TPP AMI 4.7.0 README

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The official Amazon image for TPP 4.7.0 is available for your use either directly on Amazon EC2 or can be modified and re-bundled as your own AMI.

Contents

Overview

  • Operating system: Ubuntu 13.10 (Saucy Salamander)
  • Constructed from: ami-e04428d0
  • TPP Version: 4.7.0
  • AMI Version: 1

Additional Open Source Proteomics Software

  • OMSSA - The Open Mass Spectrometry Search Algorithm
    • Version 2.1.9 (reports itself as 2.1.8)
    • Source: omssa-linux.tar.gz
    • md5sum: cd4839fd295fce49f36dce70840e92b0
  • InsPecT - Tool for fast and accurate identification of post-translationally modified peptides from tandem mass spectra
    • Release: 20120109 (patched to correct linker and buffer overrun issues)
    • Source: Inspect.20120109.zip
    • md5sum: d79001469984ae5a563afb4a8d05ee89
  • MyriMatch - highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis
    • Version: 2.1.138
    • Source: myrimatch-bin-linux-x86-gcc41-release-2_1_138.tar.bz2
    • md5sum: b1816b9f566ffff4fbd9b2776eefc294

Additional Open Source RNA Seq Software

  • bowtie
    • Version: 1.0.0
    • Source: bowtie-1.0.0-linux-x86_64.zip
    • md5sum: c1c3b6599fd0d92213b130cbccfc5e92
  • cufflinks
    • Version: 2.1.1
    • Source: cufflinks-2.1.1.Linux_x86_64.tar.gz
    • md5sum: 59d5d54889bcc4bd9e427d3587b7973a
  • samtools
    • Version: 0.1.19
    • Source: samtools-0.1.19.tar.bz2
    • md5sum: ff8b46e6096cfb452003b1ec5091d86a
  • SnpEff
    • Version: 3.5f (build 2014-03-18)
    • Source: snpEff_latest_core.zip
    • md5sum: b38e0a7093f7868419eb763d614bb9d6
  • tophat
    • Version: 2.0.8b
    • Source: tophat-2.0.8b.Linux_x86_64.tar.gz
    • md5sum: a189c762a3d5194d8d94440ee5a9e9e3
  • SRA Toolkit
    • Version: 2.3.2-5
    • Source: sratoolkit.2.3.2-5-ubuntu64.tar.gz
    • md5sum: b00dda8ea86c7d70d9eb8adc32cb1a2f
  • FastQC
    • Version: 0.01.1
    • Source: fastqc_v0.10.1.zip
    • md5sum: c93815ddfc0259bd58430e52ae4fb429

Ubuntu Software Packages

  • ant
  • apache2
  • build-essential
  • cabextract
  • g++
  • gnuplot
  • libbz2-dev
  • libamazon-sqs-simple-perl
  • libnet-amazon-s3-perl
  • libclass-insideout-perl
  • libcurl4-openssl-dev
  • libexpat1
  • libexpat1-dev
  • libfile-pushd-perl
  • libfile-which-perl
  • libfuse-dev
  • libgd2-xpm-dev
  • libio-compress-perl
  • libparallel-forkmanager-perl
  • libperl-dev
  • libpng12-dev
  • libxml-parser-perl
  • libxml2-dev
  • libyaml-perl
  • openjdk-6-jdk
  • ruby
  • s3cmd
  • subversion
  • swig
  • xsltproc
  • zip

Additional Notes

  • TPP's web interface, petunia, was modified to include EC2 information when checking for newer versions of TPP on session log in. These changes have been incorporated into the TPP source tree and will be available in future releases.
Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=TPP_AMI_4.7.0_README"