Ycarus Gentoo ebuild

science

These ebuilds come from .

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

sci-libs

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} )

aocl-sparse : AMD library for optimized sparse BLAS operations ( https://developer.amd.com/amd-aocl/ )

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

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

awkward-array : Manipulate arrays of complex data structures as easily as Numpy. ( https://github.com/scikit-hep/awkward-array )

bids-validator : Validator for the Brain Imaging Data Structure ( https://github.com/bids-standard/bids-validator )

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

blis-amd : AMD optimized BLAS-like Library Instantiation Software Framework ( https://developer.amd.com/amd-aocl/ )

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

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

ciftilib : C++ Library for reading and writing CIFTI-2 and CIFTI-1 files ( https://github.com/Washington-University/CiftiLib )

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/ )

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 )

ensmallen : header only C++ library for numerical optimization ( https://ensmallen.org )

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/ )

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 )

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 )

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

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/ )

libflame-amd : AMD optimized high-performance object-based library for DLA computations ( https://developer.amd.com/amd-aocl/ )

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

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/ )

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

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 )

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/ )

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

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

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

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 )

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

pytorch : Tensors and Dynamic neural networks in Python with strong GPU acceleration ( https://pytorch.org/ )

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

scikits_video : Video processing in Python ( https://scikit-image.org/ )

spams-python : Optimization toolbox for solving various sparse estimation problems ( http://spams-devel.gforge.inria.fr/index.html )

spyking-circus : Fast and scalable spike sorting in Python ( http://spyking-circus.rtfd.org )

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 )

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