Info2: << Package: viennarna Version: 2.1.8 Revision: 7 Source: http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-%v.tar.gz Source-Checksum: SHA256(37a0a0b7c8a167bcdab1a85d88bcb1025ad8e00a4b00a147bf36d45dc8ca7560) SourceDirectory: ViennaRNA-%v Type: perl (5.16.2) Distribution: 10.9 #only in unused codepaths of static-only lib: #Depends: gd2-shlibs, x11 Depends: << system-perl%type_pkg[perl] << #BuildDepends: graphviz BuildDepends: << doxygen, gd2, fink-package-precedence, texlive-base, x11-dev << GCC: 4.0 UpdatePOD: true Description: RNA structural prediction DescDetail: << The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. The package allows you to - predict minimum free energy secondary structures - calculate the partition function for the ensemble of structures - calculate suboptimal structures in a given energy range - predict consensus secondary structures from a multiple sequence alignment - predict melting curves - search for sequences folding into a given structure - compare two secondary structures - The package includes a Perl5 module that gives access to almost all functions of the C library from Perl. - The following executables are provided in /sw/bin: RNA2Dfold Compute MFE structure, partition function and representative sample structures of k,l neighborhoods RNAaliduplex Predict conserved RNA-RNA interactions between two alignments RNAalifold Calculate secondary structures for a set of aligned RNA sequences RNAcofold Calculate secondary structures of two RNAs with dimerization RNAdistance Calculate distances between RNA secondary structures RNAduplex Compute the structure upon hybridization of two RNA strands RNAeval Evaluate free energy of RNA sequences with given secondary structure RNAfold Calculate minimum free energy secondary structures and partition function of RNAs RNAheat Calculate the specific heat (melting curve) of an RNA sequence RNAinverse Find RNA sequences with given secondary structure (sequence design) RNALalifold Calculate locally stable secondary structures for a set of aligned RNAs RNALfold Calculate locally stable secondary structures of long RNAs RNApaln RNA alignment based on sequence base pairing propensities RNApdist Calculate distances between thermodynamic RNA secondary structures ensembles RNAparconv Convert energy parameter files from ViennaRNA 1.8 to 2.0 format RNAPKplex Predict RNA secondary structures including pseudoknots RNAplex Find targets of a query RNA RNAplfold Calculate average pair probabilities for locally stable secondary structures RNAplot Draw RNA Secondary Structures in PostScript, SVG, or GML RNAsnoop Find targets of a query H/ACA snoRNA RNAsubopt Calculate suboptimal secondary structures of RNAs RNAup Calculate the thermodynamics of RNA-RNA interactions Several small but helpful Perl Utilities are in /sw/share/ViennaRNA/bin which is not added to your PATH by default. These include the following: ct2db Produce dot bracket notation of an RNA secondary structure given as mfold .ct file b2mt.pl Produce coordinates for a mountain plot from bracket notation cmount.pl Produce a colored mountain plot of a consensus structure coloraln.pl Colorize an alignment with consensus structure colorrna.pl Colorize an alirna.ps file mountain.pl Produce coordinates for a mountain plot from a dot plot refold.pl Refold using consensus structure as constraint relplot.pl Annotate a secdonary structure plot with reliability information rotate_ss.pl Rotate or mirror coordinates of secondary structure plot switch.pl Design bistable RNA sequences -- For more detailed information on these please enter the command info RNA or visit the website http://www.tbi.univie.ac.at/RNA/manpages.html << # dmacks--fixed a ton of -I ordering and local -L flags so that # external libs are correctly detected and build-directory files are # correctly used PatchFile: %n.patch PatchFile-MD5: 1fb2358ece4980f5a0c2118329e28346 PatchScript: << #!/bin/zsh -efv %{default_script} perl -pi -e 's|ersion 1.6|ersion 2.1.8|g' README perl -pi -e 's|ersion 1.6|ersion 2.1.8|g' man/RNAlib.info perl -pi -e 's|(\* libRNA.a)( \(texinfo\).)|\1:\2|' man/RNAlib.info << CompileScript: << #!/bin/zsh -efv export ARCHFLAGS='' ./configure %c --prefix=%p PerlCmd=/usr/bin/perl PythonCmd=/usr/bin/python make V=1 fink-package-precedence --prohibit-bdep=%n-dev . fink-package-precedence --prohibit-bdep=%n-dev --no-libs --depfile-ext='\.d' . << InfoTest: << TestScript: << make check || exit 2 << << InstallScript: << #!/bin/zsh -efv perl -pi.bak -e 's|/usr/local|%p/share|g' Perl/Makefile.perl perl -pi.bak -e 's;/usr/share/man;%p/share/man;g' Perl/Makefile.perl mkdir -p %i/share/man/man3/ mkdir -p %i/lib mkdir -p %i/include/ViennaRNA %i/lib/ViennaRNA make -j1 install DESTDIR=%d INSTALLPRIVLIB=%p/lib/perl5/%type_raw[perl]/ INSTALLARCHLIB=%p/lib/perl5/%type_raw[perl]/darwin-thread-multi-2level/ INSTALLSITELIB=%p/lib/perl5/%type_raw[perl]/ INSTALLSITEARCH=%p/lib/perl5/%type_raw[perl]/darwin-thread-multi-2level INSTALLSCRIPT=%p/share/viennarna/scripts << ############################################################################### # SplitOff: << Package: %N-dev BuildDependsOnly: True Replaces: %N Files: << include lib/libg2.a lib/libRNA.a lib/pkgconfig share/info << InfoDocs: RNAlib.info << ############################################################################### DocFiles: AUTHORS ChangeLog COPYING INSTALL INSTALL.configure NEWS README THANKS License: GPL Homepage: http://www.tbi.univie.ac.at/RNA/ Maintainer: W. G. Scott # end of Info2 field: <<