fix tools

container.yaml

@@ -14,12 +14,14 @@ containers: [
 ,{ 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: "cd-hit", version: "4.6.8", description: "CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.", documentation: "http://weizhongli-lab.org/cd-hit/", install: ["conda install -c bioconda cd-hit=4.6.8"]}
 ,{ 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: "CNVnator", version: "0.3.3", description: "an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.", documentation: "https://github.com/abyzovlab/CNVnator", install: ["cd /opt/biotools/ ; wget --quiet https://root.cern.ch/download/root_v6.10.08.Linux-ubuntu16-x86_64-gcc5.4.tar.gz ; tar zxf root_v6.10.08.Linux-ubuntu16-x86_64-gcc5.4.tar.gz",	"export ROOTSYS=/opt/biotools/root", "export LD_LIBRARY_PATH=\"$ROOTSYS/lib:$LD_LIBRARY_PATH\"", "echo 'export ROOTSYS=/opt/biotools/root' >> $SINGULARITY_ENVIRONMENT", "echo 'export LD_LIBRARY_PATH=\"$ROOTSYS/lib:$LD_LIBRARY_PATH\"' >> $SINGULARITY_ENVIRONMENT", "cd /opt/biotools/ ; wget https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2 -O bcftools.tar.bz2 ; tar -xjvf bcftools.tar.bz2 ; cd bcftools-1.3.1/ ; make ; make prefix=/usr/local/bin install", "ln -s /usr/local/bin/bin/bcftools /usr/bin/bcftools ", "cd /opt/biotools/ ; wget --quiet https://github.com/abyzovlab/CNVnator/releases/download/v0.3.3/CNVnator_v0.3.3.zip ; unzip CNVnator_v0.3.3.zip ; cd CNVnator_v0.3.3/src/samtools/htslib-1.3.1/ ;	make ; make install ; cd ../ ; make ; make install ; cd ../ ; make", "ln -s /opt/biotools/CNVnator_v0.3.3/src/cnvnator /opt/biotools/bin/cnvnator"] }
 ,{ name: "cnv-seq", version: "1.0", description: "CNV-seq, a new method to detect copy number variation using high-throughput sequencing", documentation: "http://tiger.dbs.nus.edu.sg/cnv-seq/", install: ["cd /opt/biotools/ ; wget http://tiger.dbs.nus.edu.sg/cnv-seq/cnv-seq.tar.gz; tar -xvf cnv-seq.tar.gz; ln -s /opt/biotools/cnv-seq/cnv-seq.pl bin/cnv-seq"]}
 ,{ name: "cross-species-scaffolding", version: "0.1", description: "Generate in silico mate-pair reads from single-/paired-end reads of your organism of interest", documentation: "https://github.com/thackl/cross-species-scaffolding", install: ["cd /opt/biotools; rm -rf cross-species-scaffolding; git clone https://github.com/thackl/cross-species-scaffolding.git ; cd cross-species-scaffolding; mkdir samples; make util/bcftools; make util/samtools; make dependencies;"], env: "export PATH=/opt/biotools/cross-species-scaffolding/bin:/opt/biotools/cross-species-scaffolding/util/samtools:$PATH" }
 ,{ name: "crux", version: "2.1", description: "a software toolkit for tandem mass spectrometry analysis", documentation: "http://cruxtoolkit.sourceforge.net/", install: [] }
+,{ name: "dDocent", version: "2.5.5", description: "dDocent is an interactive bash wrapper to QC, assemble, map, and call SNPs from all types of RAD data", documentation: "http://ddocent.com/", install: ["conda install -c bioconda ddocent=2.5.5"]}
 ,{ 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"] }
@@ -30,6 +32,7 @@ containers: [
 ,{ 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: "freebayes", version: "1.2.0", description: "Bayesian haplotype-based genetic polymorphism discovery and genotyping.", documentation: "https://github.com/ekg/freebayes", install: ["conda install -c bioconda freebayes=1.2.0"]}
 ,{ 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"] }
@@ -57,9 +60,11 @@ containers: [
 ,{ 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: "rad_haplotyper", version: "1.1.9", description: "A program for building SNP haplotypes from RAD sequencing data", documentation: "https://github.com/chollenbeck/rad_haplotyper", install: ["git clone https://github.com/chollenbeck/rad_haplotyper.git && \\", "cp ./rad_haplotyper/rad_haplotyper.pl /opt/biotools/bin/ && \\", "apt-get install -y vcftools && \\", "cpan App::cpanminus && \\", "cpanm Vcf && \\", "cpanm Data::Dumper && \\", "cpanm Getopt::Long && \\", "cpanm Pod::Usage && \\", "cpanm Bio::Cigar && \\", "cpanm List::MoreUtils && \\",     "cpanm Term::ProgressBar && \\", "cpanm Parallel::ForkManager"]}
 ,{ 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: "repeatmasker", version: "4.0.6", description: "RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.", documentation: "http://www.repeatmasker.org/", install: ["conda install -c bioconda repeatmasker=4.0.6; mkdir /share; ln -s /opt/conda/share/RepeatMasker /share/RepeatMasker"]}
 #,{ name: "root", version: "6.04", description: "", documentation: "", install: ["conda install -c nlesc root=6.04"]}
+,{ name: "sambamba", version: "0.6.6", description: "Tools for working with SAM/BAM data", documentation: "http://lomereiter.github.io/sambamba/", install: [" conda install -c bioconda sambamba=0.6.6"]}
 ,{ 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"] }
@@ -84,5 +89,6 @@ containers: [
 ,{ name: "trimmomatic", version: "0.36", description: "Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.", documentation: "http://www.usadellab.org/cms/?page=trimmomatic", install: ["conda install -c bioconda trimmomatic=0.36"] }
 ,{ 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: "vcflib", version: "1.0.0_rc1", description: "a simple C++ library for parsing and manipulating VCF files, + many command-line utilities", documentation: "https://github.com/vcflib/vcflib", install: ["conda install -c bioconda vcflib=1.0.0_rc1"]}
 ,{ 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" ] }
 ]