prime-phylo-1.0.11/install_macports_and_prime.sh000644 010617 000144 00000002656 12063637725 023037 0ustar00esjolundusers000000 000000 #!/bin/sh # Run this script like this: # # mkdir ~/installdir # sh install_ports_and_prime.sh ~/installdir set -e macports_version=2.0.4 installdir="$1" if [ -d "$installdir" ]; then cd "$installdir" export PATH="$installdir/macports/bin:$PATH" # curl -O http://codesynthesis.com/download/xsd/3.3/macosx/i686/xsd-3.3.0-i686-macosx.tar.bz2 # tar xfj xsd-3.3.0-i686-macosx.tar.bz2 curl -O https://distfiles.macports.org/MacPorts/MacPorts-${macports_version}.tar.gz tar xfz MacPorts-${macports_version}.tar.gz cd MacPorts-${macports_version} ./configure --prefix="$installdir/macports" --with-no-root-privileges make make install port -v selfupdate # maybe we need to install fortran like this: # port install gcc44 +gfortran port install openmpi libxml2 bison flex gengetopt port install boost +openmpi port install cmake port install subversion cd "$installdir" svn co --trust-server-cert --non-interactive https://svn.sbc.su.se/repos/PrIME/trunk prime-trunk tmpdir=`mktemp -d /tmp/prime_build.XXXX` cd $tmpdir && cmake "-DCMAKE_PREFIX_PATH=$installdir;$installdir/xsd-3.3.0-i686-macosx/" -DCMAKE_INSTALL_PREFIX=$installdir/primeinstall "-DCMAKE_Fortran_COMPILER=$installdir/macports/bin/gfortran-mp-4.4" "$installdir/prime-trunk/" make -j 8 make install # make test echo export "PATH=$installdir/primeinstall/bin:$installdir/macports/bin:$PATH" else echo "The directory $installdir doesn't exist" fi prime-phylo-1.0.11/FILE_FORMATS000644 010617 000144 00000006353 12063637725 016742 0ustar00esjolundusers000000 000000 * Newick format with extensions The Newick format is documented here: http://evolution.genetics.washington.edu/phylip/newick_doc.html Gene and species trees are saved in Newick format with some additional tags defined. Our extensions come in comments of the from "[&&PRIME ]". The part follows this grammar: ::=