TPP AMI 4.7.1 README

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The official Amazon image for TPP 4.7.1 is available for your use either directly on Amazon EC2 or can be modified and re-bundled as your own AMI.

Contents

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Overview

  • Operating system: Ubuntu 14.04 LTS
  • Constructed from: ami-ecc9a3dc
  • TPP Version: 4.7.1
  • AMI Version: 1
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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
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Additional Open Source RNA Seq Software

  • bowtie - an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers.
    • Version: 1.0.0
    • Source: bowtie-1.0.0-linux-x86_64.zip
    • md5sum: c1c3b6599fd0d92213b130cbccfc5e92
  • cufflinks - assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
    • Version: 2.1.1
    • Source: cufflinks-2.1.1.Linux_x86_64.tar.gz
    • md5sum: 59d5d54889bcc4bd9e427d3587b7973a
  • samtools - provides efficient utilities on manipulating alignments in the SAM format.
    • Version: 0.1.19
    • Source: samtools-0.1.19.tar.bz2
    • md5sum: ff8b46e6096cfb452003b1ec5091d86a
  • SnpEff - a fast variant effect predictor (SNP, MNP and InDels) for genomic data.
    • Version: 3.5f (build 2014-03-18)
    • Source: snpEff_latest_core.zip
    • md5sum: b38e0a7093f7868419eb763d614bb9d6
  • tophat - a fast splice junction mapper for RNA-Seq reads.
    • Version: 2.0.8b
    • Source: tophat-2.0.8b.Linux_x86_64.tar.gz
    • md5sum: a189c762a3d5194d8d94440ee5a9e9e3
  • SRA Toolkit - used to directly download SRA data files and reference sequences (see the “Reference Compression” section above).
    • Version: 2.3.2-5
    • Source: sratoolkit.2.3.2-5-ubuntu64.tar.gz
    • md5sum: b00dda8ea86c7d70d9eb8adc32cb1a2f
  • FastQC - quality control tool for high throughput sequence data.
    • Version: 0.01.1
    • Source: fastqc_v0.10.1.zip
    • md5sum: c93815ddfc0259bd58430e52ae4fb429
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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
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Additional Notes

  • None
Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=TPP_AMI_4.7.1_README"
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