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Commit cfcbf3b2 authored by jlopez's avatar jlopez
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Add more biocontainer tools

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container.yaml
View file @ cfcbf3b2
......@@ -14,51 +14,38 @@ containers: [
,{ 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: "2015011", description: "an open source tandem mass spectrometry sequence database search tool", documentation: "http://comet-ms.sourceforge.net/parameters/parameters_201601/", install: [] }
,{ name: "comet", version: "2015012", description: "an open source tandem mass spectrometry sequence database search tool", documentation: "http://comet-ms.sourceforge.net/parameters/parameters_201601/", install: [] }
,{ name: "comet", version: "2015020", description: "an open source tandem mass spectrometry sequence database search tool", documentation: "http://comet-ms.sourceforge.net/parameters/parameters_201601/", install: [] }
,{ name: "comet", version: "2015025", description: "an open source tandem mass spectrometry sequence database search tool", documentation: "http://comet-ms.sourceforge.net/parameters/parameters_201601/", install: [] }
,{ name: "comet", version: "2016010", description: "an open source tandem mass spectrometry sequence database search tool", documentation: "http://comet-ms.sourceforge.net/parameters/parameters_2016010/", install: [] }
,{ name: "comet", version: "2016011", description: "an open source tandem mass spectrometry sequence database search tool", documentation: "http://comet-ms.sourceforge.net/parameters/parameters_2016010/", install: [] }
,{ name: "comet", version: "2016012", description: "an open source tandem mass spectrometry sequence database search tool", documentation: "http://comet-ms.sourceforge.net/parameters/parameters_2016010/", install: [] }
,{ 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: "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: "1.4256", description: "computational analysis of data independent acquisition (DIA) mass spectrometry-based proteomics data", documentation: "http://diaumpire.sourceforge.net", install: [] }
,{ name: "dia-umpire", version: "2.1.2", description: "computational analysis of data independent acquisition (DIA) mass spectrometry-based proteomics data", documentation: "http://diaumpire.sourceforge.net", 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: [] }
,{ name: "discovardenovo", version: "52488", description: "Genome variant discovery through assembly", documentation: "http://www.broadinstitute.org/software/discovar/blog/?page_id=19", 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: "7.50.20171103", description: "Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected Entrez databases", documentation: "https://ncbi.github.io/magicblast/", install: [] }
,{ 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: [] }
,{ 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: [] }
,{ 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-r6", 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: [] }
,{ 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: "gcta", version: "1.24.7", description: "", documentation: "", install: [] }
,{ name: "htslib", version: "1.2.1", description: "", documentation: "", install: [] }
,{ name: "jbrowse", version: "1.11.6", description: "", documentation: "", install: [] }
,{ name: "jellyfish", version: "2.2.3", description: "", documentation: "", install: [] }
,{ 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: "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: "1.11.1-3", description: "C++ libraries ans tools for MS/MS data analysis", documentation: "http://open-ms.sourceforge.net/", install: [] }
,{ name: "openms", version: "2.0.0", description: "C++ libraries ans tools for MS/MS data analysis", documentation: "http://open-ms.sourceforge.net/", install: [] }
,{ 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: "20120423", description: "de novo sequencing of low precision MS/MS data", documentation: "http://proteomics.ucsd.edu/Software/PepNovo/", 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: "1.10.3", description: "interpretation of proteomics identification results", documentation: "http://compomics.github.io/projects/peptide-shaker.html", install: [] }
,{ name: "peptideshaker", version: "1.16.16", description: "interpretation of proteomics identification results", documentation: "http://compomics.github.io/projects/peptide-shaker.html", install: [] }
,{ name: "peptideshaker", version: "1.16.17", description: "interpretation of proteomics identification results", documentation: "http://compomics.github.io/projects/peptide-shaker.html", install: [] }
,{ name: "percolator", version: "3.0", description: "Semi-supervised learning for peptide identification from shotgun proteomics datasets", documentation: "http://percolator.ms/", 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: "pia-web-server", version: "1.1.0-SNAPSHOT", description: "Web server for PIA - Protein Inference Algorithms", documentation: "https://github.com/mpc-bioinformatics/pia", install: [] }
,{ name: "picard", version: "1.139", 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=1.139"] }
,{ name: "picard", version: "1.141", 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=1.141"] }
,{ name: "picard", version: "2.3.0", 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=2.3.0"] }
,{ 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"] }
......@@ -80,7 +67,6 @@ containers: [
,{ 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: "4.8", description: "a collection of integrated tools for MS/MS proteomics", documentation: "http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP", 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"] }
......
pages/pages_def_home.R
View file @ cfcbf3b2
......@@ -23,14 +23,10 @@ tabHome = fluidPage(align="left",
actionButton("createContainer", label = "Create", icon("paper-plane"), style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
downloadButton('downloadContainerFile', label = "Dowload", style="color: #fff; background-color: #337ab7; border-color: #2e6da4")
)),
column(width = 10,
box(
title = "R Packages",
title = "Packages and tools",
width = NULL,
collapsible = TRUE,
solidHeader = TRUE,
......@@ -40,16 +36,21 @@ tabHome = fluidPage(align="left",
withSpinner(DT::dataTableOutput('dtrcranpackage'), type = 4, proxy.height = "150px")
),
tabPanel('Bioconductor',
DT::dataTableOutput('dtrbioconductorpackage')),
div(id = "formBioconductor",
# br(),
#selectizeInput('selectedBioconductor', 'R Bioconductor selected:', choices = NULL, multiple=TRUE, options = list(maxItems = 30000)),
DT::dataTableOutput('dtrbioconductorpackage'))),
tabPanel('Github',
textInput("inputGithub", "Package name:", ""),
actionButton("findGithub", label = "Find", icon("paper-plane"), style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
div(id = "formGithub",
br(), br(),
selectizeInput('rgithubpackagelist', 'R Github selected:', choices = NULL, multiple=TRUE, options = list(maxItems = 30000)),
br(), br(),
DT::dataTableOutput('dtrgithubpackage'))),
tabPanel('BioContainer tools',
div(id = "formContainer",
br(),
selectizeInput('selectedBiocontainer', 'Biocontainer tools selected:', choices = NULL, multiple=TRUE, options = list(maxItems = 30000))),
DT::dataTableOutput('dtbiocontainer')
)
......
server/opt_home.R
View file @ cfcbf3b2
......@@ -165,29 +165,38 @@ createContentFile <- function() {
selectBIO <- allBIO[input$dtrbioconductorpackage_rows_all,]
selectBIO <- selectBIO[,"Package"]
sizeBIO <- length(selectBIO)
if(!is.null(sizeBIO)) {
if(sizeBIO < length(allBIO[,"Package"])) {
if(sizeBIO >= 1) {
result <- paste(result, '\tR --slave -e "source(\'https://bioconductor.org/biocLite.R\'); \\', sep = "\n")
result <- paste(result, '\tbiocLite()"\n', sep = "\n")
listRBIO <- '\tR --slave -e "source(\'https://bioconductor.org/biocLite.R\'); \\'
listRBIO <- paste0(listRBIO, "\n\tbiocLite(")
for (pkg in 1:sizeBIO){
if(pkg < sizeBIO) {
listRBIO <- paste0(listRBIO, '\'',selectBIO[pkg],'\', ')
} else {
listRBIO <- paste0(listRBIO, '\'',selectBIO[pkg],'\')"')
}
}
result <- paste(result, listRBIO, sep = "\n")
}
}
# if(!is.null(input$selectedBioconductor)) {
#print(input$selectedBioconductor)
sizeBIO <- length(selectBIO)
if(!is.null(sizeBIO)) {
if(sizeBIO < length(allBIO[,"Package"])) {
if(sizeBIO >= 1) {
result <- paste(result, '\tR --slave -e "source(\'https://bioconductor.org/biocLite.R\'); \\', sep = "\n")
result <- paste(result, '\tbiocLite()"\n', sep = "\n")
listRBIO <- '\tR --slave -e "source(\'https://bioconductor.org/biocLite.R\'); \\'
listRBIO <- paste0(listRBIO, "\n\tbiocLite(")
for (pkg in 1:sizeBIO){
if(pkg < sizeBIO) {
listRBIO <- paste0(listRBIO, '\'',selectBIO[pkg],'\', ')
} else {
listRBIO <- paste0(listRBIO, '\'',selectBIO[pkg],'\')"')
}
}
result <- paste(result, listRBIO, sep = "\n")
}
}
# }
}
result <- paste(result, "\n", sep = "\n")
if(!is.null(input$rgithubpackagelist)) {
......
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