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System News

LONI CLuster News:

▶ QB2

Jul-2017

  • Hardware

    • no news
  • Software

    • Newly installed packages
      • Key: beagle_lib/2.1.2/INTEL-14.0.2
        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: bioperl/1.7.1
        Description: The Bioperl Project is an international association of users & developers of open source Perl tools for bioinformatics, genomics and life science.
      • Key: bwa/0.7.15/INTEL-14.0.2
        Description: Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.
      • Key: canu/1.5/GCC-4.9.0
        Description: Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION).
      • Key: fastx_toolkit/0.0.13.2/INTEL-14.0.2
        Description: The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
      • Key: garli/2.1/INTEL-140-MVAPICH2-2.0
        Description: GARLI is a program that performs phylogenetic inference using the maximum-likelihood criterion. Two versions are available on QB2 - OpenMP and MPI.
      • Key: ima2p/20170629/INTEL-140-MVAPICH2-2.0
        Description: IMa2p is a parallel implementation of IMa2, using OpenMPI-C++ - a Bayesian MCMC based method for inferring population demography under the IM (Isolation with Migration) model. Please refer to Sethuraman and Hey (2015) for details of implementation.
      • Key: libgtextutils/0.6.1/INTEL-14.0.2
        Description: ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream
      • Key: mafft/7.310/INTEL-14.0.2
        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: mrbayes/3.2.6/INTEL-140-MVAPICH2-2.0
        Description: MrBayes is a program for the Bayesian estimation of phylogeny.
      • Key: novoplasty/2.5.9
        Description: NOVOPlasty is a de novo assembler for short circular genomes.
      • Key: openbabel/2.4.1
        Description: A chemical toolbox designed to speak the many languages of chemical data URL: http://openbabel.org
      • Key: pigz/2.3.4
        Description: pigz is parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data.
      • Key: poretools/0.6.0
        Description: Poretools: a toolkit for working with nanopore sequencing data from Oxford Nanopore.
      • Key: racon/20170629/GCC-4.9.0
        Description: Consensus module for raw de novo DNA assembly of long uncorrected reads.
      • Key: raxml/8.2.3/INTEL-14.0.2-mt-sse3
        Description: RAxML search algorithm for maximum likelihood based inference of phylogenetic trees.
      • Key: remora/1.8
        Description: Resource Monitoring for Remote Applications
      • Key: spades/3.10.1
        Description: SPAdes – St. Petersburg genome assembler – is an assembly toolkit containing various assembly pipelines.
      • Key: sparsehash/2.0.2/INTEL-14.0.2
        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: stacks/1.46/GCC-4.9.0
        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.
      • Key: stampy/1.0.31/GCC-4.9.0
        Description: Stampy is a package for the mapping of short reads from illumina sequencing machines onto a reference genome.
      • Key: structure/2.3.4
        Description: The program structure is a free software package for using multi-locus genotype data to investigate population structure.
      • Key: trinity/2.4.0/INTEL-14.0.2
        Description: Trinity assembles transcript sequences from Illumina RNA-Seq data.
    • Updated packages
      • Key: beast/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.
  • Maintenance Scheduled

    • Not scheduled
  • Known Problems

    • No impact on users

▶ Eric

LSU CLuster News:

▶ SuperMIC

Jul-2017

  • Hardware

    • no news
  • Software

    • Newly installed packages
      • Key: pigz/2.3.4
        Description: pigz is parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data.
      • Key: remora/1.8
        Description: Resource Monitoring for Remote Applications
      • Key: xdinfo/1.3-1
        Description: Adds XSEDE Information Services Think Client (xdinfo) tool to paths remove-path PATH /usr/local/packages/xsede/xdinfo-1.3-1/bin
    • Updated packages
      • Key: matlab/r2017a
        Description:
      • Key: python/2.7.13-anaconda-tensorflow
        Description: Python is a programming language that lets you work more quickly and integrate your systems more effectively. -
      • Key: gateway-usage-reporting/2.0
        Description: adds gateway-submit_attributes tool to paths in the login shell environment remove-path PATH /etc/globus/gateway_submit_attributes-2.0
      • Key: xdusage/2.0-3
        Description: adds XSEDE xdusage tool to paths in the login shell environment remove-path PATH /usr/local/packages/xsede/xdusage/xdusage-2.0-3/bin
  • Maintenance Scheduled

    • Not scheduled
  • Known Problems

    • No impact on users

▶ SuperMike-II

Jul-2017

  • Hardware

    • no news
  • Software

    • Newly installed packages
      • Key: +bedtools-2.26.0
        Description: Bedtools is a powerful toolset for genome arithmetic
      • Key: +pigz-2.3.4
        Description: A parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data
      • Key: +remora-1.8
        Description: Resource Monitoring for Remote Applications
      • Key: +vcftools
        Description: vcftoolsA is a set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.
    • Updated packages
      • Key: +Intel-16.0.3
        Description: The C/C++ and Fortran compiler suite from Intel.
      • Key: +Intel-17.0.4
        Description: The C/C++ and Fortran compiler suite from Intel.
      • Key: +impi-17.3.196-Intel-17.0.4
        Description: Intel MPI implementation.
      • Key: +impi-5.1.3.210-Intel-16.0.3
        Description: Intel MPI implementation.
      • 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.
      • Key: +mvapich2-2.2-Intel-16.0.3
        Description: An MPI-2 implementation (conforming to MPI 3.0 standard) .
      • Key: +mvapich2-2.2-Intel-17.0.4
        Description: An MPI-2 implementation (conforming to MPI 3.0 standard) .
      • Key: +portland-15.10
        Description: Portland Group's high-performance compilers and tools.
      • Key: +R-3.3.3-gcc-4.7.2
        Description:
    • Retired packages
      • Key: +ddt-3.2
  • Maintenance Scheduled

    • Not scheduled
  • Known Problems

    • No impact on users

▶ Philip

Jul-2017

  • Hardware

    • no news
  • Software

    • Updated packages
      • Key: matlab/r2017a
        Description:
  • Maintenance Scheduled

    • Not scheduled
  • Known Problems

    • No impact on users

▶ Pandora

▶ Shelob

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