TPP AMI 4.7.0 README

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==== Additional Open Source RNA Seq Software ==== ==== Additional Open Source RNA Seq Software ====
-* [http://sourceforge.net/projects/bowtie-bio bowtie]+* [http://sourceforge.net/projects/bowtie-bio bowtie] - an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers.
** Version: 1.0.0 ** Version: 1.0.0
** Source: bowtie-1.0.0-linux-x86_64.zip ** Source: bowtie-1.0.0-linux-x86_64.zip
** md5sum: c1c3b6599fd0d92213b130cbccfc5e92 ** md5sum: c1c3b6599fd0d92213b130cbccfc5e92
-* [http://cufflinks.cbcb.umd.edu cufflinks]+* [http://cufflinks.cbcb.umd.edu cufflinks] - assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
** Version: 2.1.1 ** Version: 2.1.1
** Source: cufflinks-2.1.1.Linux_x86_64.tar.gz ** Source: cufflinks-2.1.1.Linux_x86_64.tar.gz
** md5sum: 59d5d54889bcc4bd9e427d3587b7973a ** md5sum: 59d5d54889bcc4bd9e427d3587b7973a
-* [http://sourceforge.net/projects/samtools samtools]+* [http://sourceforge.net/projects/samtools samtools] - provides efficient utilities on manipulating alignments in the SAM format.
** Version: 0.1.19 ** Version: 0.1.19
** Source: samtools-0.1.19.tar.bz2 ** Source: samtools-0.1.19.tar.bz2
** md5sum: ff8b46e6096cfb452003b1ec5091d86a ** md5sum: ff8b46e6096cfb452003b1ec5091d86a
-* [http://sourceforge.net/projects/snpeff SnpEff]+* [http://sourceforge.net/projects/snpeff SnpEff] - a fast variant effect predictor (SNP, MNP and InDels) for genomic data.
** Version: 3.5f (build 2014-03-18) ** Version: 3.5f (build 2014-03-18)
** Source: snpEff_latest_core.zip ** Source: snpEff_latest_core.zip
** md5sum: b38e0a7093f7868419eb763d614bb9d6 ** md5sum: b38e0a7093f7868419eb763d614bb9d6
-* [http://tophat.cbcb.umd.edu tophat]+* [http://tophat.cbcb.umd.edu tophat] - a fast splice junction mapper for RNA-Seq reads.
** Version: 2.0.8b ** Version: 2.0.8b
** Source: tophat-2.0.8b.Linux_x86_64.tar.gz ** Source: tophat-2.0.8b.Linux_x86_64.tar.gz
** md5sum: a189c762a3d5194d8d94440ee5a9e9e3 ** md5sum: a189c762a3d5194d8d94440ee5a9e9e3
-* [http://ftp-trace.ncbi.nlm.nih.gov/sra SRA Toolkit]+* [http://eutils.ncbi.nih.gov/Traces/sra/?view=software SRA Toolkit] - used to directly download SRA data files and reference sequences (see the “Reference Compression” section above).
** Version: 2.3.2-5 ** Version: 2.3.2-5
** Source: sratoolkit.2.3.2-5-ubuntu64.tar.gz ** Source: sratoolkit.2.3.2-5-ubuntu64.tar.gz
** md5sum: b00dda8ea86c7d70d9eb8adc32cb1a2f ** md5sum: b00dda8ea86c7d70d9eb8adc32cb1a2f
-* [http://www.bioinformatics.babraham.ac.uk/projects/fastqc FastQC]+* [http://www.bioinformatics.babraham.ac.uk/projects/fastqc FastQC] - quality control tool for high throughput sequence data.
** Version: 0.01.1 ** Version: 0.01.1
** Source: fastqc_v0.10.1.zip ** Source: fastqc_v0.10.1.zip

Revision as of 22:53, 19 March 2014

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 - 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

  • 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.
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