixos.org/releases/"/>
  <autotools id="patchelf" autogenargs="--bindir=${prefix}/devbin">
    <branch repo="nixos" module="patchelf/patchelf-0.8/patchelf-0.8.tar.gz"
            version="0.8" size="144271"/>
  </autotools>

  <autotools id="libgnurx">
    <branch repo="files" module="libgnurx-2.5.1.tar.gz"
            version="2.5.1" size="379950"/>
  </autotools>

  <repository type="tarball" name="tukaani" href="http://tukaani.org/"/>
  <autotools id="xz" autogen-sh="configure" autogenargs="--disable-rpath">
    <branch repo="tukaani" module="xz/xz-5.0.4.tar.gz"
            version="5.0.4" size="1281166">
    </branch>
  </autotools>

  <!-- we don't need python bindings, but -DRDK_BUILD_PYTHON_WRAPPERS=OFF
     prevents installing some headers that are included from other headers -->
  <cmake id="rdkit" cmakeargs="-DRDK_INSTALL_INTREE=OFF -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_BUILD_SLN_SUPPORT=OFF -DRDK_TEST_MMFF_COMPLIANCE=OFF -DRDK_BUILD_CPP_TESTS=OFF -DBoost_NO_SYSTEM_PATHS=ON -DBOOST_ROOT=${prefix}">
    <branch module="rdkit/rdkit/Q1_2015/RDKit_${version}.tgz"
            repo="sf" version="2015_03_1" size="24859988"
            checkoutdir="rdkit-Release_${version}">
      <patch file="rdkit-DebugTrace-mingw.patch" strip="0" />
    </branch>
    <dependencies>
      <dep package="boost"/>
      <dep package="numpy"/>
      <dep package="sqlite3"/>
    </dependencies>
  </cmake>


  <repository type="tarball" name="bitbucket" href="https://bitbucket.org/"/>
  <autotools id="libgd" autogen-sh="configure"
             autogenargs="--with-png --with-jpeg --with-freetype --without-tiff --without-xpm --bindir=${prefix}/devbin">
    <branch repo="bitbucket"
            module="libgd/gd-libgd/downloads/libgd-${version}.tar.bz2"
            checkoutdir="libgd-${version}"
            version="2.1.0" size="2275327">
    </branch>
    <dependencies>
      <dep package="libpng"/>
      <dep package="libjpeg"/>
    </dependencies>
    <after>
      <dep package="pkgconf"/>
      <dep package="freetype2"/>
    </after>
  </autotools>

  <repository type="tarball" name="sqlite" href="http://sqlite.org/"/>
  <autotools id="sqlite3"
     autogenargs="--bindir=${prefix}/devbin CFLAGS=&quot;$CFLAGS -DSQLITE_ENABLE_FTS3=1 -DSQLITE_ENABLE_COLUMN_METADATA=1 -DSQLITE_ENABLE_UNLOCK_NOTIFY=1 -DSQLITE_SECURE_DELETE=1&quot;">
    <branch repo="sqlite" module="2014/sqlite-autoconf-3080401.tar.gz"
            version="3.8.4.1" size="1937368"/>
  </autotools>

  <repository type="tarball" name="python"
              href="http://www.python.org/ftp/python/"/>
  <autotools id="python" autogenargs="--bindir=${prefix}/libexec">
    <pkg-config>python-2.7.pc</pkg-config>
    <branch module="2.7.10/Python-2.7.10.tgz"
            repo="python" version="2.7.10" size="16768806">
      <patch file="python-2.7.6-osx.patch" strip="0" />
    </branch>
    <dependencies>
      <dep package="zlib"/>
      <dep package="bzip2"/>
      <dep package="openssl"/>
      <dep package="sqlite3"/>
    </dependencies>
  </autotools>

  <cmake id="zlib">
    <!-- both dynamic and static libraries are built -->
    <pkg-config>zlib.pc</pkg-config>
    <branch repo="sf" module="libpng/zlib-1.2.8.tar.gz"
            version="1.2.8" size="571091"/>
  </cmake>

  <repository type="tarball" name="sbrabec"
              href="http://ftp.suse.com/pub/people/sbrabec/"/>
  <autotools id="bzip2" autogenargs="--bindir=${prefix}/devbin">
    <pkg-config>bzip2.pc</pkg-config>
    <!-- using autotool-ized tarball from Suse -->
    <branch repo="sbrabec" module="bzip2/tarballs/bzip2-1.0.6.0.1.tar.gz"
            version="1.0.6" size="1071724">
    </branch>
  </autotools>

  <repository type="tarball" name="openssl"
              href="http://www.openssl.org/source/"/>
  <custom id="openssl"
          configure="./config --prefix=${prefix} --openssldir=${prefix}/etc/openssl no-hw shared"
          build="make" clean="make clean"
          install="touch install_docs; make INSTALL_PREFIX=${destdir} install">
    <pkg-config>openssl.pc</pkg-config>
    <branch repo="openssl" module="openssl-${version}.tar.gz"
            version="1.0.1j" size="4432964">
     <patch file="openssl-ldflags.patch" strip="0" />
    </branch>
    <dependencies>
      <dep package="zlib"/>
    </dependencies>
  </custom>

  <repository type="tarball" name="curl" href="http://curl.haxx.se/download/"/>
  <autotools id="curl" autogenargs="--disable-manual --disable-ldap --bindir=${prefix}/devbin">
    <pkg-config>libcurl.pc</pkg-config>
    <branch module="curl-${version}.tar.gz"
            repo="curl" version="7.37.1" size="4076296">
     <patch file="curl-configure.patch" strip="0" />
    </branch>
    <dependencies>
      <dep package="openssl"/>
    </dependencies>
  </autotools>

  <repository type="tarball" name="gnu" href="ftp://ftp.gnu.org/"/>
  <!-- MINGW=true is a hack to link gsl with gslcblas and avoid problems
       when programs are linked with -as-needed -->
  <autotools id="gsl" autogenargs="MINGW=true">
    <pkg-config>gsl.pc</pkg-config>
    <branch repo="gnu" module="gnu/gsl/gsl-${version}.tar.gz"
            version="1.16" size="3534080"/>
  </autotools>

  <autotools id="guile-gtk" autogenargs="--without-glade --without-gtkgl">
    <branch repo="gnu" module="gnu/guile-gtk/guile-gtk-2.1.tar.gz"
            version="2.1" size="781985"/>
    <dependencies>
      <dep package="guile"/>
      <dep package="gtk2"/>
    </dependencies>
  </autotools>

  <repository type="tarball" name="gnome"
              href="http://ftp.gnome.org/pub/gnome/sources/"/>
  <autotools id="libgnomecanvas" autogen-sh="configure" autogenargs="">
    <pkg-config>libgnomecanvas-2.0.pc</pkg-config>
    <branch repo="gnome"
            module="libgnomecanvas/2.30/libgnomecanvas-${version}.tar.bz2"
            version="2.30.3" size="574139"/>
    <!--branch repo="gnome"
            module="libgnomecanvas/2.20/libgnomecanvas-${version}.tar.bz2"
            version="2.20.1" size="583613"/-->
    <dependencies>
      <dep package="gtk2"/>
      <dep package="libart_lgpl"/>
      <!--dep package="libglade"/-->
    </dependencies>
  </autotools>
  <autotools id="libart_lgpl" autogen-sh="configure" autogenargs="">
    <branch repo="gnome"
            module="libart_lgpl/2.3/libart_lgpl-${version}.tar.bz2"
            version="2.3.21" size="329102"/>
  </autotools>
  <autotools id="goocanvas" autogen-sh="configure" autogenargs=""
             makeargs="SUBDIRS=src"
             makeinstallargs="SUBDIRS=src install">
    <pkg-config>goocanvas.pc</pkg-config>
    <branch repo="gnome" module="goocanvas/1.0/goocanvas-1.0.0.tar.bz2"
            version="1.0.0" size="570552"/>
    <dependencies>
      <dep package="gtk2"/>
      <dep package="cairo"/>
    </dependencies>
  </autotools>
  <autotools id="pygtk" autogenargs="--without-glade">
    <branch repo="gnome" module="pygtk/2.24/pygtk-2.24.0.tar.bz2"
            version="2.24.0" size="2361097"/>
    <dependencies>
      <dep package="pygobject2"/>
      <dep package="py2cairo"/>
    </dependencies>
  </autotools>
  <autotools id="pygobject2" autogenargs="--disable-introspection">
    <branch repo="gnome" module="pygobject/2.28/pygobject-2.28.6.tar.bz2"
            version="2.28.6" size="888240"/>
    <dependencies>
      <dep package="glib"/>
      <dep package="py2cairo"/>
    </dependencies>
  </autotools>

  <repository type="tarball" name="cairo" href="http://cairographics.org/"/>
  <autotools id="cairo" autogen-sh="configure"
              autogenargs="--enable-xlib --disable-trace">
    <pkg-config>cairo.pc</pkg-config>
    <!--
    <branch repo="cairo" module="releases/cairo-1.8.10.tar.gz"
            version="1.8.10" size="7102657"/>
    -->
    <branch repo="cairo" module="releases/cairo-1.10.2.tar.gz"
            version="1.10.2" size="23558405"/>
    <dependencies>
      <dep package="pixman"/>
      <dep package="libpng"/>
    </dependencies>
    <after>
      <dep package="freetype2"/>
    </after>
  </autotools>
  <autotools id="pixman" autogen-sh="configure" autogenargs="--disable-gtk">
    <branch repo="cairo" module="releases/pixman-0.28.2.tar.gz"
            version="0.28.2" size="734094"/>
    <dependencies>
    </dependencies>
  </autotools>

  <autotools id="intltool" autogenargs="--bindir=${prefix}/devbin">
    <branch repo="lp" module="intltool/trunk/0.50.2/+download/intltool-${version}.tar.gz"
            version="0.50.2" size="189483"/>
  </autotools>

  <!-- only libintl.dylib is used by glib
       GCJ=none is set to avoid checking java and OSX popup  -->
  <autotools id="gettext"
   autogenargs="--bindir=${prefix}/devbin --disable-java --disable-libasprintf --disable-curses GCJ=none">
    <branch repo="gnu" module="pub/gnu/gettext/gettext-${version}.tar.gz"
            version="0.18.3.2" size="16189249"/>
  </autotools>

  <autotools id="py2cairo">
    <branch repo="cairo" module="releases/pycairo-1.2.2.tar.gz"
            version="1.2.2" size="482417">
    </branch>
    <dependencies>
      <dep package="cairo"/>
    </dependencies>
    <after>
      <dep package="python"/>
    </after>
  </autotools>

  <autotools id="glib" autogenargs="--disable-modular-tests --disable-selinux --disable-dtrace ac_cv_func_splice=no">
    <pkg-config>glib-2.0.pc</pkg-config>
    <branch repo="gnome" module="glib/2.34/glib-2.34.3.tar.xz"
            version="2.34.3" size="6334872">
      <patch file="glib-osx-gcc-fix.patch" strip="1" />
    </branch>
    <dependencies>
      <dep package="libffi"/>
      <dep package="gettext"/> <!-- skipped by default on non-OSX -->
    </dependencies>
  </autotools>

  <!-- ver. 3.1 has a new problem in libffi.pc.
       configure patch will stay anyway to avoid ../lib64 -->
  <repository type="tarball" name="sourceware"
              href="ftp://sourceware.org/pub/"/>
  <autotools id="libffi" autogenargs="--enable-portable-binary">
    <pkg-config>libffi.pc</pkg-config>
    <branch repo="sourceware" module="libffi/libffi-${version}.tar.gz"
            version="3.0.13" size="845747">
      <patch file="libffi-configure.patch" strip="1" />
      <patch file="libffi_intel_define.patch" strip="0" />
    </branch>
  </autotools>

  <!-- pango 1.23 requires fontconfig >= 2.5 (not on CentOS 5) -->
  <!-- with included-modules there is no need to call pango-querymodules -->
  <autotools id="pango" autogen-sh="configure"
             autogenargs="--disable-introspection --with-included-modules">
    <pkg-config>pango.pc</pkg-config>
    <branch repo="gnome" module="pango/1.22/pango-1.22.4.tar.bz2"
            version="1.22.4" size="1496168"/>
    <dependencies>
      <dep package="cairo"/>
      <dep package="glib"/>
      <!-- <dep package="harfbuzz"/> -->
    </dependencies>
  </autotools>
  <autotools id="pangox" autogen-sh="configure">
    <pkg-config>pangox.pc</pkg-config>
    <branch repo="gnome" module="pangox-compat/0.0/pangox-compat-0.0.2.tar.xz"
            version="0.0.2" size="267396"/>
    <dependencies>
      <dep package="pango"/>
    </dependencies>
  </autotools>

  <repository type="tarball" name="freedesktop"
               href="http://www.freedesktop.org/software/"/>
  <autotools id="harfbuzz" autogen-sh="configure">
    <pkg-config>harfbuzz.pc</pkg-config>
    <branch repo="freedesktop"
            module="harfbuzz/release/harfbuzz-0.9.16.tar.bz2"
            version="0.9.16" size="902208"/>
    <dependencies>
      <dep package="glib"/>
      <dep package="libicu"/>
    </dependencies>
  </autotools>
  <autotools id="fontconfig" autogen-sh="configure" autogenargs="">
    <pkg-config>fontconfig.pc</pkg-config>
    <branch repo="freedesktop" module="fontconfig/release/fontconfig-${version}.tar.gz"
            version="2.10.1" size="1700168"/>
    <dependencies>
      <!--<dep package="iconv"/>-->
      <!--<dep package="expat"/>-->
    </dependencies>
  </autotools>

  <repository type="tarball" name="icu"
              href="http://download.icu-project.org/files/"/>
  <autotools id="libicu" autogen-sh="source/configure"
             autogenargs="--disable-tests --disable-samples --disable-rpath">
    <pkg-config>icu-i18n.pc</pkg-config>
    <branch repo="icu" module="icu4c/51.1/icu4c-51_1-src.tgz"
            checkoutdir="libicu-51.1" version="51.1" size="21815174"/>
  </autotools>

  <autotools id="gdk-pixbuf" autogen-sh="configure"
             autogenargs="--disable-introspection --without-libtiff --disable-rpath --disable-glibtest --disable-nls --with-included-loaders=png --disable-gio-sniffing">
    <branch repo="gnome" module="gdk-pixbuf/2.28/gdk-pixbuf-2.28.1.tar.xz"
            version="2.28.1" size="1191084">
      <patch file="gdk-pixbuf-hack.patch" strip="0" />
    </branch>
    <dependencies>
      <dep package="libpng"/>
      <dep package="libjpeg"/>
      <dep package="glib"/>
    </dependencies>
  </autotools>

  <autotools id="librsvg" autogen-sh="configure"
             autogenargs="--disable-introspection --disable-gtk-theme --disable-tools --disable-vala">
    <!--
    <branch repo="gnome" module="librsvg/2.36/librsvg-${version}.tar.xz"
            version="2.36.4" size="513028"/>
    -->
    <branch repo="gnome" module="librsvg/2.32/librsvg-2.32.1.tar.bz2"
            version="2.32.1" size="517170"/>
    <dependencies>
      <dep package="gdk-pixbuf"/>
      <dep package="libcroco"/>
    </dependencies>
  </autotools>
  <autotools id="libcroco" autogen-sh="configure"
             autogenargs="--enable-Bsymbolic=auto">
    <branch repo="gnome" module="libcroco/0.6/libcroco-0.6.8.tar.xz"
            version="0.6.8" size="464992"/>
    <dependencies>
      <dep package="glib"/>
      <dep package="libxml2"/>
      <dep package="pango"/>
    </dependencies>
  </autotools>

  <autotools id="atk" autogen-sh="configure"
             autogenargs="--disable-introspection --disable-glibtest">
    <branch repo="gnome" module="atk/2.8/atk-2.8.0.tar.xz"
            version="2.8.0" size="634052"/>
    <dependencies>
      <dep package="glib"/>
    </dependencies>
  </autotools>

  <autotools id="gtk2" autogen-sh="configure"
             autogenargs="--disable-visibility --disable-introspection --disable-glibtest --disable-cups --disable-papi --with-included-immodules">
    <branch repo="gnome" module="gtk+/2.24/gtk+-2.24.23.tar.xz"
            version="2.24.23" size="13316276"/>
    <dependencies>
      <dep package="glib"/>
      <dep package="cairo"/>
      <dep package="pango"/>
      <dep package="atk"/>
      <dep package="gdk-pixbuf"/>
    </dependencies>
  </autotools>

  <autotools id="gtkglext" autogen-sh="configure"
             autogenargs="--disable-introspection --disable-glibtest">
    <branch repo="gnome" module="gtkglext/1.2/gtkglext-1.2.0.tar.bz2"
            version="1.2.0" size="703821">
      <patch file="gtkglext-1.2.0-bz677457.diff" strip="1" />
    </branch>
    <dependencies>
      <dep package="gtk2"/>
      <dep package="pangox"/>
    </dependencies>
  </autotools>

  <autotools id="libglade"
     autogenargs="--disable-gtktest CPPFLAGS=&quot;$CPPFLAGS -UG_DISABLE_DEPRECATED&quot; --with-xml-catalog=/dev/null">
    <pkg-config>libglade-2.0.pc</pkg-config>
    <branch repo="gnome" module="libglade/2.6/libglade-2.6.4.tar.bz2"
            version="2.6.4" size="356119"/>
    <dependencies>
      <dep package="gtk2"/>
      <dep package="gdk-pixbuf"/>
      <dep package="libxml2"/>
    </dependencies>
  </autotools>

  <autotools id="guile" autogenargs="--disable-rpath --disable-error-on-warning">
    <branch repo="gnu" module="gnu/guile/guile-1.8.8.tar.gz"
            version="1.8.8" size="3956654">
      <patch file="guile-configure.patch" strip="0"/>
      <patch file="guile-fink.patch" strip="1"/>
    </branch>
    <dependencies>
      <dep package="libtool"/>
      <dep package="gmp"/>
      <dep package="readline"/>
    </dependencies>
  </autotools>
  <autotools id="gmp" autogenargs="--disable-assembly">
    <branch repo="gnu" module="gnu/gmp/gmp-5.1.1.tar.bz2"
            version="5.1.1" size="2213841"/>
  </autotools>
  <autotools id="libtool" autogenargs="">
    <branch repo="gnu" module="gnu/libtool/libtool-2.4.tar.gz"
            version="2.4" size="2580417"/>
  </autotools>
  <autotools id="readline" autogenargs="">
    <branch repo="gnu" module="gnu/readline/readline-${version}.tar.gz"
            version="6.3" size="2468560">
      <patch file="readline-shobj-conf.patch" strip="0"/>
    </branch>
  </autotools>

  <repository type="tarball" name="savannah"
              href="http://download.savannah.gnu.org/releases/"/>
  <autotools id="guile-lib">
    <branch repo="savannah" module="guile-lib/guile-lib-0.2.2.tar.gz"
            version="0.2.2" size="476723"/>
    <dependencies>
      <dep package="guile"/>
    </dependencies>
  </autotools>

  <autotools id="freetype2">
    <pkg-config>freetype2.pc</pkg-config>
    <branch repo="savannah" module="freetype/freetype-${version}.tar.bz2"
            version="2.5.3" size="1703842"/>
  </autotools>

  <repository type="tarball" name="pypi"
              href="https://pypi.python.org/packages/source/"/>
  <distutils id="setuptools" installargs="--install-scripts=${prefix}/libexec">
    <branch repo="pypi" module="s/setuptools/setuptools-${version}.tar.gz"
            version="2.0" size="783643" />
    <dependencies/>
    <after>
      <dep package="python"/>
    </after>
  </distutils>
  <distutils id="pip" installargs="--install-scripts=${prefix}/libexec">
    <branch repo="pypi" module="p/pip/pip-${version}.tar.gz"
            version="1.5.6" size="938120" />
    <dependencies/>
    <after>
      <dep package="python"/>
    </after>
  </distutils>

  <distutils id="numpy">
    <branch repo="pypi" module="n/numpy/numpy-${version}.tar.gz"
            version="1.8.2" size="3792998">
      <patch file="numpy-intelcompiler.patch" strip="0"/>
    </branch>
    <dependencies>
      <dep package="lapack"/>
    </dependencies>
    <after>
      <dep package="python"/>
    </after>
  </distutils>


  <!--osx intel <distutils id="scipy" buildargs="\-\-compiler=intelem \-\-fcompiler=intelem" > -->
  <distutils id="scipy">
    <branch repo="pypi" module="s/scipy/scipy-${version}.tar.gz"
            version="0.16.0" size="18137295" />
    <dependencies>
      <dep package="numpy"/>
    </dependencies>
  </distutils>

  <distutils id="biopython">
    <branch repo="pypi" module="b/biopython/biopython-${version}.tar.gz"
            version="1.64" size="11671556" />
    <dependencies>
      <dep package="numpy"/>
    </dependencies>
  </distutils>

<!--
  <distutils id="docutils">
    <branch repo="pypi" module="d/docutils/docutils-${version}.tar.gz"
            version="0.12" size="3792998" />
    <after>
      <dep package="python"/>
    </after>
  </distutils>

  <distutils id="ipython">
    <branch repo="pypi" module="i/ipython/ipython-${version}.tar.gz"
            version="2.1.0" size="3792998" />
    <after>
      <dep package="python"/>
    </after>
  </distutils>

  <distutils id="pyopengl">
    <branch repo="pypi" module="p/pyopengl/PyOpenGL-${version}.tar.gz"
            version="3.1.0" size="3792998" />
    <after>
      <dep package="python"/>
    </after>
  </distutils>

  <distutils id="numpydoc">
    <branch repo="pypi" module="n/numpydoc/numpydoc-${version}.tar.gz"
            version="0.5" size="3792998" />
    <after>
      <dep package="python"/>
    </after>
  </distutils>

  <distutils id="reportlab">
    <branch repo="pypi" module="r/reportlab/reportlab-${version}.tar.gz"
            version="2.6" size="3792998" />
    <after>
      <dep package="python"/>
    </after>
  </distutils>

  <distutils id="send2trash">
    <branch repo="pypi" module="s/Send2Trash/Send2Trash-${version}.tar.gz"
            version="1.3.0" size="3792998" />
    <after>
      <dep package="python"/>
    </after>
  </distutils>

  <distutils id="sphinx">
    <branch repo="pypi" module="s/sphinx/Sphinx-${version}.tar.gz"
            version="1.2.2" size="3792998" />
    <dependencies>
      <dep package="numpydoc"/>
    </dependencies>
    <after>
      <dep package="python"/>
    </after>
  </distutils>
-->

  <distutils id="pycrypto">
    <branch repo="pypi" module="p/pycrypto/pycrypto-${version}.tar.gz"
            version="2.6.1" size="446240" />
    <dependencies>
      <dep package="gmp"/>
    </dependencies>
    <after>
      <dep package="python"/>
    </after>
  </distutils>

  <distutils id="pillow">
    <branch repo="pypi" module="P/Pillow/Pillow-${version}.tar.gz"
            version="2.6.1" size="7321920" />
    <dependencies>
      <dep package="libjpeg"/>
      <dep package="zlib"/>
      <dep package="tiff"/>
    </dependencies>
    <after>
      <dep package="python"/>
      <dep package="setuptools"/>
    </after>
  </distutils>

  <distutils id="paramiko">
    <branch repo="pypi" module="p/paramiko/paramiko-${version}.tar.gz"
            version="1.15.2" size="1220578" />
    <dependencies>
      <dep package="pycrypto"/>
    </dependencies>
  </distutils>

  <distutils id="python-dateutil">
    <branch repo="pypi" module="p/python-dateutil/python-dateutil-1.5.tar.gz"
            version="1.5.0" size="233747" />
    <dependencies/>
    <after>
      <dep package="python"/>
    </after>
  </distutils>

  <distutils id="pyparsing">
    <branch repo="pypi" module="p/pyparsing/pyparsing-2.0.1.tar.gz"
            version="2.0.1" size="1129563" />
    <dependencies/>
    <after>
      <dep package="python"/>
    </after>
  </distutils>

  <distutils id="matplotlib">
    <!-- matplotlib 1.4 requires freetype2 2.4+, on RHEL5 it's 2.2.1 -->
    <branch repo="pypi" module="m/matplotlib/matplotlib-${version}.tar.gz"
            version="1.3.1" size="42702580">
      <patch file="matplotlib-setup-cfg.patch" strip="0"/>
    </branch>
    <dependencies>
       <dep package="numpy"/>
       <dep package="python-dateutil"/>
       <dep package="pyparsing"/>
       <dep package="libpng"/>
       <dep package="pyqt4"/>
    </dependencies>
    <after>
      <dep package="python"/>
    </after>
  </distutils>

  <repository type="tarball" name="lp" href="https://launchpad.net/"/>
  <distutils id="bzr" installargs="--install-scripts=${prefix}/libexec">
    <branch repo="lp" module="bzr/2.6/2.6.0/+download/bzr-2.6.0.tar.gz"
            version="2.6.0" size="11301124" />
    <after>
      <dep package="python"/>
    </after>
  </distutils>

  <repository type="tarball" name="hdf5" href="http://www.hdfgroup.org/ftp/"/>
  <cmake id="hdf5"
      cmakeargs="-DBUILD_TESTING=OFF -DHDF5_BUILD_EXAMPLES=OFF -DHDF5_BUILD_TOOLS=OFF -DHDF5_BUILD_CPP_LIB=OFF -DHDF5_BUILD_HL_LIB=OFF -DHDF5_INSTALL_DATA_DIR=share/hdf5 -DHDF5_INSTALL_CMAKE_DIR=share/cmake">
    <branch repo="hdf5"
            module="HDF5/releases/hdf5-${version}/src/hdf5-${version}.tar.gz"
            version="1.8.15-patch1" size="12244820"/>
    <dependencies>
      <dep package="zlib"/>
    </dependencies>
  </cmake>

  <distutils id="h5py">
    <branch repo="pypi" module="h/h5py/h5py-${version}.tar.gz"
            version="2.3.1" size="1072766"/>
    <dependencies>
      <dep package="hdf5"/>
      <dep package="numpy"/>
    </dependencies>
  </distutils>

  <distutils id="ecdsa">
    <branch repo="pypi" module="e/ecdsa/ecdsa-${version}.tar.gz"
            version="0.13" size="55579"/>
    <dependencies/>
  </distutils>

  <repository type="tarball" name="xmlsoft.org" href="ftp://xmlsoft.org/"/>
  <autotools id="libxml2" autogenargs="--without-python --without-threads --with-zlib --bindir=${prefix}/devbin">
    <pkg-config>libxml-2.0.pc</pkg-config>
    <branch module="libxml2/libxml2-${version}.tar.gz"
            repo="xmlsoft.org" version="2.9.1" size="5172503"/>
    <dependencies>
      <dep package="zlib"/>
    </dependencies>
  </autotools>
  <!-- on Windows patched using: mingw32-libxslt-use-correct-mkdir.patch -->
  <autotools id="libxslt" autogenargs="--without-python --without-crypto --bindir=${prefix}/devbin">
    <pkg-config>libxslt.pc</pkg-config>
    <branch module="libxml2/libxslt-${version}.tar.gz"
            repo="xmlsoft.org" version="1.1.28" size="3435907"/>
    <dependencies>
      <dep package="libxml2"/>
    </dependencies>
  </autotools>

  <repository type="tarball" name="gc"
              href="http://www.hboehm.info/gc/gc_source/"/>
  <autotools id="gc" autogen-sh="configure"
             autogenargs="--disable-threads --enable-cplusplus">
    <branch module="gc-7.2e.tar.gz"
            repo="gc" version="7.2e" checkoutdir="gc-7.2e" size="1291186"/>
  </autotools>

  <repository type="tarball" name="lapack_site"
              href="http://www.netlib.org/lapack/"/>
  <cmake id="lapack" cmakeargs="-DBUILD_TESTING=OFF">
    <branch repo="lapack_site" version="3.5.0" module="lapack-${version}.tgz"
            size="6313139"/>
  </cmake>

  <!-- compile in-source, otherwise fftw.h in srcdir is not modified by
       configure; since the source could be already built by different
       compiler we run make clean first (and -j1 to prevent clean and make
       running in parallel -->
  <repository type="tarball" name="fftw_site" href="http://www.fftw.org/"/>
  <autotools id="fftw2" autogenargs="--enable-float"
             supports-non-srcdir-builds="no" makeargs="-j1 clean all">
    <branch repo="fftw_site" module="fftw-2.1.5.tar.gz"
            version="2.1.5" size="1256888">
      <patch file="fftw2-configure.patch" strip="0" />
    </branch>
  </autotools>

  <repository type="tarball" name="jpeg" href="http://www.ijg.org/files/"/>
  <autotools id="libjpeg" autogenargs="--bindir=${prefix}/devbin">
    <branch repo="jpeg" module="jpegsrc.v8d.tar.gz" version="8d" size="991456"
            checkoutdir="jpeg-8d"/>
  </autotools>

  <autotools id="libpng" autogenargs="--bindir=${prefix}/devbin">
    <pkg-config>libpng.pc</pkg-config>
    <branch repo="sf" module="libpng/libpng-${version}.tar.gz"
            version="1.6.12" size="1354223"/>
    <dependencies>
      <dep package="zlib"/>
    </dependencies>
  </autotools>

  <autotools id="freeglut" autogenargs="">
    <branch repo="sf" module="freeglut/freeglut-2.8.1.tar.gz"
            version="2.8.1" size="1005343">
      <patch file="freeglut-smooth_opengl3.patch" strip="0" />
      <patch file="freeglut-strokechar.patch" strip="0" />
    </branch>
    <dependencies>
    </dependencies>
  </autotools>

  <custom id="boost"
          configure="./bootstrap.sh --with-libraries=chrono,date_time,filesystem,iostreams,program_options,thread,system,python"
          build="./b2 -q -d+2 -sNO_BZIP2=1 --layout=system variant=release link=shared linkflags=&quot;${LDFLAGS}&quot; stage"
          install="./b2 -q -d+2 -sNO_BZIP2=1 --layout=system variant=release link=shared linkflags=&quot;${LDFLAGS}&quot; install --prefix=${dest}"
          clean="./b2 --clean-all">
    <branch repo="sf" module="boost/boost/1.56.0/boost_1_56_0.tar.gz"
            version="1.56.0" size="119485170">
      <patch file="boost-boot.patch" strip="0" />
    </branch>
    <dependencies>
      <dep package="zlib"/>
    </dependencies>
  </custom>

  <repository type="tarball" name="tiff" href="ftp://ftp.remotesensing.org"/>
  <autotools id="tiff" autogenargs="--disable-lzma"
             makeargs="SUBDIRS='port libtiff'"
             makeinstallargs="SUBDIRS='port libtiff' install">
   <branch repo="tiff" module="libtiff/tiff-4.0.3.tar.gz"
            version="4.0.3" size="2051630"/>
   <pkg-config>libtiff-4.pc</pkg-config>
   <dependencies>
     <dep package="zlib"/>
     <dep package="libjpeg"/>
   </dependencies>
  </autotools>

  <!-- sdr files in the tarball have \r\n line endings and don't work on Unix,
       they are regenerated after installation (triggers/pixie.trigger).
       $PIXIEHOME is respected only on OSX, on Linux $SHADERS and $DISPLAY
       need to be set.
  -->
  <autotools id="pixie"
             autogenargs="--bindir=${prefix}/libexec --disable-selfcontained"
             supports-non-srcdir-builds="no">
    <branch repo="sf" module="pixie/Pixie-src-2.2.6.tgz"
            checkoutdir="Pixie-2.2.6" version="2.2.6" size="9993504">
      <patch file="pixie-2.2.6-zlib-1.2.5.2.patch" strip="0"/>
      <patch file="pixie-generated.patch" strip="0"/>
    </branch>
    <dependencies>
      <dep package="tiff"/>
    </dependencies>
  </autotools>

  <!--
  on Linux qt4 compilation requires dev files for fontconfig and xrender
  -->
  <repository type="tarball" name="qt4"
              href="http://download.qt-project.org/archive/qt/4.8/"/>
  <!-- the first lines (before -release) are unix-specific -->
  <custom id="qt4"
   configure="${srcdir}/configure -prefix ${prefix} -bindir ${prefix}/devbin
   -plugindir ${libdir}/qt4/plugins
   -no-sse3 -no-ssse3 -no-sse4.1 -no-sse4.2 -no-avx
   -fontconfig -opengl -no-sm -no-xshape -no-xvideo
   -release -opensource -xmlpatterns
   -no-3dnow -no-neon
   -no-sql-sqlite -no-qt3support -qt-libmng
   -no-phonon -no-phonon-backend -no-multimedia
   -no-audio-backend -webkit -no-declarative -no-declarative-debug
   -no-scripttools
   -no-cups -no-openvg
   -no-s60 -nomake examples -nomake demos -nomake tools -confirm-license"
   build="${}" install="make INSTALL_ROOT=${destdir} install" clean="${}"
   supports-non-srcdir-builds="yes">
    <branch repo="qt4" module="4.8.6/qt-everywhere-opensource-src-4.8.6.tar.gz"
            version="4.8.6" size="241623667"/>
    <dependencies>
      <dep package="zlib"/>
      <dep package="libpng"/>
      <dep package="libjpeg"/>
      <dep package="openssl"/>
      <dep package="tiff"/>
    </dependencies>
    <after> <!-- on Linux it may use glib -->
      <dep package="glib"/>
    </after>
  </custom>

  <custom id="sip" configure="python ${srcdir}/configure.py --bindir=${prefix}/devbin --destdir=${prefix}/lib/python2.7/site-packages --incdir=${prefix}/include --sipdir=${prefix}/share/sip LFLAGS+=&quot;${LDFLAGS}&quot;"
          build="${}" install="${}" clean="${}"
          supports-non-srcdir-builds="no">
    <branch repo="sf" module="pyqt/sip/sip-${version}/sip-${version}.tar.gz"
            version="4.16.3" size="794305"/>
    <after>
      <dep package="python"/>
    </after>
  </custom>

  <custom id="pyqt4"
          configure="python ${srcdir}/configure.py --confirm-license --no-designer-plugin --no-qsci-api -e QtCore -e QtGui -e QtNetwork -e QtScript -e QtXml -e QtOpenGL -e QtSql -e QtSvg -e QtTest -e QtWebKit -e QtXmlPatterns --bindir=${prefix}/devbin --destdir=${prefix}/lib/python2.7/site-packages --sipdir=${prefix}/share/sip LFLAGS+=&quot;${LDFLAGS}&quot;"
          build="${}" install="${} INSTALL_ROOT=${destdir}" clean="${}"
          supports-non-srcdir-builds="yes">
    <!-- no real differences between PyQt-mac and PyQt-x11, only differences
         in doc/html/ and in comments in sip/ -->
    <branch repo="sf"
            module="pyqt/PyQt4/PyQt-${version}/PyQt-x11-gpl-${version}.tar.gz"
            version="4.11.2" size="11120742"/>
    <dependencies>
      <dep package="sip"/>
    </dependencies>
    <after>
      <dep package="qt4"/>
    </after>
  </custom>

  <distutils id="suds">
    <branch repo="pypi" module="s/suds/suds-${version}.tar.gz"
            version="0.4" size="104013"/>
    <dependencies/>
    <after>
      <dep package="python"/>
      <dep package="setuptools"/>
    </after>
  </distutils>

  <distutils id="psutil">
    <branch repo="pypi" module="p/psutil/psutil-${version}.tar.gz"
            version="3.2.2" size="253502"/>
    <dependencies/>
    <after>
      <dep package="python"/>
      <dep package="setuptools"/>
    </after>
  </distutils>

  <distutils id="lxml">
    <branch repo="pypi" module="l/lxml/lxml-${version}.tar.gz"
            version="3.2.4" size="3347893"/>
    <dependencies>
      <dep package="libxml2"/>
      <dep package="libxslt"/>
    </dependencies>
    <after>
      <dep package="python"/>
      <dep package="setuptools"/>
    </after>
  </distutils>

  <repository type="tarball" name="raster3d"
              href="http://skuld.bmsc.washington.edu/raster3d/"/>
  <cmake id="raster3d">
    <branch repo="raster3d" module="Raster3D_${version}.tar.gz" version="3.0-3">
      <patch file="raster3d-cmake.patch" strip="1" />
    </branch>
    <dependencies>
      <dep package="libgd"/>
    </dependencies>
  </cmake>

  <cmake id="plplot" cmakeargs="-DENABLE_DYNDRIVERS=0 -DDEFAULT_NO_BINDINGS=1 -DHAVE_QHULL=0 -DWITH_CSA=0 -DDEFAULT_NO_DEVICES=1 -DPLD_png=1">
    <branch repo="sf"
            module="plplot/plplot/${version}%20Source/plplot-${version}.tar.gz"
            version="5.11.0" size="15892751">
      <patch file="plplot-home-env.patch" strip="0" />
    </branch>
    <dependencies>
      <dep package="libgd"/>
    </dependencies>
  </cmake>

  <cmake id="macapp">
    <branch/>
  </cmake>

  <!--osx intel <autotools id="wxwidgets" autogenargs=" /-/-enable-unicode /-/-with-osx_cocoa /-/-with-opengl /-/-enable-sound /-/-enable-graphics_ctx /-/-disable-mediactrl /-/-enable-display /-/-enable-geometry /-/-enable-debug_flag /-/-enable-optimise /-/-disable-debugreport /-/-enable-uiactionsim /-/-enable-monolithic /-/-disable-precomp-headers "> -->

  <autotools id="wxwidgets" autogenargs=" --enable-unicode --with-opengl --enable-sound --enable-graphics_ctx --disable-mediactrl --enable-display --enable-geometry --enable-debug_flag --enable-optimise --disable-debugreport --enable-uiactionsim --enable-monolithic ">
    <branch repo="sf" module="wxpython/wxPython-src-${version}.tar.bz2"
            version="3.0.2.0" size="58304944">
       <patch file="wxpython-init.patch" strip="0" />
       <patch file="wxpython-build.patch" strip="0" />
       <patch file="wxPython-3.0.2.0-plot.patch" strip="1"/>
    </branch>
  </autotools>

  <!--osx intel <custom id="wxpython"
          build="python ${srcdir}/wxPython/build-wxpython.py  /-/-prefix=${prefix} /-/-wxpy_installdir=${prefix} /-/-installdir=${prefix} /-/-no_wxbuild /-/-osx_cocoa "
          install="python ${srcdir}/wxPython/build-wxpython.py /-/-prefix=${prefix} /-/-install /-/-no_wxbuild /-/-osx_cocoa" clean="python ${srcdir}/build-wxpython.py /-/-clean"
          supports-non-srcdir-builds="no"> -->
  <custom id="wxpython"
          build="python ${srcdir}/wxPython/build-wxpython.py  --prefix=${prefix} --wxpy_installdir=${prefix} --installdir=${prefix} --no_wxbuild "
          install="python ${srcdir}/wxPython/build-wxpython.py --prefix=${prefix} --install --no_wxbuild " clean="python ${srcdir}/build-wxpython.py --clean"
          supports-non-srcdir-builds="no"> -->
    <branch repo="sf" module="wxpython/wxPython-src-${version}.tar.bz2"
            version="3.0.2.0" size="58304944">
       <patch file="wxpython-init.patch" strip="0" />
       <patch file="wxpython-build.patch" strip="0" />
       <patch file="wxPython-3.0.2.0-plot.patch" strip="1"/>
    </branch>
    <dependencies>
      <dep package="wxwidgets"/>
    </dependencies>
  </custom>

  <cmake id="probe">
    <branch repo="github-zip"
        module="rlabduke/probe/archive/${version}.zip"
        version="acc7f517c3e3830b2489f71cbc53049399f86909"
        checkoutdir="probe-${version}">
      <patch file="probe-cmake.patch" strip="0" />
    </branch>
  </cmake>

  <cmake id="reduce">
    <branch repo="github-zip"
        module="rlabduke/reduce/archive/${version}.zip"
        version="9fb41bbc04a2b611832231fcfc7ab8f670083bef"
        checkoutdir="reduce-${version}">
      <patch file="reduce-cmake.patch" strip="0" />
    </branch>
  </cmake>

<!--
  <custom id="arcimboldo" install_to="bin/* bin/, arcimboldo lib/py2/">
    <branch repo="files" version="3.0.1-test1"
            module="arcimboldo-${version}.tar.gz"/>
-->
  <cmake id="arcimboldo">
    <branch/>
    <dependencies>
      <dep package="scipy"/>
      <dep package="biopython"/>
      <dep package="matplotlib"/>
      <dep package="paramiko"/>
      <dep package="ecdsa"/>
    </dependencies>
  </cmake>

  <cmake id="lorestr">
    <branch/>
    <dependencies />
  </cmake>

  <metamodule id="default">
    <dependencies>
      <dep package="ccp4-base"/>
      <dep package="ccp4-lib-data"/>
      <dep package="mmdb2"/>
      <dep package="ccif"/>
      <dep package="libccp4"/>
      <dep package="ssm"/>
      <dep package="ccp4srs"/>
      <dep package="gesamt"/>
      <dep package="molrep"/>
      <dep package="sfcheck"/>
      <dep package="procheck"/>
      <dep package="scala"/>
      <dep package="dm21"/>
      <dep package="refmac"/>
      <dep package="monomers"/>
      <dep package="ccp4-progs"/>
      <dep package="ccp4i"/>
      <dep package="imosflm"/>
      <dep package="clipper"/>
      <dep package="pointless"/>
      <dep package="aimless"/>
      <dep package="feckless"/>
      <dep package="clipper-progs"/>
      <dep package="cprodrg"/>
      <dep package="prosmart"/>
      <dep package="crank"/>
      <dep package="crank2"/>
      <dep package="examples"/>
      <dep package="documentation"/>
      <dep package="ccp4dispatchers"/>
      <!--<dep package="xia2"/> -->
      <dep package="edstats"/>
      <dep package="dimple"/>
      <dep package="mrbump"/>
      <dep package="tgutils"/>
      <dep package="spicker"/>
      <dep package="prelyscar"/>
      <dep package="theseus"/>
      <!-- may depend on Tcl -->
      <dep package="diff-image"/>
      <dep package="ccp4mapwish"/>
      <!-- requires javac -->
      <dep package="jligand"/>
      <!-- pulls libxml, gc -->
      <dep package="rapper"/>
      <!-- requires Qt, OpenGL -->
      <dep package="pisa"/>
      <dep package="viewhkl"/>
      <dep package="qtrview"/>
      <!-- for now Ample is tested/working only on Unix -->
      <dep package="ample"/>
      <dep package="raster3d"/>
      <dep package="xssp"/>
      <dep package="blend"/>
      <dep package="acedrg"/>
      <dep package="libg"/>
      <dep package="privateer"/>
      <dep package="clustalw2"/>
      <dep package="mafft"/>
      <dep package="hmmer"/>
      <dep package="ccp4mg"/>
      <dep package="biopython"/>
      <dep package="jsrview"/>
      <dep package="clipper-python"/>
      <dep package="ccp4srs-python"/>
      <dep package="ccp4i2"/>
      <dep package="probe"/>
      <dep package="reduce"/>
    </dependencies>
  </metamodule>

  <metamodule id="ccp4-linux"> <!-- for Linux binaries  -->
    <dependencies>
      <dep package="default"/>
      <dep package="tcltk84"/>
      <dep package="hklview"/>
      <dep package="rotgen"/>
      <dep package="mosflm"/>
      <dep package="chooch"/>
      <dep package="pdb-extract"/>
      <dep package="arcimboldo"/>
      <dep package="lorestr"/>
    </dependencies>
  </metamodule>

  <metamodule id="ccp4-osx"> <!-- for OSX binaries  -->
    <dependencies>
      <dep package="pkgconf"/>
      <dep package="freetype2"/>
      <dep package="default"/>
      <dep package="tcltk84"/>
      <dep package="hklview"/>
      <dep package="rotgen"/>
      <dep package="mosflm"/>
      <dep package="chooch"/>
      <dep package="pdb-extract"/>
      <dep package="arcimboldo"/>
      <dep package="lorestr"/>
    </dependencies>
  </metamodule>

  <metamodule id="coot-osx"> <!-- extra for coot on os x -->
    <dependencies>
      <dep package="pkgconf"/>
      <dep package="freetype2"/>
      <dep package="intltool"/>
      <!--<dep package="gettext"/>-->
      <!--<dep package="fontconfig"/>-->
      <!--<dep package="readline"/>-->
      <dep package="coot"/>
    </dependencies>
    <after>
      <dep package="python"/>
    </after>
  </metamodule>

  <metamodule id="ccp4-windows"> <!-- for Windows -->
    <dependencies>
      <dep package="pkgconf"/>
      <dep package="libgnurx"/>
      <dep package="freetype2"/>
      <dep package="default"/>
    </dependencies>
  </metamodule>

  <metamodule id="balbes">
    <dependencies>
      <dep package="balbes-pipeline"/>
      <dep package="balbesdb"/>
    </dependencies>
  </metamodule>

  <metamodule id="all-sources"> <!-- sources for ccp4 source bundle -->
    <dependencies>
      <dep package="ccp4-linux"/>
      <dep package="ccp4-windows"/>
      <dep package="ccp4-osx"/>
      <dep package="ccp4-deprecated"/>
      <!-- <dep package="setup"/> -->
      <dep package="devtools"/>
      <dep package="python"/>
      <dep package="setuptools"/>
      <dep package="pip"/>
      <dep package="pillow"/>
      <dep package="wxwidgets"/>
      <dep package="bzr"/>
      <dep package="cmake"/>
      <dep package="coot"/>
    </dependencies>
  </metamodule>

</moduleset>
<!-- vim:set ts=2 sw=2 expandtab: -->
