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Makefile.CP2
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Makefile.CP2
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#
# Makefile for CellProfiler 2 prerequisites
#
#
# CellProfiler is distributed under the GNU General Public License.
# See the accompanying file LICENSE for details.
#
# Copyright (c) 2003-2009 Massachusetts Institute of Technology
# Copyright (c) 2009-2015 Broad Institute
# All rights reserved.
#
# Please see the AUTHORS file for credits.
#
# Website: http://www.cellprofiler.org
#
# WARNING: this Makefile is unlikely to work correctly for
# CellProfiler revisions much beyond the most recent update to the
# Makefile itself.
#
# This Makefile will download, unpack, compile and install all
# prerequisites for CP2, except for Java. It requires a fairly
# recent compiler (gcc) to compile ATLAS with optimal performance.
# Please disable CPU frequency scaling before compilation.
#
# PREREQUISITES:
# - It is recommended to have development files for GTK+. If you don't
# have (or want) GTK+, you can compile with a less optimal user interface
# using the WXUSEGTK="no" parameter for this Makefile.
# RedHat: yum install gtk2-devel
# Debian/Ubuntu: aptitude install libgtk2.0-dev
# Generic: "make gtk" with this Makefile
#
# VARIABLES:
# - set PREFIX to where you want to install your CellProfiler2 directory
# Ensure that JAVA_HOME points to your JDK
# Define HOSTTYPE to be the processor type if not "amd64"
#
# USAGE:
# - always invoke 'make' with the name of this Makefile, i.e.:
# make -f Makefile.CP2
# - supply variables that you want to set on the command line, i.e.:
# make -f Makefile.CP2 PREFIX="$HOME/usr/CellProfiler2" ...
# - if you want to first download all sources, use the "download" target:
# make -f Makefile.CP2 download
#
# After installation, you need to run the following every time
# you want to start CellProfiler (or place it in your SHELL
# startup scripts, e.g., ~/.bashrc for bash):
# CP2DEST="$HOME/usr/CellProfiler2"
# export PATH="${CP2DEST}/bin:${PATH}"
# export LD_LIBRARY_PATH="${CP2DEST}/lib:${CP2DEST}/lib64:${LD_LIBRARY_PATH}":${CP2DEST}/lib/mysql
# export PYTHONPATH="${CP2DEST}/lib/python2.5/site-packages:${PYTHONPATH}"
# export JAVA_HOME="<your path to JDK or JRE>"
#
# and set your locale to use UTF-8 encoding, e.g.
#
# export LC_ALL=en_US.UTF-8
#
# To run CellProfiler:
# cd ${CP2DEST}
# python CellProfiler.py -b
#
# To run Ilastik:
# python -m ilastik.ilastikMain
#
# MAKE_FLAGS is used for "make" compilation. -jN specifies N parallel
# build jobs for packages that support parallel compilation. Change or
# add other parameters as you like:
PACKAGEHOST ?= http://cellprofiler.org/linux/SOURCES
MAKE_FLAGS ?= -j4
PREFIX ?= /usr/CellProfiler
SRCDIR ?= $(PREFIX)/src
TMPDIR ?= $(PWD)/tmp
HOSTTYPE ?=amd64
#
# TGTDIR holds the target files touched when making multipart dependencies
# The target directory must be present before the dependencies are calculated
# so it must be created in this backhanded fashion.
#
TGTDIR ?= $(TMPDIR)/targets
export MAKETGTDIRCMD := "mkdir -p "$(TGTDIR)";echo "$(TGTDIR)
VPATH = $(shell "$(MAKETGTDIRCMD)")
unexport MAKETGTDIRCMD
# Set DISABLE_PRECHECKS to "YES" (case sensitive!) to explicitly
# disable prechecks. Disabling is not recommended. It may lead
# to failed builds because of missing/wrong dependencies.
DISABLE_PRECHECKS ?= NO
WXUSEGTK ?= yes
WGETFLAGS ?= --continue --tries=10 --timeout=60 --no-check-certificate
# Versions and prefixes of packages:
CELLPROFILERPREFIX ?= $(PREFIX)
CELLPROFILER_CO_URL = https://github.com/CellProfiler/CellProfiler.git
PYVERSION = 2.7
PYTHONVERSION = Python-$(PYVERSION).2
PYTHONPREFIX ?= $(PREFIX)
PYTHON = $(PYTHONPREFIX)/bin/python
SITEPKGPREFIX = $(PYTHONPREFIX)/lib/python$(PYVERSION)/site-packages
AMDVERSION = AMD-2.2.2
AMDURL = $(PACKAGEHOST)
ATLASVERSION = atlas3.11.8
ATLASPREFIX ?= /usr/lib64/atlas/
ATLASURL = http://sourceforge.net/projects/math-atlas/files/
BIOFORMATSVERSION = python-bioformats-1.0.4
BIOFORMATSURL = $(PACKAGEHOST)
BOOSTVERSION = boost_1_53_0
BOOSTPREFIX ?= $(PREFIX)
CAMDVERSION = CAMD-2.2.2
CAMDPREFIX ?= $(PREFIX)
CAMDURL = $(PACKAGEHOST)
CELLH5VERSION = cellh5-1.2.0
CCOLAMDVERSION = CCOLAMD-2.7.3
CCOLAMDPREFIX ?= $(PREFIX)
CCOLAMDURL = $(PACKAGEHOST)
CHOLMODVERSION = CHOLMOD-1.7.2
CHOLMODPREFIX ?= $(PREFIX)
CHOLMODURL = $(PACKAGEHOST)
COLAMDVERSION = COLAMD-2.7.3
COLAMDPREFIX ?= $(PREFIX)
COLAMDURL = $(PACKAGEHOST)
CYTHONVERSION = Cython-0.20.2
CYTHONPREFIX ?= $(PREFIX)
CYTHONURL = $(PACKAGEHOST)#download
DATEUTILVERSION = python-dateutil-2.2
DECORATORVERSION = decorator-3.2.0
FFTWVERSION = fftw-3.2.2
FFTWPREFIX ?= $(PREFIX)
HDF5VERSION = hdf5-1.8.10-patch1
HDF5PREFIX ?= $(PREFIX)
H5PYVERSION = h5py-2.2.0
H5PYPREFIX ?= $(PREFIX)
H5PYURL = $(PACKAGEHOST)
ILASTIKMAJVERSION = 0.5
ILASTIKMINVERSION = 05
ILASTIKVERSION = $(ILASTIKMAJVERSION).$(ILASTIKMINVERSION)
ILASTIKPREFIX ?= $(PREFIX)
ILASTIKURL = $(PACKAGEHOST)
JAVABRIDGEVERSION = javabridge-1.0.11
JAVABRIDGEURL = $(PACKAGEHOST)
JPEGVERSION = 8b
JPEGPREFIX ?= $(PREFIX)
LAPACKVERSION = lapack-3.3.0
LAPACKFLAGS = -fPIC -m64
LAPACKURL = http://www.netlib.org/lapack/
LXMLVERSION = lxml-3.4.2
LIBXML2VERSION = libxml2-2.9.2
LIBXSLTVERSION = libxslt-1.1.28
LIBICONVVERSION = libiconv-1.9.2
MATPLOTLIBVERSION = matplotlib-1.0.1
MATPLOTLIBURL = $(PACKAGEHOST)
MYSQLVERSION = mysql-5.1.55
MYSQLPREFIX ?= $(PREFIX)
MYSQLURL = $(PACKAGEHOST)
MYSQLPYTHONVERSION = MySQL-python-1.2.3
MYSQLPYTHONURL = $(PACKAGEHOST)
NCURSESVERSION = ncurses-5.7
NCURSESPREFIX ?= $(PREFIX)
NUMPYVERSION = numpy-1.9.0
NUMPYPREFIX ?= $(PREFIX)
NUMPYURL = $(PACKAGEHOST)
PANDASVERSION = pandas-0.16.0
PCREVERSION = pcre-8.35
PCREPREFIX ?= $(PREFIX)
PCREURL = $(PACKAGEHOST)
PILVERSION = Imaging-1.1.7
PILPREFIX ?= $(PREFIX)
PILURL = $(PACKAGEHOST)
#PNGVERSION = libpng-1.4.5
#PNGPREFIX ?= $(PREFIX)
#PNGURL = $(PACKAGEHOST)
PYOPENGLVERSION = PyOpenGL-3.0.1
PYOPENGLPREFIX ?= $(PREFIX)
PYOPENGLURL = http://pyopengl.sourceforge.net/documentation/installation.html
PYOPENGLACCELVERSION = PyOpenGL-accelerate-3.0.1
PYOPENGLACCELPREFIX ?= $(PREFIX)
PYOPENGLACCELURL = http://pyopengl.sourceforge.net/documentation/installation.html
PYPIVERSION = setuptools-1.1.6
PYPIPREFIX ?= $(PREFIX)
PYQTVERSION = PyQt-x11-gpl-4.8.3
PYQTPREFIX ?= $(PREFIX)
PYQTURL = $(PACKAGEHOST)
PYSQLITEVERSION = pysqlite-2.6.1
PYSQLITEPREFIX ?= $(PREFIX)
PYSQLITEURL = $(PACKAGEHOST)
PYTHONNOSEVERSION = nose-1.3.4
PYTHONNOSEURL = $(PACKAGEHOST)
PYTZVERSION = pytz-2013.7
PYZMQVERSION = pyzmq-13.1.0
PYZMQURL = $(PACKAGEHOST)
QIMGTOARRVERSION = qimage2ndarray-1.0
QIMGTOARRPREFIX ?= $(PREFIX)
QIMGTOARRURL = $(PACKAGEHOST)
QTVERSION = qt-everywhere-opensource-src-4.7.1
QTMAKE = $(PREFIX)/bin/qmake
READLINEVERSION = readline-6.3
SKLEARNVERSION = scikit-learn-0.15.2
SCIPYVERSION = scipy-0.10.1
SCIPYPREFIX ?= $(PREFIX)
SCIPYURL = $(PACKAGEHOST)
SIPVERSION = sip-4.12.1
SIPPREFIX ?= $(PREFIX)
SIPURL = $(PACKAGEHOST)
SIXVERSION = six-1.4.1
SQLITEVERSION = sqlite-autoconf-3070500
SQLITEPREFIX ?= $(PREFIX)
SQLITEURL = $(PACKAGEHOST)
SWIGVERSION = swig-2.0.1
SWIGPREFIX ?= $(PREFIX)
SWIGURL = $(PACKAGEHOST)
TIFFVERSION = tiff-3.9.4
TIFFPREFIX ?= $(PREFIX)
UFCONFIGVERSION = UFconfig-3.6.0
UFCONFIGURL = $(PACKAGEHOST)
UMFPACKVERSION = UMFPACK-5.5.1
UMFPACKPREFIX ?= $(PREFIX)
UMFPACKURL = $(PACKAGEHOST)
VIGRAVERSION = vigra-1.7.1
VIGRAPREFIX ?= $(PREFIX)
VIGRAURL = $(PACKAGEHOST)
WXVERSION = 2.8.11
WXPYTHONTOOLKIT_no = --without-gtk --disable-unicode --disable-gtktest --with-x11
WXPYTHONTOOLKIT_yes = --with-gtk --enable-unicode
WXPYTHONVERSION = 2.8.11.0
WXFLAGS = --with-opengl --enable-graphics_ctx --enable-shared --disable-compat24 --enable-compat26 --disable-sound --enable-monolithic --with-libpng=sys --with-libjpeg --with-libtiff --with-zlib
WXPYTHONPREFIX ?= $(PREFIX)
WXPYTHONURL = http://www.wxpython.org/download.php#sources
YATTAGVERSION = yattag-1.5.0.tar.gz
ZLIBVERSION = zlib-1.2.5
ZLIBPREFIX ?= $(PREFIX)
# optional packages:
GTKVERSION = gtk+-2.22.1
GTKPREFIX = $(PREFIX)
GLIBVERSION = glib-2.26.1
GLIBPREFIX = $(PREFIX)
PANGOVERSION = pango-1.28.3
PANGOPREFIX = $(PREFIX)
PIXMANVERSION = pixman-0.20.2
PIXMANPREFIX = $(PREFIX)
GDKPIXBUFVERSION = gdk-pixbuf-2.22.1
GDKPIXBUFPREFIX = $(PREFIX)
ATKVERSION = atk-1.32.0
ATKPREFIX = $(PREFIX)
CAIROVERSION = cairo-1.10.2
CAIROPREFIX = $(PREFIX)
FONTCFGVERSION = fontconfig-2.8.0
FONTCFGPREFIX = $(PREFIX)
GETTEXTPREFIX = $(PREFIX)
GETTEXTVERSION = gettext-0.18.1.1
DOLLAR =\$$
default: all
all: precheck cellprofiler
gtk: precheck libgtk
#Identify host type and set relevant variables
sethost:
@if echo $${HOSTTYPE} | grep -q 64; then \
echo "using 64 bit version" ; \
fi
#
# Here we have all the tests for prerequisites of this Makefile
# Add as many (useful) tests as you like, the more the better.
# They just need to perform quickly!
# NOTE: Some of these prechecks where kindly provided by
# the XuvTools project at http://xuvtools.org/
#
precheck-java: $(SRCDIR)/findlibjvm.class
@if test "$(DISABLE_PRECHECKS)" != "YES" ; then \
if test -z "$(JAVA_HOME)" ; then \
echo "Could not detect JAVA_HOME variable. Please export JAVA_HOME from" ; \
echo "your SHELL to the path of the JRE, and add it to LD_LIBRARY_PATH." ; \
false ; \
elif ! echo "$(LD_LIBRARY_PATH)"|grep -qs "$(JAVA_HOME)" ; then \
echo "It seems JAVA_HOME is missing from the LD_LIBRARY_PATH variable." ; \
echo "Please read the setup guide on how to fix that." ; \
false ; \
else \
cd "$(SRCDIR)" && \
LIBJVMPATH=$$($${JAVA_HOME}/bin/java findlibjvm 2>/dev/zero) && \
if ! test -r "$${LIBJVMPATH}/libjvm.so" ; then \
echo "Could not find 'libjvm.so' in the following path:" ; \
echo " '$${LIBJVMPATH}'" ; \
echo "Please read the setup guide on how to fix that." ; \
false ; \
fi ; \
fi ; \
fi
precheck-env:
@if test "$(DISABLE_PRECHECKS)" != "YES" ; then \
if test -z "$(HOSTTYPE)" ; then \
echo "Could not detect HOSTTYPE variable. Please export HOSTTYPE from" ; \
echo "your SHELL to set the default architecture of the build." ; \
false ; \
elif test -n "$(CPPFLAGS)" -o -n "$(LDFLAGS)" ; then \
echo "The CPPFLAGS and/or LDFLAGS variables are set. Likely, numpy" ; \
echo "will not compile because external flags override theirs." ; \
echo "Please unset these variables unless you know what you are doing." ; \
false ; \
fi ; \
fi
precheck-git:
@if ! git --version 2>&1|grep -iqs '^git.*version [1-9][0-9]*\.[0-9][0-9]*\.[0-9][0-9]*' && test "$(DISABLE_PRECHECKS)" != "YES" ; then \
echo "Could not detect GIT revision management system, please compile" ; \
echo "or install git for your platform. Alternatively, you can disable" ; \
echo "ilastik (it is optional), or download and compile it manually." ; \
false ; \
fi
precheck-svn:
@if ! svn --version 2>&1|grep -iqs '^svn.*version [1-9][0-9]*\.[0-9][0-9]*\.[0-9][0-9]*' && test "$(DISABLE_PRECHECKS)" != "YES" ; then \
echo "Could not detect a recent version of Subversion (>= 1.4.0)," ; \
echo "please compile or install Subversion/SVN." ; \
echo "You can also try to install SVN for your Linux distribution." ; \
false ; \
fi
precheck-wget:
@if ! wget --help 2>&1|grep -qs -- '--no-check-certificate' && test "$(DISABLE_PRECHECKS)" != "YES" ; then \
echo "Your wget does not support the '--no-check-certificate' attribute." ; \
echo "You need a newer wget, or you need to disable the use of the" ; \
echo "attribute '--no-check-certificate' in this Makefile. To do that," ; \
echo "try to add to the command-line WGETFLAGS=\"\"." ; \
false ; \
fi
precheck-cmake:
@if ! cmake --version 2>/dev/zero|grep -iqs '^cmake.* 2\.[6-9]\|^cmake.* [0-9]\.' && test "$(DISABLE_PRECHECKS)" != "YES" ; then \
echo "Could not detect a recent cmake build system (>=2.6.0)," ; \
echo "it is unlikely that ilastik will compile! Please install cmake" ; \
echo "separately, or remove ilastik from the default build." ; \
false ; \
fi
precheck-gcc:
@if ! gcc --version 2>/dev/zero|grep -iqs '^gcc.* [4-9]\.[1-9][0-9]*\.[0-9][0-9]*' && test "$(DISABLE_PRECHECKS)" != "YES" ; then \
echo "Could not detect a recent GCC C compiler version (>=4.1.0)," ; \
echo "it is very unlikely that you will be able to compile fast code!" ; \
false ; \
fi
precheck-gpp:
@if ! g++ --version 2>/dev/zero|grep -iqs '^g++.* [4-9]\.[1-9][0-9]*\.[0-9][0-9]*' && test "$(DISABLE_PRECHECKS)" != "YES" ; then \
echo "Could not detect a recent GCC C++ compiler version (>=4.1.0)," ; \
echo "it is very unlikely that you will be able to compile fast code!" ; \
false ; \
fi
precheck-gfortran:
@if ! gfortran --version 2>/dev/zero|grep -iqs '^GNU Fortran.* [4-9]\.[1-9][0-9]*\.[0-9][0-9]*' && test "$(DISABLE_PRECHECKS)" != "YES" ; then \
echo "Could not detect a recent GCC Fortran 95 compiler version (>=4.1.0)," ; \
echo "it is very unlikely that you will be able to compile fast code!" ; \
false ; \
fi
precheck-success:
@echo "All pre-checks executed successfully."
precheck: $(TMPDIR)/create-dirs sethost precheck-java precheck-env precheck-svn precheck-git precheck-gcc precheck-gpp precheck-gfortran precheck-wget precheck-cmake precheck-success
.PHONY: precheck-java precheck-env precheck-svn precheck-git precheck-gcc precheck-gpp precheck-gfortran precheck-wget precheck-cmake precheck-success precheck clean update
#
# The temporary build directories and source directories
#
$(TMPDIR)/create-dirs:
mkdir -p "$(TGTDIR)"
mkdir -p "$(TMPDIR)/lib"
mkdir -p "$(SRCDIR)"
touch $@
#
# Here come the actual compile instructions for CP2 prerequisites,
# package by package. There is no strict ordering, but it was coded
# top-to-bottom, so you may assume that later specified packages
# depend on earlier specified packages.
#
$(TGTDIR)/python: $(SRCDIR)/$(PYTHONVERSION).tar.bz2 sqlite readline
cd "$(TMPDIR)" && \
rm -fr "$(PYTHONVERSION)" && \
tar -xjf "$(SRCDIR)/$(PYTHONVERSION).tar.bz2" && \
cd "$(PYTHONVERSION)" && \
export LD_LIBRARY_PATH="$(PYTHONPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
export LDFLAGS="-L$(PREFIX)/lib $${LDFLAGS}" && \
export C_INCLUDE_PATH="$(PYTHONPREFIX)/include:$(C_INCLUDE_PATH)" && \
./configure \
--prefix="$(PYTHONPREFIX)" \
--enable-shared \
--enable-unicode=ucs4 && \
make install MACHDEP=linux2
touch $@
$(TGTDIR)/readline: $(SRCDIR)/$(READLINEVERSION).tar.gz
cd "$(TMPDIR)" && \
rm -fr "$(READLINEVERSION)" && \
tar -zxvf "$(SRCDIR)/$(READLINEVERSION).tar.gz" && \
cd "$(READLINEVERSION)" && \
export LD_LIBRARY_PATH="$(PREFIX)/lib:$${LD_LIBRARY_PATH}" && \
export C_INCLUDE_PATH="$(PREFIX)/include:$(C_INCLUDE_PATH)" && \
./configure \
--prefix="$(PREFIX)" \
--enable-shared && \
$(MAKE) $(MAKE_FLAGS) && \
$(MAKE) -j1 install
touch $@
$(TGTDIR)/cython: $(SRCDIR)/$(CYTHONVERSION).tar.gz pypi
cd "$(TMPDIR)" && \
rm -fr "$(CYTHONVERSION)" && \
tar -xzf "$(SRCDIR)/$(CYTHONVERSION).tar.gz" && \
cd "$(CYTHONVERSION)" && \
export PATH="$(PYTHONPREFIX)/bin:$(PATH)" && \
export LD_LIBRARY_PATH="$(PYTHONPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
$(PYTHON) setup.py install
touch $@
$(TGTDIR)/umfpack: $(SRCDIR)/$(UMFPACKVERSION).tar.gz $(SRCDIR)/$(CAMDVERSION).tar.gz $(SRCDIR)/$(CCOLAMDVERSION).tar.gz $(SRCDIR)/$(COLAMDVERSION).tar.gz $(SRCDIR)/$(CHOLMODVERSION).tar.gz $(SRCDIR)/$(UFCONFIGVERSION).tar.gz $(SRCDIR)/$(AMDVERSION).tar.gz
cd "$(TMPDIR)" && \
rm -fr "CHOLMOD" && \
rm -fr "COLAMD" && \
rm -fr "CCOLAMD" && \
rm -fr "CAMD" && \
rm -fr "UMFPACK" && \
rm -fr "UFconfig" && \
rm -fr "AMD" && \
tar -xzf "$(SRCDIR)/$(CHOLMODVERSION).tar.gz" && \
tar -xzf "$(SRCDIR)/$(COLAMDVERSION).tar.gz" && \
tar -xzf "$(SRCDIR)/$(CCOLAMDVERSION).tar.gz" && \
tar -xzf "$(SRCDIR)/$(CAMDVERSION).tar.gz" && \
tar -xzf "$(SRCDIR)/$(UMFPACKVERSION).tar.gz" && \
tar -xzf "$(SRCDIR)/$(UFCONFIGVERSION).tar.gz" && \
tar -xzf "$(SRCDIR)/$(AMDVERSION).tar.gz" && \
perl -pi -e 's@(^CHOLMOD_CONFIG )=.*@$$1= -DNPARTITION@g' UFconfig/UFconfig.mk && \
perl -pi -e 's@(^CC )=.*@$$1= gcc@g' UFconfig/UFconfig.mk && \
perl -pi -e 's@(^CFLAGS .*)@$$1 -m64 -fPIC@g' UFconfig/UFconfig.mk && \
perl -pi -e 's@(^F77 )=.*@$$1= gfortran@g' UFconfig/UFconfig.mk && \
perl -pi -e 's@(^F77FLAGS .*)@$$1 -m64 -fPIC@g' UFconfig/UFconfig.mk && \
perl -pi -e 's@(^BLAS )=.*@$$1= -L$(ATLASPREFIX) -llapack -lblas -latlas -lgfortran@g' UFconfig/UFconfig.mk && \
perl -pi -e 's@(^LAPACK )=.*@$$1= -L$(ATLASPREFIX) -llapack -lblas -latlas -lgfortran@g' UFconfig/UFconfig.mk && \
perl -pi -e 's@(^METIS_PATH )=.*@$$1= @g' UFconfig/UFconfig.mk && \
perl -pi -e 's@(^METIS )=.*@$$1= @g' UFconfig/UFconfig.mk && \
perl -pi -e 's@(^INSTALL_LIB )=.*@$$1= $(UMFPACKPREFIX)/lib@g' UFconfig/UFconfig.mk && \
perl -pi -e 's@(^INSTALL_INCLUDE )=.*@$$1= $(UMFPACKPREFIX)/include@g' UFconfig/UFconfig.mk && \
export PATH="$(PYTHONPREFIX)/bin:$(PATH)" && \
export LD_LIBRARY_PATH="$(PYTHONPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
cd "UMFPACK" && \
$(MAKE) $(MAKE_FLAGS) && \
$(MAKE) -j1 install && \
cp -p "../AMD/Include/amd.h" "$(UMFPACKPREFIX)/include/" && \
cp -p "../UFconfig/UFconfig.h" "$(UMFPACKPREFIX)/include/"
touch $@
$(TGTDIR)/fftw: $(FFTWPREFIX)/lib/libfftw3.la $(FFTWPREFIX)/lib/libfftw3l.la $(FFTWPREFIX)/lib/libfftw3f.la
touch $@
$(FFTWPREFIX)/lib/libfftw3.la: $(SRCDIR)/$(FFTWVERSION).tar.gz
cd "$(TMPDIR)" && \
rm -fr "$(FFTWVERSION)" && \
tar -xzf "$(SRCDIR)/$(FFTWVERSION).tar.gz" && \
cd "$(FFTWVERSION)" && \
./configure \
--enable-sse2 \
--enable-shared \
--prefix="$(FFTWPREFIX)" && \
$(MAKE) $(MAKE_FLAGS) && \
$(MAKE) -j1 install
$(FFTWPREFIX)/lib/libfftw3l.la: $(SRCDIR)/$(FFTWVERSION).tar.gz
cd "$(TMPDIR)" && \
rm -fr "$(FFTWVERSION)" && \
tar -xzf "$(SRCDIR)/$(FFTWVERSION).tar.gz" && \
cd "$(FFTWVERSION)" && \
./configure \
--enable-long-double \
--enable-shared \
--prefix="$(FFTWPREFIX)" && \
$(MAKE) $(MAKE_FLAGS) && \
$(MAKE) -j1 install
$(FFTWPREFIX)/lib/libfftw3f.la: $(SRCDIR)/$(FFTWVERSION).tar.gz $(FFTWPREFIX)/lib/libfftw3.la $(FFTWPREFIX)/lib/libfftw3l.la
cd "$(TMPDIR)" && \
rm -fr "$(FFTWVERSION)" && \
tar -xzf "$(SRCDIR)/$(FFTWVERSION).tar.gz" && \
cd "$(FFTWVERSION)" && \
./configure \
--enable-float \
--enable-sse \
--enable-shared \
--prefix="$(FFTWPREFIX)" && \
$(MAKE) $(MAKE_FLAGS) && \
$(MAKE) -j1 install
$(TGTDIR)/numpy: $(SRCDIR)/$(NUMPYVERSION).tar.gz $(SRCDIR)/mtrand.pyx.patch umfpack fftw pypi
cd "$(TMPDIR)" && \
rm -fr "$(NUMPYVERSION)" && \
tar -zxf "$(SRCDIR)/$(NUMPYVERSION).tar.gz" && \
cd "$(NUMPYVERSION)" && \
cp site.cfg.example site.cfg && \
perl -pi -e 's@#(\[DEFAULT\])@$$1@g' site.cfg && \
perl -pi -e 's@#(library_dirs.*)@$$1:/usr/lib64:$(PYTHONPREFIX)/lib@g' site.cfg && \
perl -pi -e 's@#(include_dirs.*)@$$1:$(PYTHONPREFIX)/include@g' site.cfg && \
perl -pi -e 's@#(\[lapack_opt\])@$$1@g' site.cfg && \
perl -pi -e 's@#(libraries = lapack, blas, atlas)@$$1, gfortran@g' site.cfg && \
perl -pi -e 's@#(\[amd\])@$$1@g' site.cfg && \
perl -pi -e 's@#(amd_libs)@$$1@g' site.cfg && \
perl -pi -e 's@#(\[umfpack\])@$$1@g' site.cfg && \
perl -pi -e 's@#(umfpack_libs)@$$1@g' site.cfg && \
perl -pi -e 's@#(\[fftw\])@$$1@g' site.cfg && \
perl -pi -e 's@#(libraries = fftw3)@$$1@g' site.cfg && \
perl -pi -e 's@#(\[djbfft\])@$$1@g' site.cfg && \
patch -p0 < $(SRCDIR)/mtrand.pyx.patch && \
export MKL="None" && \
export PATH="$(PYTHONPREFIX)/bin:$(PATH)" && \
export LD_LIBRARY_PATH="$(PYTHONPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
cd numpy/random/mtrand && \
$(PYTHON) generate_mtrand_c.py && \
cd ../../.. && \
$(PYTHON) setup.py build --fcompiler=gfortran && \
$(PYTHON) setup.py install
touch $@
$(TGTDIR)/pcre: $(SRCDIR)/$(PCREVERSION).tar.bz2
cd "$(TMPDIR)" && \
rm -fr "$(PCREVERSION)" && \
tar -xjf "$(SRCDIR)/$(PCREVERSION).tar.bz2" && \
cd "$(PCREVERSION)" && \
./configure \
--prefix="$(PCREPREFIX)" && \
$(MAKE) $(MAKE_FLAGS) && \
$(MAKE) -j1 install
touch $@
$(TGTDIR)/swig: $(SRCDIR)/$(SWIGVERSION).tar.gz pcre
cd "$(TMPDIR)" && \
rm -fr "$(SWIGVERSION)" && \
tar -xzf "$(SRCDIR)/$(SWIGVERSION).tar.gz" && \
cd "$(SWIGVERSION)" && \
export PCRE_CONFIG="$(PCREPREFIX)/bin/pcre-config" && \
export LD_LIBRARY_PATH="$(PCREPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
./configure \
--prefix="$(SWIGPREFIX)" \
--with-python="$(PYTHON)" \
--without-python3 && \
$(MAKE) $(MAKE_FLAGS) && \
$(MAKE) -j1 install
touch $@
$(TGTDIR)/scipy: $(SRCDIR)/$(SCIPYVERSION).tar.gz umfpack numpy pypi swig
cd "$(TMPDIR)" && \
rm -fr "$(SCIPYVERSION)" && \
tar -zxf "$(SRCDIR)/$(SCIPYVERSION).tar.gz" && \
cd "$(SCIPYVERSION)" && \
export PATH="$(PYTHONPREFIX)/bin:$(PATH)" && \
export LD_LIBRARY_PATH="$(PYTHONPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
$(PYTHON) setup.py build --fcompiler=gfortran && \
$(PYTHON) setup.py install
touch $@
$(TGTDIR)/matplotlib: $(SRCDIR)/$(MATPLOTLIBVERSION).tar.gz tiff jpeg python numpy wxpython
cd "$(TMPDIR)" && \
rm -fr "$(MATPLOTLIBVERSION)" && \
tar -zxf "$(SRCDIR)/$(MATPLOTLIBVERSION).tar.gz" && \
cd "$(MATPLOTLIBVERSION)" && \
export PATH="$(PYTHONPREFIX)/bin:$(PATH)" && \
export LD_LIBRARY_PATH="$(PYTHONPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
export PKG_CONFIG_PATH="$(GLIBPREFIX)/lib/pkgconfig:$(PANGOPREFIX)/lib/pkgconfig:$${PKG_CONFIG_PATH}" && \
export CPPFLAGS="-I$(JPEGPREFIX)/include -I$(TIFFPREFIX)/include -I$(ZLIBPREFIX)/include $${CPPFLAGS}" && \
export LDFLAGS="-L$(JPEGPREFIX)/lib -L$(TIFFPREFIX)/lib -L$(ZLIBPREFIX)/lib $${LDFLAGS}" && \
export LD_LIBRARY_PATH="$(JPEGPREFIX)/lib:$(TIFFPREFIX)/lib:$(ZLIBPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
$(PYTHON) setup.py build && \
$(PYTHON) setup.py install
touch $@
$(TGTDIR)/pypi: $(SRCDIR)/$(PYPIVERSION).tar.gz python
export PATH="$(PYTHONPREFIX)/bin:$(PATH)" && \
export LD_LIBRARY_PATH="$(PYTHONPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
cd "$(TMPDIR)" && \
rm -fr "$(PYPIVERSION)" && \
tar -zxf "$(SRCDIR)/$(PYPIVERSION).tar.gz" && \
cd "$(PYPIVERSION)" && \
$(PYTHON) setup.py build && \
$(PYTHON) setup.py install
touch $@
$(TGTDIR)/decorator: $(SRCDIR)/$(DECORATORVERSION).tar.gz pypi
cd "$(TMPDIR)" && \
rm -fr "$(DECORATORVERSION)" && \
tar -xzf "$(SRCDIR)/$(DECORATORVERSION).tar.gz" && \
cd "$(DECORATORVERSION)" && \
export PATH="$(PYTHONPREFIX)/bin:$(PATH)" && \
export LD_LIBRARY_PATH="$(PYTHONPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
$(PYTHON) setup.py install
touch $@
$(TGTDIR)/ncurses: $(SRCDIR)/$(NCURSESVERSION).tar.gz
cd "$(TMPDIR)" && \
rm -fr "$(NCURSESVERSION)" && \
tar -xzf "$(SRCDIR)/$(NCURSESVERSION).tar.gz" && \
cd "$(NCURSESVERSION)" && \
./configure \
--prefix="$(NCURSESPREFIX)" \
--with-shared \
--without-ada \
--without-debug \
--enable-widec && \
$(MAKE) $(MAKE_FLAGS) && \
$(MAKE) -j1 install
touch $@
$(TGTDIR)/sqlite: $(SRCDIR)/$(SQLITEVERSION).tar.gz zlib readline
cd "$(TMPDIR)" && \
rm -fr "$(SQLITEVERSION)" && \
tar -zxf "$(SRCDIR)/$(SQLITEVERSION).tar.gz" && \
cd "$(SQLITEVERSION)" && \
export CPPFLAGS="-I$(ZLIBPREFIX)/include $${CPPFLAGS}" && \
export LDFLAGS="-L$(ZLIBPREFIX)/lib -L$(PREFIX)/lib $${LDFLAGS}" && \
export LD_LIBRARY_PATH="$(ZLIBPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
./configure \
--prefix="$(SQLITEPREFIX)" && \
$(MAKE) $(MAKE_FLAGS) && \
$(MAKE) -j1 install
touch $@
$(TGTDIR)/pysqlite: $(SRCDIR)/$(PYSQLITEVERSION).tar.gz python sqlite zlib
cd "$(TMPDIR)" && \
rm -fr "$(PYSQLITEVERSION)" && \
tar -zxf "$(SRCDIR)/$(PYSQLITEVERSION).tar.gz" && \
cd "$(PYSQLITEVERSION)" && \
export PATH="$(PYTHONPREFIX)/bin:$(PATH)" && \
export LD_LIBRARY_PATH="$(PYTHONPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
export CPPFLAGS="-I$(SQLITEPREFIX)/include $${CPPFLAGS}" && \
export LDFLAGS="-L$(SQLITEPREFIX)/lib $${LDFLAGS}" && \
export LD_LIBRARY_PATH="$(SQLITEPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
$(PYTHON) setup.py build && \
$(PYTHON) setup.py install
touch $@
$(TGTDIR)/mysql: $(SRCDIR)/$(MYSQLVERSION).tar.gz zlib ncurses
cd "$(TMPDIR)" && \
rm -fr "$(MYSQLVERSION)" && \
tar -zxf "$(SRCDIR)/$(MYSQLVERSION).tar.gz" && \
cd "$(MYSQLVERSION)" && \
export CPPFLAGS="-I$(NCURSESPREFIX)/include $${CPPFLAGS}" && \
export LDFLAGS="-L$(NCURSESPREFIX)/lib $${LDFLAGS}" && \
export LD_LIBRARY_PATH="$(NCURSESPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
./configure \
--prefix="$(MYSQLPREFIX)" \
--with-zlib-dir="$(ZLIBPREFIX)" \
--disable-community-features \
--enable-local-infile \
--without-server \
--without-docs && \
$(MAKE) $(MAKE_FLAGS) && \
$(MAKE) -j1 install
touch $@
$(TGTDIR)/mysqlpython: $(SRCDIR)/$(MYSQLPYTHONVERSION).tar.gz pypi mysql
cd "$(TMPDIR)" && \
rm -fr "$(MYSQLPYTHONVERSION)" && \
tar -xzf "$(SRCDIR)/$(MYSQLPYTHONVERSION).tar.gz" && \
cd "$(MYSQLPYTHONVERSION)" && \
export PATH="$(PYTHONPREFIX)/bin:$(PATH)" && \
export LD_LIBRARY_PATH="$(PYTHONPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
$(PYTHON) setup.py build && \
$(PYTHON) setup.py install
touch $@
$(TGTDIR)/pyopengl: $(SRCDIR)/$(PYOPENGLVERSION).tar.gz numpy pil
cd "$(TMPDIR)" && \
rm -fr "$(PYOPENGLVERSION)" && \
tar -zxf "$(SRCDIR)/$(PYOPENGLVERSION).tar.gz" && \
cd "$(PYOPENGLVERSION)" && \
export PATH="$(PYTHONPREFIX)/bin:$(PATH)" && \
export LD_LIBRARY_PATH="$(PYTHONPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
$(PYTHON) setup.py build && \
$(PYTHON) setup.py install
touch $@
$(TGTDIR)/pyopenglaccel: $(SRCDIR)/$(PYOPENGLACCELVERSION).tar.gz $(PYTHON) pyopengl
cd "$(TMPDIR)" && \
rm -fr "$(PYOPENGLACCELVERSION)" && \
tar -zxf "$(SRCDIR)/$(PYOPENGLACCELVERSION).tar.gz" && \
cd "$(PYOPENGLACCELVERSION)" && \
export PATH="$(PYTHONPREFIX)/bin:$(PATH)" && \
export LD_LIBRARY_PATH="$(PYTHONPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
$(PYTHON) setup.py build && \
$(PYTHON) setup.py install
touch $@
$(TGTDIR)/qt: $(SRCDIR)/$(QTVERSION).tar.gz zlib jpeg
cd "$(TMPDIR)" && \
rm -fr "$(QTVERSION)" && \
tar -zxf "$(SRCDIR)/$(QTVERSION).tar.gz" && \
cd "$(QTVERSION)" && \
export PATH="$(PYTHONPREFIX)/bin:$(PATH)" && \
export LD_LIBRARY_PATH="$(PYTHONPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
./configure \
--prefix="$(PREFIX)" \
-developer-build \
-opengl \
-opensource \
-confirm-license \
-no-xmlpatterns \
-no-audio-backend \
-no-phonon \
-no-webkit \
-no-script && \
$(MAKE) $(MAKE_FLAGS) && \
$(MAKE) -j1 install
touch $@
$(TGTDIR)/pyqt: $(SRCDIR)/$(PYQTVERSION).tar.gz sip pyopenglaccel qt
cd "$(TMPDIR)" && \
rm -fr "$(PYQTVERSION)" && \
tar -zxf "$(SRCDIR)/$(PYQTVERSION).tar.gz" && \
cd "$(PYQTVERSION)" && \
export PATH="$(PYTHONPREFIX)/bin:$(PATH)" && \
export LD_LIBRARY_PATH="$(PYTHONPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
$(PYTHON) configure.py --confirm-license -g -q $(QTMAKE) \
--enable=QtCore --enable=QtGui --enable=QtDeclarative \
--enable=QtMultimedia --enable=QtNetwork --enable=QtOpenGL \
--enable=QtTest --no-designer-plugin && \
$(MAKE) $(MAKE_FLAGS) && \
$(MAKE) -j1 install
touch $@
$(TGTDIR)/sip: $(SRCDIR)/$(SIPVERSION).tar.gz python
cd "$(TMPDIR)" && \
rm -fr "$(SIPVERSION)" && \
tar -zxf "$(SRCDIR)/$(SIPVERSION).tar.gz" && \
cd "$(SIPVERSION)" && \
export PATH="$(PYTHONPREFIX)/bin:$(PATH)" && \
export LD_LIBRARY_PATH="$(PYTHONPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
$(PYTHON) configure.py && \
$(MAKE) $(MAKE_FLAGS) && \
$(MAKE) -j1 install
touch $@
$(TGTDIR)/wx: $(SRCDIR)/wxX11-$(WXVERSION).tar.bz2
cd "$(TMPDIR)" && \
rm -rf "wxX11-$(WXVERSION)" && \
tar xvf "$(SRCDIR)/wxX11-$(WXVERSION).tar.bz2" && \
cd "wxX11-$(WXVERSION).tar.bz2" && \
./configure && \
$(MAKE) $(MAKE_FLAGS) && \
$(MAKE) -j1 install
touch $@
$(TGTDIR)/wxpython: $(SRCDIR)/wxPython-src-$(WXPYTHONVERSION).tar.bz2 python jpeg zlib tiff
cd "$(TMPDIR)" && \
rm -fr "wxPython-src-$(WXPYTHONVERSION)" && \
tar -xjf "$(SRCDIR)/wxPython-src-$(WXPYTHONVERSION).tar.bz2" && \
rm -fr "wxPython-src-$(WXPYTHONVERSION)-$(HOSTTYPE)" && \
mkdir "wxPython-src-$(WXPYTHONVERSION)-$(HOSTTYPE)" && \
cd "wxPython-src-$(WXPYTHONVERSION)-$(HOSTTYPE)" && \
export PATH="$(PYTHONPREFIX)/bin:$(PATH)" && \
export LD_LIBRARY_PATH="$(PYTHONPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
export CPPFLAGS="-I$(JPEGPREFIX)/include -I$(TIFFPREFIX)/include -I$(ZLIBPREFIX)/include -I$(SQLITEPREFIX)/include $${CPPFLAGS}" && \
export LDFLAGS="-L$(JPEGPREFIX)/lib -L$(TIFFPREFIX)/lib -L$(ZLIBPREFIX)/lib -L$(SQLITEPREFIX)/lib $${LDFLAGS}" && \
export LD_LIBRARY_PATH="$(JPEGPREFIX)/lib:$(TIFFPREFIX)/lib:$(ZLIBPREFIX)/lib:$(SQLITEPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
if test -f "$(GTKPREFIX)/lib/libgtk-x11-2.0.la" ; then \
export CPPFLAGS="-I$(GTKPREFIX)/include $${CPPFLAGS}" && \
export LDFLAGS="-L$(GTKPREFIX)/lib $${LDFLAGS}" && \
export LD_LIBRARY_PATH="$(GTKPREFIX)/lib:$${LD_LIBRARY_PATH}" ; \
fi && \
if test -d "$(GLIBPREFIX)/lib/pkgconfig" ; then \
export PKG_CONFIG_PATH="$(GLIBPREFIX)/lib/pkgconfig:$${PKG_CONFIG_PATH}" ; \
fi && \
"../wxPython-src-$(WXPYTHONVERSION)/configure" \
--prefix="$(WXPYTHONPREFIX)" \
$(WXPYTHONTOOLKIT_$(WXUSEGTK)) \
$(WXFLAGS) && \
$(MAKE) $(MAKE_FLAGS) && \
$(MAKE) $(MAKE_FLAGS) -C contrib/src/gizmos && \
$(MAKE) $(MAKE_FLAGS) -C contrib/src/stc && \
$(MAKE) -j1 install && \
$(MAKE) -j1 install -C contrib/src/gizmos && \
$(MAKE) -j1 install -C contrib/src/stc && \
cd "../wxPython-src-$(WXPYTHONVERSION)/wxPython/" && \
$(PYTHON) setup.py build_ext --inplace && \
$(PYTHON) setup.py install
touch $@
$(TGTDIR)/nose: $(SRCDIR)/$(PYTHONNOSEVERSION).tar.gz python
cd "$(TMPDIR)" && \
rm -fr "$(PYTHONNOSEVERSION)" && \
tar -xzf "$(SRCDIR)/$(PYTHONNOSEVERSION).tar.gz" && \
cd "$(PYTHONNOSEVERSION)" && \
export PATH="$(PYTHONPREFIX)/bin:$(PATH)" && \
export LD_LIBRARY_PATH="$(PYTHONPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
$(PYTHON) setup.py install
touch $@
$(TGTDIR)/pil: $(SRCDIR)/$(PILVERSION).tar.gz python jpeg zlib tiff
cd "$(TMPDIR)" && \
rm -fr "$(PILVERSION)" && \
tar -xzf "$(SRCDIR)/$(PILVERSION).tar.gz" && \
cd "$(PILVERSION)" && \
perl -pi -e 's@(^JPEG_ROOT.*?)=.*@$$1= "$(JPEGPREFIX)"@g' setup.py && \
perl -pi -e 's@(^ZLIB_ROOT.*?)=.*@$$1= "$(ZLIBPREFIX)"@g' setup.py && \
perl -pi -e 's@(^TIFF_ROOT.*?)=.*@$$1= "$(TIFFPREFIX)"@g' setup.py && \
export PATH="$(PYTHONPREFIX)/bin:$(PATH)" && \
export LD_LIBRARY_PATH="$(PYTHONPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
$(PYTHON) setup.py build_ext -i && \
$(PYTHON) selftest.py && \
$(PYTHON) setup.py install
touch $@
$(TGTDIR)/jpeg: $(SRCDIR)/jpegsrc.v$(JPEGVERSION).tar.gz
cd "$(TMPDIR)" && \
rm -fr "jpeg-$(JPEGVERSION)" && \
tar -xzf "$(SRCDIR)/jpegsrc.v$(JPEGVERSION).tar.gz" && \
cd "jpeg-$(JPEGVERSION)" && \
./configure \
CC="gcc" CPP="cpp" \
--prefix="$(JPEGPREFIX)" && \
$(MAKE) $(MAKE_FLAGS) && \
$(MAKE) -j1 install
touch $@
$(TGTDIR)/zlib: $(SRCDIR)/$(ZLIBVERSION).tar.bz2
cd "$(TMPDIR)" && \
rm -fr "$(ZLIBVERSION)" && \
tar -xjf "$(SRCDIR)/$(ZLIBVERSION).tar.bz2" && \
cd "$(ZLIBVERSION)" && \
./configure \
--prefix="$(ZLIBPREFIX)" && \
$(MAKE) $(MAKE_FLAGS) && \
$(MAKE) -j1 install && \
if ! test -r "$(ZLIBPREFIX)/include/zlib.h" ; then \
echo "error finding zlib.h" && \
exit 1 ; \
fi
touch $@
#$(TGTDIR)/png: $(SRCDIR)/$(PNGVERSION).tar.bz2
# cd "$(TMPDIR)" && \
# rm -fr "$(PNGVERSION)" && \
# tar -xjf "$(SRCDIR)/$(PNGVERSION).tar.bz2" && \
# cd "$(PNGVERSION)" && \
# ./configure \
# --prefix="$(PNGPREFIX)" && \
# $(MAKE) $(MAKE_FLAGS) && \
# $(MAKE) -j1 install
# touch $@
$(TGTDIR)/tiff: $(SRCDIR)/$(TIFFVERSION).tar.gz zlib jpeg
mkdir -p "$(TMPDIR)" && cd "$(TMPDIR)" && \
rm -fr "$(TIFFVERSION)" && \
tar -xzf "$(SRCDIR)/$(TIFFVERSION).tar.gz" && \
cd "$(TIFFVERSION)" && \
./configure \
--prefix="$(TIFFPREFIX)" \
--enable-cxx \
--with-zlib-include-dir="$(ZLIBPREFIX)/include" \
--with-zlib-lib-dir="$(ZLIBPREFIX)/lib" \
--with-jpeg-include-dir="$(JPEGPREFIX)/include" \
--with-jpeg-lib-dir="$(JPEGPREFIX)/lib" && \
$(MAKE) $(MAKE_FLAGS) && \
$(MAKE) -j1 install
touch $@
$(TGTDIR)/hdf5: $(SRCDIR)/$(HDF5VERSION).tar.bz2 zlib
cd "$(TMPDIR)" && \
rm -fr "$(HDF5VERSION)" && \
tar -xjf "$(SRCDIR)/$(HDF5VERSION).tar.bz2" && \
cd "$(HDF5VERSION)" && \
./configure \
--prefix="$(HDF5PREFIX)" \
--with-pic \
--enable-hl \
--enable-cxx \
--enable-fortran \
--enable-production \
--with-zlib="$(ZLIBPREFIX)" && \
$(MAKE) $(MAKE_FLAGS) && \
$(MAKE) -j1 install
touch $@
$(TGTDIR)/h5py: $(SRCDIR)/$(H5PYVERSION).tar.gz hdf5 numpy
cd "$(TMPDIR)" && \
rm -fr "$(H5PYVERSION)" && \
tar -xzf "$(SRCDIR)/$(H5PYVERSION).tar.gz" && \
cd "$(H5PYVERSION)" && \
export PATH="$(PYTHONPREFIX)/bin:$(PATH)" && \
export LD_LIBRARY_PATH="$(PYTHONPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
$(PYTHON) setup.py build \
--hdf5="$(HDF5PREFIX)" && \
$(PYTHON) setup.py install
touch $@
$(TGTDIR)/pyzmq: $(SRCDIR)/$(PYZMQVERSION).tar.gz python
cd "$(TMPDIR)" && \
rm -fr "$(PYZMQVERSION)" && \
tar -xzf "$(SRCDIR)/$(PYZMQVERSION).tar.gz" && \
cd "$(PYZMQVERSION)" && \
export PATH="$(PYTHONPREFIX)/bin:$(PATH)" && \
export LD_LIBRARY_PATH="$(PYTHONPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
$(PYTHON) setup.py build && \
$(PYTHON) setup.py install
touch $@
$(TGTDIR)/javabridge: $(SRCDIR)/$(JAVABRIDGEVERSION).tar.gz python numpy
cd "$(TMPDIR)" && \
rm -fr "$(JAVABRIDGEVERSION)" && \
tar -xzf "$(SRCDIR)/$(JAVABRIDGEVERSION).tar.gz" && \
cd "$(JAVABRIDGEVERSION)" && \
export PATH="$(PYTHONPREFIX)/bin:$(PATH)" && \
export LD_LIBRARY_PATH="$(PYTHONPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
$(PYTHON) setup.py build && \
$(PYTHON) setup.py install
touch $@
$(TGTDIR)/bioformats: $(SRCDIR)/$(BIOFORMATSVERSION).tar.gz python javabridge
cd "$(TMPDIR)" && \
rm -fr "$(BIOFORMATSVERSION)" && \
tar -xzf "$(SRCDIR)/$(BIOFORMATSVERSION).tar.gz" && \
cd "$(BIOFORMATSVERSION)" && \
export PATH="$(PYTHONPREFIX)/bin:$(PATH)" && \
export LD_LIBRARY_PATH="$(PYTHONPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
$(PYTHON) setup.py build && \
$(PYTHON) setup.py install
touch $@
$(TGTDIR)/boost: $(SRCDIR)/$(BOOSTVERSION).tar.bz2 python
cd "$(TMPDIR)" && \
rm -fr "$(BOOSTVERSION)" && \
tar -xjf "$(SRCDIR)/$(BOOSTVERSION).tar.bz2" && \
cd "$(BOOSTVERSION)" && \
export PATH="$(PYTHONPREFIX)/bin:$(PATH)" && \
export LD_LIBRARY_PATH="$(PYTHONPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
./bootstrap.sh \
--prefix="$(BOOSTPREFIX)" \
--with-python-root="$(PYTHONPREFIX)" \
--with-libraries="python" && \
./bjam install
touch $@
#
# Vigra work-arounds: gcc 4.7.7 distributed with Red Hat 6 segfaults when
# it encounters an optimization that can't work for RGB iterators but can
# for RGBA (but the code path is never taken for RGB).
#
# impex.hxx.patch removes the optimization
#
$(TGTDIR)/vigra: $(SRCDIR)/$(VIGRAVERSION)-src.tar.gz numpy fftw hdf5 tiff jpeg boost
cd "$(TMPDIR)" && \
rm -fr "$(VIGRAVERSION)" && \
tar -zxf "$(SRCDIR)/$(VIGRAVERSION)-src.tar.gz" && \
cd "$(TMPDIR)/$(VIGRAVERSION)/include/vigra" && \
wget $(WGETFLAGS) "$(PACKAGEHOST)/impex.hxx.patch" && \
patch < impex.hxx.patch && \
cd "$(TMPDIR)/$(VIGRAVERSION)" && \
export PATH="$(PYTHONPREFIX)/bin:$(PATH)" && \
export LD_LIBRARY_PATH="$(PYTHONPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
cmake \
-DCMAKE_INSTALL_PREFIX="$(VIGRAPREFIX)" \
-DPYTHON_EXECUTABLE="$(PYTHON)" \
-DPYTHON_LIBRARY="$(PYTHONPREFIX)/lib/libpython$(PYVERSION).so" \
-DCMAKE_PREFIX_PATH="$(PYTHONPREFIX)" \
-DDEPENDENCY_SEARCH_PREFIX="$(HDF5PREFIX);$(FFTWPREFIX);$(TIFFPREFIX);$(JPEGPREFIX)" && \
$(MAKE) && \
$(MAKE) install
touch $@
$(TGTDIR)/ilastik: $(SRCDIR)/ilastik-v$(ILASTIKVERSION).tar.gz vigra pyqt qimgtoarr
cd "$(TMPDIR)" && \
rm -fr "ilastik-v$(ILASTIKVERSION)" && \
tar -xzf "$(SRCDIR)/ilastik-v$(ILASTIKVERSION).tar.gz" && \
cd "$(TMPDIR)/ilastik-v$(ILASTIKVERSION)" && \
export PATH="$(PYTHONPREFIX)/bin:$(PATH)" && \
export LD_LIBRARY_PATH="$(PYTHONPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
$(PYTHON) setup.py build && \
$(PYTHON) setup.py install
touch $@
$(TGTDIR)/qimgtoarr: $(SRCDIR)/$(QIMGTOARRVERSION).tar.gz numpy pyqt
cd "$(TMPDIR)" && \
rm -fr "$(QIMGTOARRVERSION)" && \
tar -xzf "$(SRCDIR)/$(QIMGTOARRVERSION).tar.gz" && \
cd "$(QIMGTOARRVERSION)" && \
export PATH="$(PYTHONPREFIX)/bin:$(PATH)" && \
export LD_LIBRARY_PATH="$(PYTHONPREFIX)/lib:$${LD_LIBRARY_PATH}" && \
$(PYTHON) setup.py build && \
$(PYTHON) setup.py install
touch $@
$(TGTDIR)/cellh5: $(SRCDIR)/$(CELLH5VERSION).tar.gz $(SRCDIR)/$(CELLH5VERSION).patch sklearn pandas lxml
cd "$(TMPDIR)" && \
rm -fr "$(CELLH5VERSION)" && \
tar -xzf "$(SRCDIR)/$(CELLH5VERSION).tar.gz" && \
cd "$(CELLH5VERSION)" && \
dos2unix -k pysrc/cellh5write.py && \