TPP AMI 4.7.0 README

(Difference between revisions)

Current revision

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.

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

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

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.

 ** md5sum: d79001469984ae5a563afb4a8d05ee89
-* [http://www.mc.vanderbilt.edu/root/vumc.php?site=msrc/bioinformatics&doc=27121 MyriMatch] - highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis
+* [http://www.mc.vanderbilt.edu/root/vumc.php?site=msrc/bioinformatics&doc=27121 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