github.com/informationsea/shellflow@v0.1.3/examples/doc-example3/prepare.sf (about)

     1  # -*- shell-script -*-
     2  
     3  #% GATK_VERSION = "4.0.10.1"
     4  #% BWA_VERSION = "0.7.17"
     5  #% SAMTOOLS_VERSION = "1.9"
     6  
     7  # Prepare analysis tools
     8  curl -o [[bwa-{{BWA_VERSION}}.tar.bz2]] -L https://downloads.sourceforge.net/project/bio-bwa/bwa-{{BWA_VERSION}}.tar.bz2
     9  tar xjf ((bwa-{{BWA_VERSION}}.tar.bz2)) # [[bwa-{{BWA_VERSION}}/bwa.c]]
    10  make -C bwa-{{BWA_VERSION}} # [[bwa-{{BWA_VERSION}}/bwa]] ((bwa-{{BWA_VERSION}}/bwa.c))
    11  
    12  curl -L -o [[samtools-{{SAMTOOLS_VERSION}}.tar.bz2]] https://github.com/samtools/samtools/releases/download/{{SAMTOOLS_VERSION}}/samtools-{{SAMTOOLS_VERSION}}.tar.bz2
    13  tar xjf ((samtools-{{SAMTOOLS_VERSION}}.tar.bz2)) # [[samtools-{{SAMTOOLS_VERSION}}/samtools.h]]
    14  make -C samtools-{{SAMTOOLS_VERSION}} # ((samtools-{{SAMTOOLS_VERSION}}/samtools.h)) [[samtools-{{SAMTOOLS_VERSION}}/samtools]]
    15  
    16  curl -o [[artbinmountrainier2016.06.05linux64.tgz]] -L https://www.niehs.nih.gov/research/resources/assets/docs/artbinmountrainier2016.06.05linux64.tgz
    17  tar xzf ((artbinmountrainier2016.06.05linux64.tgz)) # [[art_bin_MountRainier/art_illumina]]
    18  
    19  curl -o [[gatk-{{GATK_VERSION}}.zip]] -L https://github.com/broadinstitute/gatk/releases/download/{{GATK_VERSION}}/gatk-{{GATK_VERSION}}.zip
    20  unzip ((gatk-{{GATK_VERSION}}.zip)) # [[gatk-{{GATK_VERSION}}/gatk]]
    21  
    22  # Prepare index
    23  ((samtools-{{SAMTOOLS_VERSION}}/samtools)) faidx ((e-coli-NC_011750.1.fasta)) # [[e-coli-NC_011750.1.fasta.fai]]
    24  ((bwa-{{BWA_VERSION}}/bwa)) index ((e-coli-NC_011750.1.fasta)) # [[e-coli-NC_011750.1.fasta.bwt]]
    25  ((gatk-{{GATK_VERSION}}/gatk)) --java-options "-Xmx4G" CreateSequenceDictionary -R ((e-coli-NC_011750.1.fasta)) # [[e-coli-NC_011750.1.dict]]