TPP AMI 4.8.0 README
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he official Amazon image for TPP 4.8.0 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-23337d13
- TPP Version: 4.8.0
- 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
