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Manifest configuration files for CloudBioLinux release 27 June 2012

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1 parent 4d25842 commit 16a3560d5e7bda89da6ab8a379e9757f1c14535e @chapmanb committed Jul 16, 2012
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  1. +296 −0 manifest/custom-packages.yaml
  2. +18,911 −0 manifest/debian-packages.yaml
  3. +846 −0 manifest/python-packages.yaml
  4. +1,275 −0 manifest/r-packages.yaml
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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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