container.yaml

containers: [
{name: "abyss", version: "1.9.0", description: "ABySS is a *de novo* sequence assembler", documentation: "https://github.com/bcgsc/abyss#abyss", install: ["conda install abyss=1.9.0"]}
#,{ name: "aliscore", version: "2.0", description: "Aliscore is designed to filter alignment ambiguous or randomly similar sites in multiple sequence alignments (MSA).", documentation: "https://www.zfmk.de/dateien/atoms/files/aliscore_v.2.0_manual_0.pdf", install: ["wget http://software.zfmk.de/ALISCORE_v2.0.zip && unzip /tmp/ALISCORE_v2.0.zip -d ./ \\", "&& unzip /tmp/ALISCORE_v2.0/Aliscore_v.2.0.zip -d /opt/biotools/bin/Aliscore/ \\", "&& chmod -R 755 /opt/biotools/bin/Aliscore  \\", "&& rm -rf /tmp/ALISCORE_v2.0" ] }
,{ name: "bamtools", version: "2.4.0", description: "C++ API & command-line toolkit for working with BAM data", documentation: "https://github.com/pezmaster31/bamtools/wiki", install: ["conda install bamtools=2.4.0"] }
,{ name: "bcftools", version: "1.5", description: "Bcftools is a program for variant calling and manipulating VCFs and BCFs", documentation: "https://samtools.github.io/bcftools/", install: ["conda install bcftools=1.5"] }
,{ name: "bedtools", version: "2.25.0", description: "a powerful toolset for genome arithmetic", documentation: "http://quinlanlab.org/tutorials/bedtools/bedtools.html", install: ["conda install bedtools=2.25.0"] }
,{ name: "bior_annotate", version: "2.1.1", description: "", documentation: "", install: [] }
,{ name: "blast", version: "2.2.31", description: "basic local alignment search tool", documentation: "http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome", install: ["conda install blast=2.2.31"] }
,{ name: "bowtie", version: "1.1.2", description: "an ultrafast memory-efficient short read aligner", documentation: "http://bowtie-bio.sourceforge.net/manual.shtml", install: ["conda install bowtie=1.1.2"] }
,{ name: "bowtie2", version: "2.2.8", description: "an ultrafast memory-efficient short read aligner", documentation: "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml", install: ["conda install bowtie2=2.2.8"] }
,{ name: "bowtie2", version: "2.3.0", description: "an ultrafast memory-efficient short read aligner", documentation: "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml", install: ["conda install bowtie2=2.3.0"] }
,{ name: "bwa", version: "0.7.12", description: "Burrow-Wheeler Aligner for pairwise alignment between DNA sequences", documentation: "http://bio-bwa.sourceforge.net/", install: ["conda install bwa=0.7.12"] }
,{ name: "bwa", version: "0.7.13", description: "Burrow-Wheeler Aligner for pairwise alignment between DNA sequences", documentation: "http://bio-bwa.sourceforge.net/", install: ["conda install bwa=0.7.13"] }
,{ name: "bwa", version: "0.7.15", description: "Burrow-Wheeler Aligner for pairwise alignment between DNA sequences", documentation: "http://bio-bwa.sourceforge.net/", install: ["conda install bwa=0.7.15"] }
,{ name: "cava", version: "1.1.1", description: "lightweight, fast and flexible NGS variant annotation tool", documentation: "http://www.well.ox.ac.uk/cava", install: [] }
,{ name: "clustal-omega", version: "1.2.1-1", description: "general purpose multiple sequence alignment program for proteins", documentation: "http://www.clustal.org/omega/#Documentation", install: ["apt-get install  clustalo"] }
,{ name: "comet", version: "1.1.0", description: "an open source tandem mass spectrometry sequence database search tool", documentation: "http://comet-ms.sourceforge.net/parameters/parameters_2016010/", install: ["conda install -c auto comet=1.1.0"] }
,{ name: "cross-species-scaffolding", version: "0.1", description: "Generate in silico mate-pair reads from single-/paired-end reads of your organism of interest", documentation: "https://github.com/thackl/cross-species-scaffolding", install: ["cd /opt/biotools; rm -rf cross-species-scaffolding; git clone https://github.com/thackl/cross-species-scaffolding.git ; cd cross-species-scaffolding; mkdir samples; make util/bcftools; make util/samtools; make dependencies;"], env: "export PATH=/opt/biotools/cross-species-scaffolding/bin:/opt/biotools/cross-species-scaffolding/util/samtools:$PATH" }
,{ name: "crux", version: "2.1", description: "a software toolkit for tandem mass spectrometry analysis", documentation: "http://cruxtoolkit.sourceforge.net/", install: [] }
,{ name: "denovogui", version: "1.10.4", description: "graphical user interface for de novo sequencing of tandem mass spectra", documentation: "https://github.com/compomics/denovogui", install: [] }
,{ name: "denovogui", version: "1.5.2", description: "graphical user interface for de novo sequencing of tandem mass spectra", documentation: "https://github.com/compomics/denovogui", install: [] }
,{ name: "dia-umpire", version: "2.1.3", description: "computational analysis of data independent acquisition (DIA) mass spectrometry-based proteomics data", documentation: "http://diaumpire.sourceforge.net", install: ["conda install dia_umpire=2.1.3"] }
,{ name: "DiffExpIR", version: "0.0.1", description: "Differentially expressed intron retention", documentation: "https://github.com/r78v10a07/DiffExpIR", install: [] }
,{ name: "discovar", version: "52488", description: "DISCOVAR is a new variant caller", documentation: "http://www.broadinstitute.org/software/discovar/blog/?page_id=19", install: ["conda install discovardenovo=52488"] }
,{ name: "discovardenovo", version: "52488", description: "Genome variant discovery through assembly", documentation: "http://www.broadinstitute.org/software/discovar/blog/?page_id=19", install: ["conda install discovardenovo=52488"] }
,{ name: "emboss", version: "6.5.7", description: "software analysis package", documentation: "http://emboss.sourceforge.net/docs/", install: ["conda install emboss=6.5.7"] }
,{ name: "entrez-direct", version: "5.80", description: "Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected Entrez databases", documentation: "", install: ["conda install entrez-direct=5.80"] }
,{ name: "fastqc", version: "0.11.5", description: "A quality control tool for high throughput sequence data.", documentation: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/", install: ["conda install -c bioconda fastqc=0.11.5"] }
,{ name: "fastxtools", version: "0.0.14", description: "a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing", documentation: "http://hannonlab.cshl.edu/fastx_toolkit/commandline.html", install: ["conda install -c biobuilds fastx-toolkit=0.0.14"] }
,{ name: "frc_align", version: "20150723", description: "Computes FRC from SAM/BAM file and not from afg files", documentation: "https://github.com/jts/frc_courve", install: [] }
,{ name: "gapcloser", version: "1.12", description: "A novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes", documentation: "http://soap.genomics.org.cn/gapcloser.html", install: ["conda install soapdenovo2-gapcloser=1.12"] }
,{ name: "gatk", version: "3.8", description: "The full Genome Analysis Toolkit (GATK) framework, license restricted.", documentation: "", install: ["conda install gatk=3.8"] }
,{ name: "gatk4", version: "4.0", description: "The full Genome Analysis Toolkit (GATK) framework, license restricted.", documentation: "", install: ["conda install -c bioconda gatk4"] }
,{ name: "gcta", version: "1.24.7", description: "", documentation: "", install: ["conda install -c biobuilds gcta=1.26.0"] }
,{ name: "htslib", version: "1.8", description: "", documentation: "", install: ["conda install htslib=1.8"] }
,{ name: "jbrowse", version: "1.12.1", description: "", documentation: "", install: ["conda install jbrowse=1.12.1"] }
,{ name: "jellyfish", version: "2.2.6", description: "", documentation: "", install: ["conda install jellyfish=2.2.6"] }
,{ name: "magicblast", version: "1.3.0", description: "Magic-BLAST is a new tool for mapping large sets of next-generation RNA or DNA sequencing runs against a whole genome or transcriptome", documentation: "https://ncbi.github.io/magicblast/", install: ["wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/1.3.0/ncbi-magicblast-1.3.0-x64-linux.tar.gz -O /tmp/ncbi-magicblast-1.3.0-x64-linux.tar.gz \\", "&& tar xzfv /tmp/ncbi-magicblast-1.3.0-x64-linux.tar.gz -C /opt/biotools/bin/ \\", "&& cd /opt/biotools/bin/ncbi-magicblast-1.3.0/ \\", "&& chmod -R 755 /opt/biotools/bin/ncbi-magicblast-1.3.0 \\", "&& ln -s /opt/biotools/bin/ncbi-magicblast-1.3.0/bin/magicblast /opt/biotools/bin/magicblast_1.3.0 \\", "&& ln -s /opt/biotools/bin/ncbi-magicblast-1.3.0/bin/makeblastdb /opt/biotools/bin/makeblastdb_1.3.0 \\", "&& rm -rf /tmp/ncbi-magicblast-1.3.0-x64-linux.tar.gz"] }
,{ name: "msamanda", version: "1.0.0.5242", description: "scoring system to identify peptides out of tandem mass spectrometry", documentation: "http://ms.imp.ac.at/?goto=msamanda", install: [] }
,{ name: "msgfp", version: "9949", description: "MS/MS database search tool", documentation: "http://proteomics.ucsd.edu/Software/MSGFPlus/", install: [] }
,{ name: "minimap2", version: "2.1.0",description: "a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database", documentation: "https://github.com/lh3/minimap2", install: ["cd /opt/biotools/bin/;curl -L https://github.com/lh3/minimap2/releases/download/v2.10/minimap2-2.10_x64-linux.tar.bz2 | tar -jxvf - "], env: "export PATH:'$PATH':/opt/biotools/bin/minimap2-2.10_x64-linux/"}
,{name: "nanopolish", version: "latest", description: "signal-level analysis of Oxford Nanopore sequencing data.", documentation: "https://github.com/jts/nanopolish", install: ["cd /opt/biotools/bin;git clone --recursive https://github.com/jts/nanopolish.git;cd nanopolish;make;"], env: "export PATH='$PATH':/opt/biotools/bin/nanopolish"}
,{name: "nextflow", version: "0.30.1", description: "Data-driven computational pipelines", documentation: "https://www.nextflow.io/", install: ["conda install -c bioconda nextflow=0.30.1"]}
,{ name: "novor", version: "1b", description: "real-time peptide de novo sequencing", documentation: "http://www.rapidnovor.com/", install: ["wget https://github.com/BioDocker/software-archive/releases/download/NovoR/novor_academic_latest.zip -O /tmp/novor_academic_latest.zip \\", "&& unzip /tmp/novor_academic_latest.zip -d /opt/biotools/bin/ \\", "&& bash -c 'echo -e \"#!/bin/bash\\njava -jar /opt/biotools/bin/novor_v1b/lib/novor.jar $@\" > /opt/biotools/bin/novor_1b' && \\", "&& chmod +x /opt/biotools/bin/novor_1b \\", "&& rm -rf /tmp/novor_academic_latest.zip "] }
,{ name: "openms", version: "2.2.0", description: "C++ libraries ans tools for MS/MS data analysis", documentation: "http://ftp.mi.fu-berlin.de/pub/OpenMS/release2.2.0-documentation/html/index.html", install: [] }
,{ name: "pepnovo", version: "20101117", description: "de novo sequencing of low precision MS/MS data", documentation: "http://proteomics.ucsd.edu/Software/PepNovo/", install: ["conda install pepnovo=20101117"] }
,{ name: "peptideprophet", version: "201510131012", description: "Peptide assignment statistics and validation", documentation: "http://peptideprophet.sourceforge.net/", install: [] }
,{ name: "peptideshaker", version: "1.16.16", description: "interpretation of proteomics identification results", documentation: "http://compomics.github.io/projects/peptide-shaker.html", install: ["conda install peptide-shaker=1.16.16"] }
,{ name: "peptideshaker", version: "1.16.17", description: "interpretation of proteomics identification results", documentation: "http://compomics.github.io/projects/peptide-shaker.html", install: ["conda install peptide-shaker=1.16.17"] }
#,{ name: "percolator", version: "3.1", description: "Semi-supervised learning for peptide identification from shotgun proteomics datasets", documentation: "http://percolator.ms/", install: ["conda install boost ", "conda install tokyocabinet", "conda install percolator=3.1"] }
,{ name: "pia", version: "1.1.0-SNAPSHOT", description: "Compile PIA XML files and run pipelines with this image", documentation: "https://github.com/mpc-bioinformatics/pia", install: [] }
,{ name: "pia", version: "1.3.0", description: "Compile PIA XML files and run analysis pipelines for protein inference with this image", documentation: "https://github.com/julianu/pia-tutorial", install: [] }
,{ name: "picard", version: "2.18.1", description: "A set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats.", documentation: "https://github.com/picard/picard", install: ["conda install picard=2.18.1"] }
,{ name: "progressive-cactus", version: "0.1", description: "multiple whole-genome alignment package", documentation: "https://github.com/glennhickey/progressiveCactus", install: [] }
,{ name: "proteinprophet", version: "201510131012", description: "Protein inference for MS/MS analysis", documentation: "http://proteinprophet.sourceforge.net/", install: [] }
,{ name: "proteowizard", version: "3_0_9992", description: "tools and software libraries that facilitate proteomics data analysis", documentation: "http://proteowizard.sourceforge.net/", install: ["conda install  proteowizard=3_0_9992"] }
,{ name: "raremetalworker", version: "4.13.7", description: "single variant analysis, generating summary statistics for gene level meta analyses", documentation: " http://genome.sph.umich.edu/wiki/RAREMETALWORKER", install: [] }
,{ name: "saintq", version: "0.0.2", description: "assigning confidence scores to protein-protein interactions based on quantitative proteomics", documentation: "http://saint-apms.sourceforge.net/Main.html", install: [] }
,{ name: "samtools", version: "1.2", description: "Tools for manipulating next-generation sequencing data", documentation: "https://github.com/samtools/samtools", install: ["conda install samtools=1.2"] }
,{ name: "samtools", version: "1.3", description: "Tools for manipulating next-generation sequencing data", documentation: "https://github.com/samtools/samtools", install: ["conda install samtools=1.3"] }
,{ name: "samtools", version: "1.3.1", description: "Tools for manipulating next-generation sequencing data", documentation: "https://github.com/samtools/samtools", install: ["conda install samtools=1.3.1"] }
,{ name: "searchgui", version: "2.1.4", description: "graphical user interface for proteomics identification search engines", documentation: "https://code.google.com/p/searchgui/", install: ["conda install searchgui=2.1.4"] }
,{ name: "sga", version: "0.10.15", description: "De novo sequence assembler using string graphs", documentation: "https://github.com/jts/sga/wiki", install: ["conda install sga=0.10.15"] }
,{ name: "snpeff", version: "4.3.1t", description: "Genetic variant annotation and effect prediction toolbox", documentation: "http://snpeff.sourceforge.net/", install: ["conda install snpeff=4.3.1t"] }
,{ name: "soapdenovo", version: "2.40", description: "a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes", documentation: "http://soap.genomics.org.cn/soapdenovo.html", install: ["conda install soapdenovo2=2.40"] }
,{ name: "soapec", version: "2.03", description: "A correction tool for SOAPdenovo", documentation: "http://soap.genomics.org.cn/soapdenovo.html", install: ["conda install soapec=2.03"] }
,{ name: "spades", version: "3.11.1", description: "Tools (written in C using htslib) for manipulating next-generation sequencing data", documentation: "http://bioinf.spbau.ru/spades", install: ["conda install spades=3.11.1"] }
,{ name: "spectra-cluster-cli", version: "1.0.1", description: "PRIDE Cluster algorithm to cluster heterogeneous mass spectra", documentation: "https://github.com/spectra-cluster/spectra-cluster-cli", install: ["conda install spectra-cluster-cli=1.0.1"] }
,{ name: "sra-tools", version: "latest", description: "", documentation: "", installation: ["cd /opt/biotools; wget --output-document sratoolkit.tar.gz http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz; tar -vxzf sratoolkit.tar.gz; rm sratoolkit.tar.gz; mv sratoolkit.*-ubuntu64 sratoolkit"], env: "export PATH=$PATH:/opt/biotools/sratoolkit/bin" }
,{ name: "stacks", version: "1.44", description: "Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population", documentation: "http://catchenlab.life.illinois.edu/stacks/", install: ["conda install stacks=1.44"] }
,{ name: "stacks", version: "2.0", description: "Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population", documentation: "http://catchenlab.life.illinois.edu/stacks/", install: ["wget http://catchenlab.life.illinois.edu/stacks/source/stacks-2.0.tar.gz \\",  "&& tar -zxvf stacks-2.0.tar.gz -C /opt/biotools/bin/ \\", "&& cd /opt/biotools/bin/stacks-2.0/ \\", "&& ./configure \\", "&& make \\", "&& make install"]}
,{ name: "tandem", version: "10-12-01-1", description: "software that can match tandem mass spectra with peptide sequences", documentation: "http://www.thegpm.org/tandem/", install: [] }
,{ name: "tandem", version: "15-12-15-2", description: "software that can match tandem mass spectra with peptide sequences", documentation: "http://www.thegpm.org/tandem/", install: [] }
,{ name: "tophat", version: "2.1.1", description: "TopHat is a fast splice junction mapper for RNA-Seq reads", documentation: "https://ccb.jhu.edu/software/tophat/index.shtml", install: ["conda install tophat=2.1.1"] }
,{ name: "toppas", version: "1.11.1-3", description: "a graphical workflow editor for the analysis of high-throughput proteomics data", documentation: "http://open-ms.sourceforge.net/workflow-integration/toppasworkflows/", install: [] }
,{ name: "TPMCalculator", version: "0.0.1", description: "This program calculates the TPM (Transcript per Millions) values for the exons and introns from NGS RNA-Seq aligned reads (BAM files)", documentation: "https://github.com/r78v10a07/TPMCalculator", install: [] }
,{ name: "tpp", version: "5.0", description: "a collection of integrated tools for MS/MS proteomics", documentation: "http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP", install: [] }
,{ name: "vcftools", version: "0.1.14", description: "A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project", documentation: "https://github.com/vcftools/vcftools|https://vcftools.github.io/index.html", install: ["conda install  vcftools=0.1.14"] }
,{ name: "vcftools", version: "0.1.15", description: "A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project", documentation: "https://github.com/vcftools/vcftools|https://vcftools.github.io/index.html", install: ["conda install  vcftools=0.1.15"] }
,{ name: "velvet", version: "1.2.10", description: "Short read de novo assembler using de Bruijn graphs", documentation: "https://www.zfmk.de/dateien/atoms/files/aliscore_v.2.0_manual_0.pdf", install: ["conda install velvet=1.2.10" ] }
]