Skip to main content

System News

LONI CLuster News:

▶ QB2

Jun-2018

  • Hardware

    • No news
  • Software

    • Newly installed packages
      • Key: autodock/4.2.6/INTEL-14.0.2
        Description: AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. -
    • Updated packages
      • Key: cuda/9.0.176
        Description: CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. -
      • Key: gaussian/g16-a03
        Description: Gaussian 16 is the latest in the Gaussian series of programs. It provides state-of-the-art capabilities for electronic structure modeling.
      • Key: gaussian/g16-b01
        Description: Gaussian 16 is the latest in the Gaussian series of programs. It provides state-of-the-art capabilities for electronic structure modeling.
      • Key: gcc/6.4.0
        Description: The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). -
      • Key: impi/2018.1.163/intel64
        Description: This is an intel MPI implementation. It is included in the Intel-2018.0 compiler. It is a good compiler for MPI programming on Xeon Phi.
      • Key: intel/2018.1
        Description: Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL -
      • Key: lammps/11Aug17/CUDA-80-INTEL-140-MVAPIC
        Description: LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.
      • Key: lammps/11Aug17/INTEL-140-MVAPICH2-2.0
        Description: LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.
      • Key: pgi/17.10
        Description: The Portland Group compilers for C, C++ and Fortran. It also supports OpenACC. http://www.pgroup.com/resources/docs.htm
      • Key: pgi/18.1
        Description: The Portland Group compilers for C, C++ and Fortran. It also supports OpenACC. http://www.pgroup.com/resources/docs.htm
      • Key: stacks/2.0/gcc-6.4
        Description: Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. -
    • Retired packages
      • Key: stacks/1.46/GCC-4.9.0
  • Maintenance Scheduled

    • Not scheduled
  • Known Problems

    • No impact on users

▶ Eric

LSU CLuster News:

▶ SuperMIC

Jun-2018

  • Hardware

    • No news
  • Software

    • Updated packages
      • Key: intel/2018.1
        Description: Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL -
      • Key: pgi/17.10
        Description: The Portland Group compilers for C, C++ and Fortran. It also supports OpenACC. http://www.pgroup.com/resources/docs.htm
      • Key: pgi/18.1
        Description: The Portland Group compilers for C, C++ and Fortran. It also supports OpenACC. http://www.pgroup.com/resources/docs.htm
  • Maintenance Scheduled

    • Not scheduled
  • Known Problems

    • No impact on users

▶ SuperMike-II

Jun-2018

  • Hardware

    • No news
  • Software

    • Newly installed packages
      • Key: a5_pipeline/20160825
        Description: A5 is a pipeline for assembling DNA sequence data generated on the Illumina sequencing platform. -
      • Key: abyss/1.9.0/INTEL-180-MVAPICH2-2.2
        Description: Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler -
      • Key: agalma/2.0.0
        Description: Agalma is a set of analysis pipelines for transcriptome assembly and analysis, phylogenetic analysis, expression analysis (including phylogenetic analysis of gene expression data).
      • Key: amber/16/INTEL-180-MVAPICH2-2.2
        Description: "Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.
      • Key: amos/3.1.0/INTEL-18.0.0
        Description: The AMOS consortium is committed to the development of open-source whole genome assembly software -
      • Key: ansys/18.1
        Description: The ANSYS software suites include Fluent, CFX and ANSYS Mechanical. It's only available to LSU users.
      • Key: autodock/4.2.5.1/INTEL-18.0.0
        Description: AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. -
      • Key: autodock_vina/1.1.2
        Description: AutoDock Vina is an open-source program for doing molecular docking. -
      • Key: autogrid/4.2.5.1/INTEL-18.0.0
        Description: AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. -
      • Key: bbcp/12.01.30.00.0
        Description: BBCP is an alternative to Gridftp when transferring large amounts of data, capable of breaking up your transfer into multiple simultaneous transferring streams, thereby transferring data much faster than single-streaming utilities such as SCP and SFTP. See details at http://pcbunn.cithep.caltech.edu/bbcp/using_bbcp.htm or http://www.nics.tennessee.edu/computing-resources/data-transfer/bbcp -
      • Key: beagle_lib/2.1.2/INTEL-18.0.0
        Description: beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. -
      • Key: beast/1.8.4
        Description: BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. -
      • Key: beast2/2.4.6
        Description: BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. -
      • Key: bedtools/2.26.0/INTEL-18.0.0
        Description: The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. -
      • Key: blast/2.2.28/INTEL-18.0.0
        Description: Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. -
      • Key: blast+/2.7.1/INTEL-18.0.0
        Description: Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. -
      • Key: boost/1.55.0/INTEL-18.0.0
        Description: Boost provides free peer-reviewed portable C++ source libraries. -
      • Key: boost/1.63.0/INTEL-18.0.0
        Description: Boost provides free peer-reviewed portable C++ source libraries. -
      • Key: bowtie/1.2.2/INTEL-18.0.0
        Description: Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome. -
      • Key: bowtie2/2.3.4.1/INTEL-18.0.0
        Description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. -
      • Key: bzip2/1.0.6/INTEL-18.0.0
        Description: bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression. -
      • Key: cap3/20071221
        Description: CAP3 assembly program -
      • Key: cd-hit/4.6.6/INTEL-18.0.0
        Description: CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. -
      • Key: clhep/2.3.1.1/GCC-6.4.0
        Description: The CLHEP project is intended to be a set of HEP-specific foundation and utility classes such as random generators, physics vectors, geometry and linear algebra. CLHEP is structured in a set of packages independent of any external package. -
      • Key: clonalframe/1.2/INTEL-18.0.0
        Description: ClonalFrame is a computer package for the inference of bacterial microevolution using multilocus sequence data. ClonalFrame identifies the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance. -
      • Key: clonalorigin/1.0/INTEL-18.0.0
        Description: ClonalOrigin performs a comparative analysis of the sequences of a sample of bacterial genomes in order to reconstruct the recombination events that have taken place in their ancestry. -
      • Key: cmake/3.7.2/INTEL-18.0.0
        Description: CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. -
      • Key: cmg/2017.10
        Description: CMG provides reservoir simulation software, including thermal, compositional, black oil and enhanced oil recovery processes.
      • Key: cuda/9.0.176
        Description: CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. -
      • Key: cufflinks/2.2.1/INTEL-18.0.0
        Description: Transcript assembly, differential expression, and differential regulation for RNA-Seq -
      • Key: curl/7.49.1/INTEL-18.0.0
        Description: libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more. -
      • Key: dendropy/4.4.0
        Description: DendroPy is a Python library for phylogenetic computing. It provides classes and functions for the simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in a range of formats, such as NEXUS, NEWICK, NeXML, Phylip, FASTA, etc. -
      • Key: dmtcp/2.5.1
        Description: DMTCP (Distributed MultiThreaded Checkpointing) transparently checkpoints a single-host or distributed computation in user-space -- with no modifications to user code or to the O/S. It works on most Linux applications, including Python, Matlab, R, GUI desktops, MPI, etc. -
      • Key: eigen/3.2.3/INTEL-18.0.0
        Description: Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. -
      • Key: exabayes/1.5/INTEL-180-MVAPICH2-2.2
        Description: ExaBayes is a software package for Bayesian tree inference. It is particularly suitable for large-scale analyses on computer clusters. -
      • Key: expat/2.2.0/INTEL-18.0.0
        Description: Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags) -
      • Key: fasttree/2.1.10/INTEL-18.0.0
        Description: FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.
      • Key: fastx_toolkit/0.0.13.2/INTEL-18.0.0
        Description: The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. -
      • Key: fftw/3.3.3/INTEL-180-MVAPICH2-2.2
        Description: FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. -
      • Key: freeglut/3.0.0/INTEL-18.0.0
        Description: freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library. -
      • Key: gatk/4.0.2.1
        Description: The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. -
      • Key: gaussian/g09-d01
        Description: Gaussian 09 is the latest in the Gaussian series of programs. It provides state-of-the-art capabilities for electronic structure modeling.
      • Key: gaussview/5.0.8
        Description: A graphical user interface designed to help prepare input for submission to Gaussian and to examine graphically the output that Gaussian produces.
      • Key: gcc/6.4.0
        Description: The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). -
      • Key: geant4/10.4.2/GCC-6.4.0
        Description: Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science. -
      • Key: geant4/10.4.2/INTEL-18.0.0
        Description: Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science. -
      • Key: git/2.17
        Description: Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. -
      • Key: gnuparallel/20180222/INTEL-18.0.0
        Description: GNU parallel: Build and execute shell commands in parallel -
      • Key: gnuplot/5.0.7/INTEL-18.0.0
        Description: Portable interactive, function plotting utility -
      • Key: gromacs/2016.5/INTEL-180-MVAPICH2-2.2
        Description: GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is CPU only build, containing both MPI and threadMPI builds. -
      • Key: gsl/2.4/GCC-6.4.0
        Description: The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. -
      • Key: gsl/2.4/INTEL-18.0.0
        Description: The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. -
      • Key: hdf5/1.8.18/INTEL-180-MVAPICH2-2.2
        Description: HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections. -
      • Key: hisat2/2.1.0
        Description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome). -
      • Key: hmmer/3.1b2/INTEL-18.0.0
        Description: HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST. -
      • Key: hwloc/1.11.5/INTEL-18.0.0
        Description: The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently. -
      • Key: hypre/2.12.1/INTEL-180-MVAPICH2-2.2
        Description: Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences. -
      • Key: idba/1.1.3/INTEL-18.0.0
        Description: IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions. -
      • Key: imagemagick/7.0.7_28/INTEL-18.0.0
        Description: ImageMagick is a software suite to create, edit, compose, or convert bitmap images -
      • Key: impi/2018.0.128
        Description: Intel MPI -
      • Key: intel/18.0.0
        Description: Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL -
      • Key: jdk/1.8.0_161
        Description: Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. -
      • Key: jellyfish/2.2.7/GCC-6.4.0
        Description: Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. -
      • Key: lammps/16Mar18/INTEL-180-MVAPICH2-2.2
        Description: LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.
      • Key: last/869/INTEL-18.0.0
        Description: LAST finds similar regions between sequences. The main difference between LAST and similar tools (e.g. BLAT, LASTZ) is that it copes more efficiently with repeat-rich sequences (e.g. genomes). For example: it can align reads to genomes without repeat-masking, without becoming overwhelmed by repetitive hits. -
      • Key: libgtextutils/0.6.1/INTEL-18.0.0
        Description: ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream -
      • Key: lmdb/0.9.21/INTEL-18.0.0
        Description: OpenLDAP's Lightning Memory-Mapped Database (LMDB) library. -
      • Key: lucy/1.20/INTEL-18.0.0
        Description: Lucy is used to clean sequence data from automated DNA sequencers prior to sequence assembly and other downstream uses. The quality trimming portion of lucy makes use of phred quality scores, such as those produced by many automated sequencers based on the Sanger sequencing method. As such, lucy’s quality trimming may not be appropriate for sequence data produced by some of the new “next-generation” sequencers. -
      • Key: mafft/7.245/INTEL-18.0.0
        Description: MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc. -
      • Key: mathematica/11.0
        Description: Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields, based on symbolic mathematics. It's only available to LSU users.
      • Key: matlab/r2017a
        Description: MATLAB is a high-level language and interactive environment developed by Mathworks. It is widely u sed in science and engineering across industry and academia. Parallel Computing Toolbox is available. Due to license restriction, MATLAB is only available to LSU users.
      • Key: mauve/20150213
        Description: Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignments provide a basis for research into comparative genomics and the study of genome-wide evolutionary dynamics. -
      • Key: metis/5.1.0/INTEL-18.0.0
        Description: METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes. -
      • Key: mira/4.0.2
        Description: MIRA is the swiss army knife of sequence assembly that I've used and developed during the past 16 years to get assembly jobs I work on done efficiently - and especially accurately. That is, without me actually putting too much manual work into it. -
      • Key: mothur/1.36.1/INTEL-180-MVAPICH2-2.2
        Description: Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. -
      • Key: mpich/3.2/INTEL-18.0.0
        Description: MPICH v3.x is an open source high-performance MPI 3.0 implementation. It does not support InfiniBand (use MVAPICH2 with InfiniBand devices). -
      • Key: mrbayes/3.2.6/INTEL-180-MVAPICH2-2.2
        Description: MrBayes is a program for the Bayesian estimation of phylogeny. -
      • Key: mummer/3.23/INTEL-18.0.0
        Description: MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it. -
      • Key: mummer4/4.0.0beta2/INTEL-18.0.0
        Description: MUMmer is a versatil alignment tool for DNA and protein sequences. -
      • Key: muscle/3.8.31/INTEL-18.0.0
        Description: MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes—only a handful of command-line options are needed to perform common alignment tasks. -
      • Key: mvapich2/2.2/INTEL-18.0.0
        Description: This is an MPI 3.0 implementation. It is based on MPICH2 and MVICH. -
      • Key: namd/2.12/INTEL-180-MVAPICH2-2.2
        Description: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 200,000 cores for the largest simulations. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. -
      • Key: netcdf/4.4.1.1/INTEL-180-MVAPICH2-2.2
        Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. -
      • Key: netcdf_c++/4.3.0/INTEL-18.0.0
        Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. -
      • Key: netcdf_fortran/4.4.4/INTEL-18.0.0
        Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. -
      • Key: nwchem/6.8/INTEL-180-MVAPICH2-2.2
        Description: NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. This version enables MRCC methods.
      • Key: oases/0.2.08/INTEL-18.0.0
        Description: Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. -
      • Key: openmpi/3.1.0/INTEL-18.0.0
        Description: The Open MPI Project is an open source MPI-2 implementation. -
      • Key: orthofinder/2.2.6/INTEL-18.0.0
        Description: OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. It finds orthologues and orthogroups infers rooted gene trees for all orthogroups and infers a rooted species tree for the species being analysed. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. OrthoFinder is simple to use and all you need to run it is a set of protein sequence files (one per species) in FASTA format.
      • Key: parallel_netcdf/1.9.0/INTEL-180-MVAPICH
        Description: PnetCDF is a high-performance parallel I/O library for accessing files in format compatibility with Unidata's NetCDF, specifically the formats of CDF-1, 2, and 5. -
      • Key: parmetis/4.0.3/INTEL-180-MVAPICH2-2.2
        Description: ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes. -
      • Key: pcre/8.36/INTEL-18.0.0
        Description: The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. -
      • Key: perl/5.24.0/INTEL-18.0.0
        Description: Larry Wall's Practical Extraction and Report Language -
      • Key: petsc/3.9.2/INTEL-180-MVAPICH2-2.2
        Description: Portable, Extensible Toolkit for Scientific Computation (PETSc) is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. This version is with real scalar.
      • Key: pgi/18.1
        Description: PGI compilers for C/C++, Fortran, OpenACC and CUDA Fortran -
      • Key: phylobayes_mpi/20161021/INTEL-180-MVAPI
        Description: A Bayesian software for phylogenetic reconstruction using mixture models -
      • Key: prottest/3.4.2
        Description: ProtTest is a bioinformatic tool for the selection of best-fit models of aminoacid replacement for the data at hand.
      • Key: python/2.7.14-anaconda
        Description: Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. -
      • Key: python/3.6.4-anaconda
        Description: Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. -
      • Key: qiime2/2018.4
        Description: QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.
      • Key: quantumespresso/6.2.1/INTEL-180-MVAPICH
        Description: Quantum Espresso is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.
      • Key: quorum/1.1.1/INTEL-18.0.0
        Description: QuorUM is an error corrector for Illumina reads -
      • Key: r/3.4.3/INTEL-18.0.0
        Description: R is a free software environment for statistical computing and graphics. -
      • Key: raxml/8.2.11/INTEL-18.0.0-mt-sse3
        Description: RAxML search algorithm for maximum likelihood based inference of phylogenetic trees. -
      • Key: repet/2.5
        Description: The REPET package ( Flutre et al, 2011 ) integrates bioinformatics programs in order to tackle biological issues at the genomic scale. Its two main pipelines are dedicated to the detection, annotation and analysis of repeats in genomic sequences, specifically designed for transposable elements (TEs). -
      • Key: root/6.10.08/GCC-6.4.0
        Description: The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way. -
      • Key: ruby/2.5.0/INTEL-18.0.0
        Description: Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write. -
      • Key: rum/2.0.5_06
        Description: RUM is an alignment, junction calling, and feature quantification pipeline specifically designed for Illumina RNA-Seq data. -
      • Key: samtools/0.1.19/INTEL-18.0.0
        Description: SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. -
      • Key: samtools/1.1/INTEL-18.0.0
        Description: SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. -
      • Key: sina/1.2.11
        Description: SINA will align and optionally taxonomically classify your rRNA gene sequences. The results can be combined with any other sequences aligned by SINA or taken from the SILVA databases by concatenation of FASTA files or using the ARB MERGE tool. -
      • Key: soapdenovo2/r240/INTEL-18.0.0
        Description: SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. The program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. SOAPdenovo2 is the successor of SOAPdenovo. -
      • Key: soapdenovotrans/1.0.4/INTEL-18.0.0
        Description: SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts.The assembler provides a more accurate, complete and faster way to construct the full-length transcript sets. -
      • Key: sparsehash/2.0.2/INTEL-18.0.0
        Description: An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! The SparseHash library contains several hash-map implementations, including implementations that optimize for space or speed. -
      • Key: sprng/2.0b/INTEL-180-MVAPICH2-2.2
        Description: Scalable Parallel Pseudo Random Number Generators Library -
      • Key: sspace/3.0
        Description: SSPACE standard is a stand-alone program for scaffolding pre-assembled contigs using NGS paired-read data. It is unique in offering the possibility to manually control the scaffolding process. By using the distance information of paired-end and/or matepair data, SSPACE is able to assess the order, distance and orientation of your contigs and combine them into scaffolds. Currently we offer this as a command-line tool in Perl. The input data is given by pre-assembled contig sequences (FASTA) and NGS paired-read data (Illumina/454/Solid FASTA or FASTQ). The final scaffolds are provided in FASTA format. -
      • Key: stringtie/1.3.3/INTEL-18.0.0
        Description: StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. -
      • Key: szip/2.1/INTEL-18.0.0
        Description: Szip compression software, providing lossless compression of scientific data -
      • Key: t_coffee/11.00
        Description: T-Coffee is a multiple sequence alignment package. You can use T-Coffee to align sequences or to combine the output of your favorite alignment methods (Clustal, Mafft, Probcons, Muscle...) into one unique alignment. -
      • Key: tophat/2.1.0
        Description: TopHat is a fast splice junction mapper for RNA-Seq reads. -
      • Key: totalview/8.12.0
        Description: TotalView is a GUI-based source code defect analysis tool that gives you unprecedented control over processes and thread execution and visibility into program state and variables. It's available to LSU users only. -
      • Key: transabyss/2.0.1
        Description: FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. It is developed by the Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging. -
      • Key: trinity/2.6.6/INTEL-18.0.0
        Description: Trinity assembles transcript sequences from Illumina RNA-Seq data. -
      • Key: valgrind/3.11.0/INTEL-180-MVAPICH2-2.2
        Description: Valgrind: Debugging and profiling tools -
      • Key: vcftools/0.1.14/INTEL-18.0.0
        Description: The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files. -
      • Key: velvet/1.2.10/INTEL-18.0.0
        Description: Sequence assembler for very short reads -
      • Key: vmatch/2.3.0
        Description: Vmatch is a versatile software tool for efficiently solving large scale sequence matching tasks. -
      • Key: wannier90/2.0.1/INTEL-180-MVAPICH2-2.2
        Description: A tool for obtaining maximally-localised Wannier functions -
      • Key: xz/5.2.2/INTEL-18.0.0
        Description: xz: XZ utilities -
      • Key: zlib/1.2.11
        Description: zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. -
  • Maintenance Scheduled

    • Not scheduled
  • Known Problems

    • No impact on users

▶ Philip

Jan-2018

  • Hardware

    • No news
  • Software

    • No changes
  • Maintenance Scheduled

    • Not scheduled
  • Known Problems

    • No impact on users

▶ Pandora

▶ Shelob

Old system news items are still available for viewing.


Users may direct questions to sys-help@loni.org.