Pelahi generic cyg update

generic/ant.cyg

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+##############################################################################
+# maali cygnet file for ant
+##############################################################################
+
+read -r -d '' MAALI_MODULE_WHATIS << EOF
+
+Apache Ant is a Java library and command-line tool whose mission is to drive
+processes described in build files as targets and extension points dependent
+upon each other. The main known usage of Ant is the build of Java applications.
+Ant supplies a number of built-in tasks allowing to compile, assemble, test and
+run Java applications. Ant can also be used effectively to build non Java
+applications, for instance C or C++ applications. More generally, Ant can be
+used to pilot any type of process which can be described in terms of targets
+and tasks.
+
+For further information see http://ant.apache.org/
+
+EOF
+
+# specify which compilers we want to build the tool with
+MAALI_TOOL_COMPILERS="binary"
+
+# URL to download the source code from
+MAALI_URL="http://archive.apache.org/dist/ant/binaries/apache-ant-$MAALI_TOOL_VERSION-bin.tar.gz"
+
+# location we are downloading the source code to
+MAALI_DST="$MAALI_SRC/apache-$MAALI_TOOL_NAME-$MAALI_TOOL_VERSION-bin.tar.gz"
+
+# where the unpacked source code is located
+MAALI_TOOL_BUILD_DIR=""
+
+# type of tool (eg. apps, devel, python, etc.)
+MAALI_TOOL_TYPE="devel"
+
+# tool pre-requisites
+MAALI_TOOL_PREREQ="java/8u202"
+
+# for auto-building module files
+MAALI_MODULE_SET_PATH=1
+
+##############################################################################
+
+function maali_unpack {
+  maali_wiki ".. supressing unpacking apache ant"
+}
+
+##############################################################################
+
+function maali_build {
+  cd $MAALI_INSTALL_DIR
+  cd ..
+  rmdir $MAALI_INSTALL_DIR
+  maali_run "tar zxf $MAALI_DST"
+  mv apache-$MAALI_TOOL_NAME-$MAALI_TOOL_VERSION $MAALI_INSTALL_DIR
+}
+
+##############################################################################

generic/apr-util.cyg

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+##############################################################################
+# maali cygnet file for xerces-c 
+##############################################################################
+
+# specify which compilers we want to build the tool with
+MAALI_TOOL_COMPILERS="$MAALI_DEFAULT_COMPILERS"
+
+# URL to download the source code from
+MAALI_URL="https://www.strategylions.com.au/mirror//apr/apr-util-${MAALI_TOOL_VERSION}.tar.gz"
+
+# location we are downloading the source code to
+MAALI_DST="${MAALI_SRC}/${MAALI_TOOL_NAME}-${MAALI_TOOL_VERSION}.tar.gz"
+
+# where the unpacked source code is located
+MAALI_TOOL_BUILD_DIR="${MAALI_BUILD_DIR}/${MAALI_TOOL_NAME}-${MAALI_TOOL_VERSION}"
+
+# type of tool (eg. apps, devel, python, etc.)
+MAALI_TOOL_TYPE="devel"
+
+MAALI_TOOL_PREREQ="apr"
+
+MAALI_TOOL_CONFIGURE='--with-apr=${MAALI_APR_HOME}'
+
+# for auto-building module files
+MAALI_MODULE_SET_PATH=1
+MAALI_MODULE_SET_LD_LIBRARY_PATH=1
+MAALI_MODULE_SET_PKG_CONFIG_PATH=1
+MAALI_MODULE_SET_CPATH=1
+
+##############################################################################

generic/apr.cyg

@@ -0,0 +1,28 @@
+##############################################################################
+# maali cygnet file for xerces-c 
+##############################################################################
+
+# specify which compilers we want to build the tool with
+MAALI_TOOL_COMPILERS="$MAALI_DEFAULT_COMPILERS"
+
+# URL to download the source code from
+MAALI_URL="https://www.strategylions.com.au/mirror//apr/apr-${MAALI_TOOL_VERSION}.tar.gz"
+# location we are downloading the source code to
+MAALI_DST="${MAALI_SRC}/${MAALI_TOOL_NAME}-${MAALI_TOOL_VERSION}.tar.gz"
+
+# where the unpacked source code is located
+MAALI_TOOL_BUILD_DIR="${MAALI_BUILD_DIR}/${MAALI_TOOL_NAME}-${MAALI_TOOL_VERSION}"
+
+# type of tool (eg. apps, devel, python, etc.)
+MAALI_TOOL_TYPE="devel"
+
+# add additional configure options
+MAALI_TOOL_CONFIGURE='--with-pic'
+
+# for auto-building module files
+MAALI_MODULE_SET_PATH=1
+MAALI_MODULE_SET_LD_LIBRARY_PATH=1
+MAALI_MODULE_SET_PKG_CONFIG_PATH=1
+MAALI_MODULE_SET_CPATH=1
+
+##############################################################################

generic/autoconf.cyg

@@ -0,0 +1,44 @@
+##############################################################################
+# maali cygnet file for autoconf
+##############################################################################
+
+read -r -d '' MAALI_MODULE_WHATIS << EOF
+
+Autoconf is an extensible package of M4 macros that produce shell scripts to
+automatically configure software source code packages. These scripts can adapt
+the packages to many kinds of UNIX-like systems without manual user
+intervention. Autoconf creates a configuration script for a package from a
+template file that lists the operating system features that the package can
+use, in the form of M4 macro calls.
+
+For further information see https://www.gnu.org/software/autoconf/autoconf.html
+
+EOF
+
+# specify which compilers we want to build the tool with
+MAALI_TOOL_COMPILERS="$MAALI_DEFAULT_SYSTEM_GCC"
+
+# URL to download the source code from
+MAALI_URL="http://ftp.gnu.org/gnu/$MAALI_TOOL_NAME/$MAALI_TOOL_NAME-$MAALI_TOOL_VERSION.tar.xz"
+
+# location we are downloading the source code to
+MAALI_DST="$MAALI_SRC/$MAALI_TOOL_NAME-$MAALI_TOOL_VERSION.tar.gz"
+
+# where the unpacked source code is located
+MAALI_TOOL_BUILD_DIR="$MAALI_BUILD_DIR/$MAALI_TOOL_NAME-$MAALI_TOOL_VERSION"
+
+# type of tool (eg. apps, devel, python, etc.)
+MAALI_TOOL_TYPE="devel"
+
+# tool pre-requisites modules needed to install this new tool/package
+MAALI_TOOL_PREREQ=""
+MAALI_TOOL_BUILD_PREREQ="libtool"
+
+# add additional configure options
+MAALI_TOOL_CONFIGURE=""
+
+# for auto-building module files
+MAALI_MODULE_SET_PATH=1
+MAALI_MODULE_SET_MANPATH=1
+
+##############################################################################

generic/automake.cyg

@@ -0,0 +1,42 @@
+##############################################################################
+# maali cygnet file for automake
+##############################################################################
+
+read -r -d '' MAALI_MODULE_WHATIS << EOF
+
+Automake is a tool for automatically generating Makefile.ins from files called
+Makefile.am. Each Makefile.am is basically a series of make variable
+definitions1, with rules being thrown in occasionally. The generated
+Makefile.ins are compliant with the GNU Makefile standards.
+
+For further information see https://www.gnu.org/software/automake/
+
+EOF
+
+# specify which compilers we want to build the tool with
+MAALI_TOOL_COMPILERS="$MAALI_DEFAULT_SYSTEM_GCC"
+
+# URL to download the source code from
+MAALI_URL="http://ftp.gnu.org/gnu/$MAALI_TOOL_NAME/$MAALI_TOOL_NAME-$MAALI_TOOL_VERSION.tar.xz"
+
+# location we are downloading the source code to
+MAALI_DST="$MAALI_SRC/$MAALI_TOOL_NAME-$MAALI_TOOL_VERSION.tar.gz"
+
+# where the unpacked source code is located
+MAALI_TOOL_BUILD_DIR="$MAALI_BUILD_DIR/$MAALI_TOOL_NAME-$MAALI_TOOL_VERSION"
+
+# type of tool (eg. apps, devel, python, etc.)
+MAALI_TOOL_TYPE="devel"
+
+# tool pre-requisites modules needed to install this new tool/package
+MAALI_TOOL_PREREQ=""
+MAALI_TOOL_BUILD_PREREQ="libtool autoconf"
+
+# add additional configure options
+MAALI_TOOL_CONFIGURE=""
+
+# for auto-building module files
+MAALI_MODULE_SET_PATH=1
+MAALI_MODULE_SET_MANPATH=1
+
+##############################################################################

generic/boost.cyg

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+##############################################################################
+# maali cygnet file for Boost
+##############################################################################
+
+read -r -d '' MAALI_MODULE_WHATIS << EOF
+
+Boost provides free peer-reviewed portable C++ source libraries.
+
+We emphasize libraries that work well with the C++ Standard Library. Boost
+libraries are intended to be widely useful, and usable across a broad spectrum
+of applications. The Boost license encourages both commercial and
+non-commercial use.
+
+For further information see http://www.boost.org/
+
+EOF
+
+#note that boost here is setup to be built with default compilers 
+#which might include intel, pgi, etc. There appears to be an 
+#issue with building versions of >=1.73 and intel related to
+#c++11, see https://github.com/spack/spack/issues/16328
+#for a spack focused version of this discussion
+#currently the work around is to adjust the compilers
+#if later versions of boost are required.
+
+# Request only the latest GNU and Intel compilers to be used
+MAALI_TOOL_COMPILERS="$MAALI_DEFAULT_COMPILERS"
+
+# needed  for this URL
+MAALI_BOOST_VERSION=`echo $MAALI_TOOL_VERSION| sed -e 's/\./_/g'`
+
+# URL to download the source code from
+MAALI_URL="http://sourceforge.net/projects/$MAALI_TOOL_NAME/files/$MAALI_TOOL_NAME/$MAALI_TOOL_VERSION/"$MAALI_TOOL_NAME"_"$MAALI_BOOST_VERSION".tar.bz2/download"
+
+# location we are downloading the source code to
+MAALI_DST="$MAALI_SRC/"$MAALI_TOOL_NAME"_"$MAALI_BOOST_VERSION".tar.bz2"
+
+# where the unpacked source code is located
+MAALI_TOOL_BUILD_DIR="$MAALI_BUILD_DIR/"$MAALI_TOOL_NAME"_"$MAALI_BOOST_VERSION
+
+# type of tool (eg. apps, devel, python, etc.)
+MAALI_TOOL_TYPE="devel"
+
+# tool pre-requisites
+MAALI_TOOL_PREREQ="$MAALI_DEFAULT_PYTHON"
+
+# for auto-building module files
+MAALI_MODULE_SET_LD_LIBRARY_PATH=1
+MAALI_MODULE_SET_LIBRARY_PATH=1
+MAALI_MODULE_SET_CPATH=1
+MAALI_MODULE_SET_C_INCLUDE_PATH=1
+MAALI_MODULE_SET_CPLUS_INCLUDE_PATH=1
+MAALI_MODULE_SET_BOOST_ROOT='$MAALI_APP_HOME'
+
+##############################################################################
+
+function maali_build {
+
+  cd "$MAALI_TOOL_BUILD_DIR"
+
+#https://github.com/HIT-SCIR/pyltp/pull/193
+  if [ "$MAALI_TOOL_VERSION" == "1.66.0" ]; then
+    sed -i -e 's;return PyUnicode_Check(obj) ? _PyUnicode_AsString(obj) : 0;return (void *)(PyUnicode_Check(obj) ? _PyUnicode_AsString(obj) : 0);g' libs/python/src/converter/builtin_converters.cpp
+  fi
+
+  export MAALI_CORES=12
+  # Intel-compiler specifics
+  if [[ "$MAALI_COMPILER_NAME" == "intel"* ]]; then
+
+  if [ "$MAALI_TOOL_MINOR_VERSION" -ge 66 ]; then
+    maali_run "./bootstrap.sh --prefix=$MAALI_INSTALL_DIR --with-toolset=intel-linux"
+    maali_run "./b2 -j$MAALI_CORES install toolset=intel --prefix=$MAALI_INSTALL_DIR"
+  else
+    maali_run "./bootstrap.sh --prefix=$MAALI_INSTALL_DIR --with-toolset=intel-linux"
+    maali_run "./bjam -j$MAALI_CORES toolset=intel release"
+    maali_run "./bjam install --prefix=$MAALI_INSTALL_DIR"
+  fi
+
+  # GNU compiler specifics
+  else
+
+  if [ "$MAALI_TOOL_MINOR_VERSION" -ge 66 ]; then
+    maali_run "./bootstrap.sh --prefix=$MAALI_INSTALL_DIR --with-toolset=gcc"
+    maali_run "./b2 -j$MAALI_CORES install toolset=gcc --prefix=$MAALI_INSTALL_DIR"
+  else
+    maali_run "./bootstrap.sh --prefix=$MAALI_INSTALL_DIR --without-libraries=python"
+    maali_run "./bjam -j$MAALI_CORES toolset=gcc release"
+    maali_run "./bjam install --prefix=$MAALI_INSTALL_DIR"
+  fi
+
+  fi
+
+  if [ "$MAALI_TOOL_VERSION" == "1.64.0" ]; then
+    sed -i -e 's;#include <boost/serialization/array.hpp>;#include <boost/serialization/array_wrapper.hpp>;g;' $MAALI_INSTALL_DIR/include/boost/numeric/ublas/matrix.hpp
+    sed -i -e 's;#include <boost/serialization/array.hpp>;#include <boost/serialization/array_wrapper.hpp>;g;' $MAALI_INSTALL_DIR/include/boost/numeric/ublas/storage.hpp
+  fi
+
+}
+
+##############################################################################

generic/cfitsio.cyg

@@ -0,0 +1,60 @@
+##############################################################################
+# maali cygnet file for cfitsio
+##############################################################################
+
+read -r -d '' MAALI_MODULE_WHATIS << EOF
+
+CFITSIO is a library of C and Fortran subroutines for reading and writing data
+files in FITS (Flexible Image Transport System) data format. CFITSIO provides
+simple high-level routines for reading and writing FITS files that insulate the
+programmer from the internal complexities of the FITS format. CFITSIO also
+provides many advanced features for manipulating and filtering the information
+in FITS files.
+
+For further information see https://heasarc.gsfc.nasa.gov/fitsio/fitsio.html
+
+EOF
+
+# specify which compilers we want to build the tool with
+MAALI_TOOL_COMPILERS="$MAALI_DEFAULT_COMPILERS"
+
+# URL to download the source code from
+MAALI_CFITSIO_VERSION=`echo $MAALI_TOOL_VERSION | sed -e 's/\.//g'`
+MAALI_URL="https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/cfitsio${MAALI_CFITSIO_VERSION}.tar.gz"
+# location we are downloading the source code to
+MAALI_DST="$MAALI_SRC/$MAALI_TOOL_NAME-$MAALI_TOOL_VERSION.tar.bz2"
+
+# where the unpacked source code is located
+MAALI_TOOL_BUILD_DIR="$MAALI_BUILD_DIR/$MAALI_TOOL_NAME"
+
+# type of tool (eg. apps, devel, python, etc.)
+MAALI_TOOL_TYPE="devel"
+
+# tool pre-requisites
+MAALI_TOOL_PREREQ=""
+
+# used in the wiki navigation bar - defaults to MAALI_TOOL_NAME_ORIG
+MAALI_WIKI_TOOL_NAME="CFITSIO"
+
+# for adding [[Category:Python]] to wiki page - bio-apps, devel and python automatically generate a category
+MAALI_WIKI_CATEGORY="File Formats & Data Management"
+
+# for auto-building module files
+MAALI_MODULE_SET_LD_LIBRARY_PATH=1
+MAALI_MODULE_SET_CPATH=1
+MAALI_MODULE_SET_FPATH=1
+MAALI_MODULE_SET_FCPATH=1
+MAALI_MODULE_SET_MANPATH=1
+MAALI_MODULE_SET_PKG_CONFIG_PATH=1
+MAALI_MODULE_SET_CFITSIO_ROOT='$MAALI_APP_HOME'
+
+##############################################################################
+
+function maali_build {
+  cd "$MAALI_TOOL_BUILD_DIR"
+  maali_run "./configure --prefix $MAALI_INSTALL_DIR $MAALI_TOOL_CONFIGURE"
+  maali_run "make shared"
+  maali_run "make install"
+}
+
+##############################################################################