Ycarus Gentoo ebuild

science

These ebuilds come from .

If you have some problems, go to the official site first.

sci-libs

Cgraph : C functions that generate PostScript for publication quality scientific plots ( http://neurovision.berkeley.edu/software/A_Cgraph.html )

amber99sb_phipsi : AMBER99SB PHI PSI table (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) ( https://research.chemistry.ohio-state.edu/bruschweiler/protein-force-field/ )

amber99sbnmr : AMBER99SBnmr1 force field (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) ( https://research.chemistry.ohio-state.edu/bruschweiler/protein-force-field/ )

amber99sbnmr-ildn : AMBER99SBnmr1-ILDN FF (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) ( https://research.chemistry.ohio-state.edu/bruschweiler/protein-force-field/ )

amdlibm : Optimized libm replacement from AMD for x86_64 architectures ( http://developer.amd.com/tools/cpu-development/libm/" einfo " ${HOMEPAGE} )

armadillo : Streamlined C++ linear algebra library ( http://arma.sourceforge.net/ )

arrayfire : A general purpose GPU library ( http://www.arrayfire.com/ )

asl : Hardware accelerated multiphysics simulation platform ( http://asl.org.il/ )

atlas : Automatically Tuned Linear Algebra Software ( http://math-atlas.sourceforge.net/ )

bigdft-abi : A DFT electronic structure code using a wavelet basis set ( http://www.abinit.org/downloads/plug-in-sources )

blas-reference : Reference implementation of BLAS ( http://www.netlib.org/lapack/ )

blastdb : The BLAST NR database ( http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web%26PAGE_TYPE=BlastDocs%26DOC_TYPE=ProgSelectionGuide )

bloom : C++ Bloom Filter Library ( https://github.com/arashpartow/bloom )

calculix-ccx : A Free Software Three-Dimensional Structural Finite Element Program ( http://www.calculix.de/ )

calculix-cgx : A Free Software Three-Dimensional Structural Finite Element Program ( http://www.calculix.de/ )

cblas-reference : C wrapper interface to the F77 reference BLAS implementation ( http://www.netlib.org/cblas/ )

ccif : CCP4 ccif lib ( http://www.ccp4.ac.uk/ )

cgnstools : The CFD General Notation System (CGNS) tools ( http://www.cgns.org/ )

clblas : A software library containing BLAS routines for OpenCL ( https://github.com/clMathLibraries/clBLAS )

clfft : Library containing FFT functions written in OpenCL ( https://github.com/clMathLibraries/clFFT )

clrng : A library for uniform random number generation in OpenCL ( https://github.com/clMathLibraries/clRNG )

cs-rosetta-db : System for chemical shifts based protein structure prediction using ROSETTA ( http://spin.niddk.nih.gov/bax/software/CSROSETTA/ )

dcmtk : OFFIS DICOM image files library and tools ( http://dicom.offis.de/dcmtk.php.en )

dealii : Solving partial differential equations with the finite element method ( http://www.dealii.org/ )

elmer-eio : Finite element programs, libraries, and visualization tools - elmer I/O library ( http://www.csc.fi/english/pages/elmer )

elmer-hutiter : Finite element programs, libraries, and visualization tools - hutiter library ( http://www.csc.fi/english/pages/elmer )

etsf_io : A library of F90 routines to read/write the ETSF file format ( http://www.etsf.eu/resources/software/libraries_and_tools/ )

factory : C++ library for representing multivariate polynomials ( http://www.mathematik.uni-kl.de/pub/Math/Singular/Factory )

fast5 : C++ header-only library for reading Oxford Nanopore Fast5 files ( https://github.com/mateidavid/fast5 )

fdlibm : C math library supporting IEEE 754 floating-point arithmetic ( http://www.netlib.org/fdlibm )

fgsl : A Fortran interface to the GNU Scientific Library ( http://www.lrz.de/services/software/mathematik/gsl/fortran/ )

fox : A library designed to allow the easy use of XML from Fortran ( http://www1.gly.bris.ac.uk/~walker/FoX/ )

framewave : A collection of popular image and signal processing routines ( http://framewave.sourceforge.net/ )

geom : A complete OpenCascade - OCAF based CAD framework ( http://sourceforge.net/projects/salomegeometry/ )

ghmm : General Hidden Markov Model library ( http://ghmm.sourceforge.net/ )

givaro : C++ library for arithmetic and algebraic computations ( http://ljk.imag.fr/CASYS/LOGICIELS/givaro/ )

gmsh : A three-dimensional finite element mesh generator ( http://www.geuz.org/gmsh/ )

gotoblas2 : Fast implementations of the Basic Linear Algebra Subroutines ( http://www.tacc.utexas.edu/tacc-projects/gotoblas2/ )

gsl : GNU Scientific Library ( https://www.gnu.org/software/gsl/" --url "${HOMEPAGE}" )

htslib-plugins : iRODs plugins for =htslib-1.4 ( https://github.com/samtools/htslib-plugins )

iRODS : Integrated Rule Oriented Data System, a data management software ( https://irods.org )

iml : Integer Matrix Library ( http://www.cs.uwaterloo.ca/~astorjoh/iml.html )

io_lib : General purpose trace and experiment file reading/writing interface ( http://staden.sourceforge.net/ )

ipp : Intel Integrated Performance Primitive library ( http://software.intel.com/en-us/articles/intel-ipp/ )

itk : NLM Insight Segmentation and Registration Toolkit ( http://www.itk.org )

jhdf5 : Java binding for HDF5 compatible with HDF5 1.6/1.8 ( https://wiki-bsse.ethz.ch/display/JHDF )

k3match : Fast matching of large sets of points in 3D space, in O(N log N) time ( http://pschella.github.com/k3match/ )

labbookdb : Lab Book Database Framework ( https://github.com/TheChymera/LabbookDB )

lapack-reference : Reference implementation of LAPACK ( http://www.netlib.org/lapack/ )

lapacke-reference : C Interface to LAPACK ( http://www.netlib.org/lapack/ )

lapackpp : C++ wrapper for LAPACK libraries ( http://lapackpp.sourceforge.net )

lib2bit : C library for accessing 2bit files ( https://github.com/dpryan79/lib2bit )

libStatGen : Set of classes for creating statistical genetic programs ( https://github.com/statgen/libStatGen )

libcgnsoo : Object-oriented interface to the CGNS Mid-level library ( http://openfoam-extend.sourceforge.net )

libfac : libfac is an extension of Singular-factory to finite fields ( ftp://www.mathematik.uni-kl.de/pub/Math/Singular/Libfac/ )

libgeodecomp : An auto-parallelizing library to speed up computer simulations ( http://www.libgeodecomp.org )

libmatheval : library to parse and evaluate symbolic expressions ( http://www.gnu.org/software/libmatheval/ )

libmaus : Library for biobambam ( https://github.com/gt1/libmaus )

libmaus2 : Library for biobambam2 ( https://github.com/gt1/libmaus )

libmed : A library to store and exchange meshed data or computation results ( http://www.salome-platform.org/ )

libspatialindex : General framework for developing spatial indices ( http://libspatialindex.github.com/ )

libsufr : LIBrary of Some Useful Fortran Routines ( http://libsufr.sourceforge.net/ )

libxc : A library of exchange-correlation functionals for use in DFT ( http://octopus-code.org/wiki/Libxc )

lwpr : The Locally Weighted Projection Regression Library ( http://www.ipab.inf.ed.ac.uk/slmc/software/lwpr/ )

matc : Finite element programs, libraries, and visualization tools - math C library ( http://www.csc.fi/english/pages/elmer )

med : Modeling and Exchange of Data library ( http://www.code-aster.org/outils/med/ )

mesquite : Mesh Quality Improvement Toolkit ( http://www.cs.sandia.gov/optimization/knupp/Mesquite.html )

mkl : Intel Math Kernel Library: linear algebra, fft, math functions ( http://software.intel.com/en-us/articles/intel-mkl/ )

mlpack : Scalable c++ machine learning library ( http://www.mlpack.org/ )

modglue : C++ library for handling of multiple co-processes ( http://cadabra.phi-sci.com )

mpiblacs : Basic Linear Algebra Communication Subprograms with MPI ( http://www.netlib.org/blacs/" SRC_URI="${HOMEPAGE}/mpiblacs.tgz ${HOMEPAGE}/${PN}-patch03.tgz test? ( ${HOMEPAGE}/blacstester.tgz )" URL: ${HOMEPAGE )

msms : MSMS library python extension module ( http://mgltools.scripps.edu/downloads#msms )

nexus : Data format for neutron and x-ray scattering data ( http://nexusformat.org/ )

ni-visa : Placeholder for an NI-VISA library ebuild ( http://www.ni.com/ )

nibabel : Access a cacophony of neuro-imaging file formats ( http://nipy.org/nibabel/ )

nipy : Neuroimaging tools for Python ( http://nipy.org/ )

nipy-data : Demo Data for Python Neuroimaging ( http://nipy.org/ )

nipy-templates : Normalization templates for Python Neuroimaging ( http://nipy.org/ )

nipype : Neuroimaging in Python: Pipelines and Interfaces ( http://nipy.sourceforge.net/nipype/ )

o2scl : Object-oriented Scientific Computing Library ( http://o2scl.sourceforge.net/ )

oasa : Python library for manipulation of chemical structures ( http://bkchem.zirael.org/oasa_en.html )

omalloc : omalloc is the memory management of the Singular algebra system ( http://www.singular.uni-kl.de/ )

openblas : Optimized BLAS library based on GotoBLAS2 ( http://xianyi.github.com/OpenBLAS/ )

openlibm : High quality system independent, open source libm ( http://julialang.org/ )

optpp : C++ library for non-linear optimization ( https://software.sandia.gov/opt++/" SRC_URI="${HOMEPAGE}/downloads/${P}.tar.gz )

pagmo : Parallelization engine for optimization problems ( https://github.com/esa/pagmo )

parmetis : Parallel (MPI) unstructured graph partitioning library ( http://www-users.cs.umn.edu/~karypis/metis/parmetis/" URL: ${HOMEPAGE/parmetis/metis} URL: ${HOMEPAGE )

pfft : Parallel 3d FFT ( https://www-user.tu-chemnitz.de/~potts/workgroup/pippig/software.php.en )

pg2plplot : Assist the transition from PGPlot to PLplot in Fortran programs ( http://pg2plplot.sourceforge.net )

plasma : Parallel Linear Algebra for Scalable Multi-core Architecture ( http://icl.cs.utk.edu/plasma/" URL: ${HOMEPAGE )

pmx : Python library to read PDB, GRO or Gromacs XTC files ( https://github.com/dseeliger/pmx )

pybids : Python package to access BIDS datasets ( https://github.com/INCF/pybids )

pydicom : A pure python package for parsing DICOM files ( http://www.pydicom.org/ )

rdkit : Cheminformatics and machine-learning software written in C++ and Python ( http://www.rdkit.org/ )

scalapack : Subset of LAPACK routines redesigned for heterogenous computing ( http://www.netlib.org/scalapack/" SRC_URI="${HOMEPAGE}/${P}.tgz )

scikits_image : Image processing routines for SciPy ( http://scikit-image.org/ )

shtools : Spherical harmonic transforms and reconstructions, rotations ( http://shtools.ipgp.fr )

spglib : Spglib is a C library for finding and handling crystal symmetries ( http://spglib.sourceforge.net/ )

starparse : Library for parsing NMR star files (peak-list format) and CIF files ( http://burrow-owl.sourceforge.net/ )

superlu_dist : MPI distributed sparse LU factorization library ( http://crd.lbl.gov/~xiaoye/SuperLU/" SRC_URI="${HOMEPAGE}/superlu_dist_${PV}.tar.gz )

symengine : Fast symbolic manipulation library, written in C++ ( https://github.com/sympy/symengine )

symmetrica : A collection of routine to handle a variety of topics ( http://www.neu.uni-bayreuth.de/de/Uni_Bayreuth/Fakultaeten/1_Mathematik_Physik_und_Informatik/Fachgruppe_Informatik/prof_diskrete_algorithmen/en/research/SYMMETRICA/index.html )

tensorflow : Library for numerical computation using data flow graphs ( https://www.tensorflow.or )

tmglib : Test Matrix Generator library for LAPACK ( http://www.netlib.org/lapack/ )

trilinos : Scientific library collection for large scale problems ( http://trilinos.sandia.gov/ )

vxl : C++ computer vision research libraries ( http://vxl.sourceforge.net )

wannier90 : Calculates maximally localized Wannier functions (MLWFs) ( http://www.wannier.org/ )

xblas : Extra Precise Basic Linear Algebra Subroutines ( http://www.netlib.org/xblas" SRC_URI="${HOMEPAGE}/${P}.tar.gz )

xraylib : X-ray matter interaction cross sections for X-ray fluorescence library ( https://github.com/tschoonj/xraylib )

zarja : Scientific multi-agent simulation library ( http://sourceforge.net/projects/zarja/ )

Add an ebuild in portage :

The ebuild is now in the portage tree.

You can also use layman : emerge layman then layman -a science

For Paludis use this rsync : rsync://gentoo.zugaina.org/science-portage

If you have a problem : ycarus(-at-)zugaina.org