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Manifest configuration files for CloudBioLinux release 27 June 2012
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| abyss: | ||
| description: Assembly By Short Sequences - a de novo, parallel, paired-end sequence | ||
| assembler. | ||
| homepage_uri: http://www.bcgsc.ca/platform/bioinfo/software/abyss | ||
| name: abyss | ||
| version: 1.3.3 | ||
| beast: | ||
| description: 'BEAST: Bayesian MCMC analysis of molecular sequences.' | ||
| homepage_uri: http://beast.bio.ed.ac.uk/main_page | ||
| name: beast | ||
| version: '' | ||
| bedtools: | ||
| description: A flexible suite of utilities for comparing genomic features. | ||
| homepage_uri: https://code.google.com/p/bedtools/ | ||
| name: bedtools | ||
| version: github | ||
| bfast: | ||
| description: 'BFAST: Blat-like Fast Accurate Search Tool.' | ||
| homepage_uri: http://sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page | ||
| name: bfast | ||
| version: 0.7.0 | ||
| bio4j: | ||
| description: Bio4j graph based database built on Neo4j with UniProt, GO, RefSeq | ||
| and more. | ||
| homepage_uri: http://www.bio4j.com/ | ||
| name: bio4j | ||
| version: '0.7' | ||
| bowtie: | ||
| description: The bowtie short read aligner. | ||
| homepage_uri: http://bowtie-bio.sourceforge.net/index.shtml | ||
| name: bowtie | ||
| version: 0.12.7 | ||
| bowtie2: | ||
| description: bowtie2 short read aligner, with gap support. | ||
| homepage_uri: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml | ||
| name: bowtie2 | ||
| version: 2.0.0-beta6 | ||
| bwa: | ||
| description: 'BWA: aligns short nucleotide sequences against a long reference sequence.' | ||
| homepage_uri: http://bio-bwa.sourceforge.net/ | ||
| name: bwa | ||
| version: 0.5.9 | ||
| bx_python: | ||
| description: Tools for manipulating biological data, particularly multiple sequence | ||
| alignments | ||
| homepage_uri: https://bitbucket.org/james_taylor/bx-python/wiki/Home | ||
| name: bx_python | ||
| version: bitbucket | ||
| cljr: | ||
| description: Clojure package manager, cljr. | ||
| homepage_uri: http://github.com/liebke/cljr | ||
| name: cljr | ||
| version: '' | ||
| cloudman: | ||
| description: ' A meta method for installing all of CloudMan components.' | ||
| homepage_uri: '' | ||
| name: cloudman | ||
| version: '' | ||
| crisp: | ||
| description: Detect SNPs and short indels from pooled sequencing data. | ||
| homepage_uri: https://sites.google.com/site/vibansal/software/crisp/ | ||
| name: crisp | ||
| version: '5' | ||
| cufflinks: | ||
| description: Cufflinks assembles transcripts, estimates their abundances, and tests | ||
| for differential expression and regulation in RNA-Seq samples. | ||
| homepage_uri: http://cufflinks.cbcb.umd.edu/ | ||
| name: cufflinks | ||
| version: 2.0.0 | ||
| dwgsim: | ||
| description: 'DWGSIM: simulating NGS data and evaluating mappings and variant calling.' | ||
| homepage_uri: http://sourceforge.net/apps/mediawiki/dnaa/index.php?title=Main_Page | ||
| name: dwgsim | ||
| version: 0.1.8 | ||
| echo: | ||
| description: 'ECHO: A reference-free short-read error correction algorithm' | ||
| homepage_uri: http://uc-echo.sourceforge.net/ | ||
| name: echo | ||
| version: '1_11' | ||
| emboss: | ||
| description: 'EMBOSS: A high-quality package of free, Open Source software for molecular | ||
| biology.' | ||
| homepage_uri: http://emboss.sourceforge.net/ | ||
| name: emboss | ||
| version: 6.3.1 | ||
| fastqc: | ||
| description: A quality control tool for high throughput sequence data. | ||
| homepage_uri: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ | ||
| name: fastqc | ||
| version: 0.10.1 | ||
| fastx_toolkit: | ||
| description: 'FASTX-Toolkit: collection of command line tools for Short-Reads FASTA/FASTQ | ||
| files preprocessing.' | ||
| homepage_uri: http://hannonlab.cshl.edu/fastx_toolkit/ | ||
| name: fastx_toolkit | ||
| version: 0.0.13 | ||
| freebayes: | ||
| description: Bayesian haplotype-based polymorphism discovery and genotyping. | ||
| homepage_uri: https://github.com/ekg/freebayes | ||
| name: freebayes | ||
| version: github | ||
| gatk: | ||
| description: 'GATK: library for writing efficient analysis tools using next-generation | ||
| sequencing data ' | ||
| homepage_uri: http://www.broadinstitute.org/gsa/wiki/index.php/Home_Page | ||
| name: gatk | ||
| version: 1.6-11-g3b2fab9 | ||
| gatk_queue: | ||
| description: Command-line scripting framework for defining multi-stage genomic analysis | ||
| pipelines. | ||
| homepage_uri: http://www.broadinstitute.org/gsa/wiki/index.php/GATK-Queue | ||
| name: gatk_queue | ||
| version: 1.6-11-g3b2fab9 | ||
| gmap: | ||
| description: 'GMAP and GSNAP: A Genomic Mapping and Alignment Program for mRNA EST | ||
| and short reads.' | ||
| homepage_uri: http://research-pub.gene.com/gmap/ | ||
| name: gmap | ||
| version: '2011-11-12' | ||
| hydra: | ||
| description: Hydra detects structural variation breakpoints in both unique and duplicated | ||
| genomic regions. | ||
| homepage_uri: https://code.google.com/p/hydra-sv/ | ||
| name: hydra | ||
| version: 0.5.3 | ||
| lastz: | ||
| description: LASTZ sequence alignment program. | ||
| homepage_uri: http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00a.html | ||
| name: lastz | ||
| version: 1.02.00 | ||
| leinengin: | ||
| description: Clojure tool for project configuration and automation. | ||
| homepage_uri: http://github.com/technomancy/leiningen | ||
| name: leinengin | ||
| version: '' | ||
| macs: | ||
| description: Model-based Analysis for ChIP-Seq. | ||
| homepage_uri: http://liulab.dfci.harvard.edu/MACS/ | ||
| name: macs | ||
| version: 1.4.2 | ||
| matplotlib: | ||
| description: matplotlib is a python 2D plotting library which produces publication | ||
| quality figures | ||
| homepage_uri: http://matplotlib.sourceforge.net/ | ||
| name: matplotlib | ||
| version: 1.0.1 | ||
| mosaik: | ||
| description: 'MOSAIK: reference-guided aligner for next-generation sequencing technologies' | ||
| homepage_uri: http://code.google.com/p/mosaik-aligner/ | ||
| name: mosaik | ||
| version: github | ||
| nginx: | ||
| description: Nginx open source web server. | ||
| homepage_uri: http://www.nginx.org/ | ||
| name: nginx | ||
| version: 1.2.0 | ||
| novoalign: | ||
| description: Novoalign short read aligner using Needleman-Wunsch algorithm with | ||
| affine gap penalties. | ||
| homepage_uri: http://www.novocraft.com/main/index.php | ||
| name: novoalign | ||
| version: V2.08.01 | ||
| perm: | ||
| description: Efficient mapping of short sequences accomplished with periodic full | ||
| sensitive spaced seeds. | ||
| homepage_uri: https://code.google.com/p/perm/ | ||
| name: perm | ||
| version: '3.6' | ||
| pgdspider: | ||
| description: PGDSpider format conversion for population genetics programs. | ||
| homepage_uri: http://www.cmpg.unibe.ch/software/PGDSpider/ | ||
| name: pgdspider | ||
| version: 2.0.1.2 | ||
| picard: | ||
| description: Command-line utilities that manipulate BAM files with a Java API. | ||
| homepage_uri: http://picard.sourceforge.net/ | ||
| name: picard | ||
| version: '1.68' | ||
| plink_seq: | ||
| description: A toolset for working with human genetic variation data. | ||
| homepage_uri: http://atgu.mgh.harvard.edu/plinkseq/ | ||
| name: plink_seq | ||
| version: '0.08' | ||
| proftpd: | ||
| description: Highly configurable GPL-licensed FTP server software. | ||
| homepage_uri: http://proftpd.org/ | ||
| name: proftpd | ||
| version: 1.3.4a | ||
| pydoop: | ||
| description: pydoop; provides Hadoop access for Python. | ||
| homepage_uri: http://pydoop.sourceforge.net/docs/ | ||
| name: pydoop | ||
| version: '' | ||
| rpy: | ||
| description: RPy is a very simple, yet robust, Python interface to the R Programming | ||
| Language. | ||
| homepage_uri: http://rpy.sourceforge.net/ | ||
| name: rpy | ||
| version: 1.0.3 | ||
| s3fs: | ||
| description: FUSE-based file system backed by Amazon S3. | ||
| homepage_uri: https://code.google.com/p/s3fs/ | ||
| name: s3fs | ||
| version: '1.61' | ||
| samtools: | ||
| description: SAM Tools provide various utilities for manipulating alignments in | ||
| the SAM format. | ||
| homepage_uri: http://samtools.sourceforge.net/ | ||
| name: samtools | ||
| version: 0.1.18 | ||
| seal: | ||
| description: 'Install seal: process high-throughput sequencing with Hadoop.' | ||
| homepage_uri: http://biodoop-seal.sf.net/ | ||
| name: seal | ||
| version: '' | ||
| sge: | ||
| description: Sun Grid Engine. | ||
| homepage_uri: '' | ||
| name: sge | ||
| version: '' | ||
| shrec: | ||
| description: Shrec is a bioinformatics tool for error correction of HTS read data. | ||
| homepage_uri: http://sourceforge.net/projects/shrec-ec/ | ||
| name: shrec | ||
| version: '2.2' | ||
| snpeff: | ||
| description: Variant annotation and effect prediction tool. | ||
| homepage_uri: http://snpeff.sourceforge.net/ | ||
| name: snpeff | ||
| version: '2_0_5' | ||
| solexaqa: | ||
| description: SolexaQA creates visual representations of data quality from FASTQ | ||
| files. | ||
| homepage_uri: http://solexaqa.sourceforge.net/ | ||
| name: solexaqa | ||
| version: '1.4' | ||
| stacks: | ||
| description: 'Stacks: build loci out of a set of short-read sequenced samples.' | ||
| homepage_uri: http://creskolab.uoregon.edu/stacks/ | ||
| name: stacks | ||
| version: '0.998' | ||
| stampy: | ||
| description: 'Stampy: mapping of short reads from illumina sequencing machines onto | ||
| a reference genome.' | ||
| homepage_uri: http://www.well.ox.ac.uk/project-stampy | ||
| name: stampy | ||
| version: 1.0.15 | ||
| tassel: | ||
| description: 'TASSEL: evaluate traits associations, evolutionary patterns, and linkage | ||
| disequilibrium.' | ||
| homepage_uri: http://www.maizegenetics.net/index.php?option=com_content&task=view&id=89&Itemid=119 | ||
| name: tassel | ||
| version: '3.0' | ||
| tophat: | ||
| description: TopHat is a fast splice junction mapper for RNA-Seq reads | ||
| homepage_uri: http://tophat.cbcb.umd.edu/ | ||
| name: tophat | ||
| version: 2.0.0 | ||
| tracer: | ||
| description: A program for analysing results from Bayesian MCMC programs such as | ||
| BEAST & MrBayes. | ||
| homepage_uri: http://beast.bio.ed.ac.uk/main_page | ||
| name: tracer | ||
| version: '' | ||
| transabyss: | ||
| description: Analyze ABySS multi-k-assembled shotgun transcriptome data. | ||
| homepage_uri: http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss | ||
| name: transabyss | ||
| version: 1.3.2 | ||
| trinity: | ||
| description: Efficient and robust de novo reconstruction of transcriptomes from | ||
| RNA-seq data. | ||
| homepage_uri: http://trinityrnaseq.sourceforge.net/ | ||
| name: trinity | ||
| version: r2012-05-18 | ||
| ucsc_tools: | ||
| description: Useful executables from UCSC. | ||
| homepage_uri: http://hgdownload.cse.ucsc.edu/admin/jksrc.zip | ||
| name: ucsc_tools | ||
| version: '' | ||
| varianttools: | ||
| description: Annotation, selection, and analysis of variants in the context of next-gen | ||
| sequencing analysis. | ||
| homepage_uri: http://varianttools.sourceforge.net/ | ||
| name: varianttools | ||
| version: 1.0.1 | ||
| vcftools: | ||
| description: Work with VCF files, such as those generated by the 1000 Genomes Project. | ||
| homepage_uri: http://vcftools.sourceforge.net/ | ||
| name: vcftools | ||
| version: 0.1.7 | ||
| velvet: | ||
| description: Sequence assembler for very short reads. | ||
| homepage_uri: http://www.ebi.ac.uk/~zerbino/velvet/ | ||
| name: velvet | ||
| version: 1.2.05 |
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