Add Dockerfile generator

R/helper_functions.R

@@ -61,7 +61,7 @@ getBioconductorPackage <- function() {
   return(result)
 }
 
-getInstallToolPackageBioContainer <- function(tool) {
+getInstallToolPackageBioContainer <- function(tool, containerType) {
   
   data <- allBIOCONTAINER
 
@@ -76,7 +76,7 @@ getInstallToolPackageBioContainer <- function(tool) {
       
       if(tools$name == name) {
         if(tools$version == version) {
-          res <- paste0("\t", tools$install, collapse='\n' )
+            res <- paste0("\t", tools$install, collapse='\n' )
           return(res)
         }
       }

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: "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"] }
@@ -33,7 +33,7 @@ containers: [
 ,{ 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: "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 "] }

pages/pages_def_home.R

@@ -10,7 +10,7 @@ tabHome = fluidPage(align="left",
                                
                                textInput("imageName", "Image Name", ""),
                                br(),
-                               radioButtons("containerType", "Container type:", choices = list("Singularity" = "singularity"), selected = "singularity"),
+                               radioButtons("containerType", "Container type:", choices = list("Singularity" = "singularity", "Docker" = "docker"), selected = "singularity"),
                                br(),
                                #selectizeInput('rcranpackagelist', 'R CRAN:', choices = NULL, multiple=TRUE, options = list(maxItems = 30000)),
                                selectizeInput('rtemplate', 'R origin:', choices = c(`None` = 'none', `R from source` = 'source', `R from r-base` = 'base', `R from CRAN depo` = 'cran'), selected = "source", multiple = FALSE),