Changes between Version 28 and Version 29 of InstallPyCml


Ignore:
Timestamp:
May 22, 2014, 11:28:50 AM (6 years ago)
Author:
jonc@…
Comment:

Only document prefered libraries; alternatives are now deprecated.

Legend:

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  • InstallPyCml

    v28 v29  
    6868== RELAX NG validator ==
    6969
    70 === Preferred option: lxml ===
    71 
    7270As of r15854 Chaste includes support for [http://lxml.de/validation.html#relaxng lxml].  This may be available in your distribution, or you can use `easy_install`.
    7371
     
    7876See http://lxml.de/installation.html for further details if required.
    7977
    80 === Alternative option: RNV ===
    81 
    82 RNV needs to be downloaded from http://ftp.davidashen.net/PreTI/RNV/RNV.ZIP and built from source:
    83 {{{
    84 wget "http://ftp.davidashen.net/PreTI/RNV/RNV.ZIP"
    85 unzip RNV.ZIP
    86 cd rnv-*
    87 make -f Makefile.gnu
    88 cp rvp /home/scratch/chaste-libs/bin/
    89 cd ..
    90 rm RNV.ZIP
    91 }}}
    92 The `cp` line ensures that the tool is available on your path and so can be found by !PyCml.  As usual, edit `/home/scratch/chaste-libs` to match your system.
    93 
    9478== RDF library ==
    9579
    96 In order to handle CellML metadata, an RDF library is needed.  !PyCml supports either [http://www.rdflib.net/ RDFLib] or the [http://librdf.org/ Redland RDF library].
    97 
    98 === Preferred option: RDFLib ===
    99 
    100 This is the easier library to install, being available both as packages in many distributions, or via easy_install.
     80In order to handle CellML metadata, an RDF library is needed.  !PyCml supports version 2 of [http://www.rdflib.net/ RDFLib]; the alternative [http://librdf.org/ Redland RDF library] is now deprecated.
    10181
    10282Ubuntu:
     
    11292easy_install:
    11393{{{
    114 easy_install rdflib
     94easy_install "rdflib==2.4.2"
    11595}}}
    11696
    117 === Alternative option: Redland library ===
    118 
    119 On Ubuntu (hardy or above) this is a simple matter of:
     97pip:
    12098{{{
    121 sudo apt-get install python-librdf
     99pip install "rdflib==2.4.2"
    122100}}}
    123 
    124 Other systems may have an equivalent, or you'll have to compile it yourself.  Online documentation is available [http://librdf.org/INSTALL.html here] and [http://librdf.org/docs/python.html here].
    125 The following instructions may work for you, if you have a few prerequisites installed on your system.
    126 {{{
    127 export CHASTE_LIBS=/home/scratch/chaste-libs
    128 export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CHASTE_LIBS/rdf/lib
    129 cd $CHASTE_LIBS
    130 wget http://download.librdf.org/source/redland-1.0.10.tar.gz
    131 wget http://download.librdf.org/source/redland-bindings-1.0.10.1.tar.gz
    132 wget http://download.librdf.org/source/rasqal-0.9.19.tar.gz
    133 wget http://download.librdf.org/source/raptor-1.4.21.tar.gz
    134 
    135 tar -zxf raptor-1.4.21.tar.gz
    136 cd raptor-1.4.21/
    137 ./configure --prefix=$CHASTE_LIBS/rdf
    138 make install
    139 cd ..
    140 
    141 export PKG_CONFIG_PATH=$CHASTE_LIBS/rdf/lib/pkgconfig/
    142 
    143 tar -zxf rasqal-0.9.19.tar.gz
    144 cd rasqal-0.9.19/
    145 ./configure --prefix=$CHASTE_LIBS/rdf
    146 make install
    147 cd ..
    148 
    149 # You may find you need the mysql development headers before this will build (eg. on Fedora: sudo yum install mysql-devel.x86_64.
    150 # Debian: sudo aptitude install libmysqlclient-dev. Alternatively (and untested): http://dev.mysql.com/downloads/mysql/ *)
    151 tar -zxf redland-1.0.10.tar.gz
    152 cd redland-1.0.10
    153 ./configure --prefix=$CHASTE_LIBS/rdf
    154 make install
    155 cd ..
    156 
    157 tar -zxf redland-bindings-1.0.10.1.tar.gz
    158 cd redland-bindings-1.0.10.1
    159 ./configure --with-python --prefix=$CHASTE_LIBS/rdf --without-perl --without-php --without-ruby
    160 make
    161 mkdir -p $CHASTE_LIBS/lib/python
    162 cp python/RDF.py python/Redland.so $CHASTE_LIBS/lib/python/
    163 }}}
    164 
    165 The following lines will then need to be added to your `~/.bashrc` file:
    166 {{{
    167 export PYTHONPATH=$CHASTE_LIBS/lib/python
    168 export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CHASTE_LIBS/rdf/lib
    169 }}}
    170 
    171 * Note: if none of these is viable (e.g., you don't have any root privileges), you can pass `--with-mysql=no` as an option to the configure script.
    172101
    173102== !PyCml itself ==