TPP AMI 4.7.1 README

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.

Overview

• Operating system: Ubuntu 14.04 LTS
• Constructed from: ami-ecc9a3dc
• TPP Version: 4.7.1
• 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 - 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

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

• None