Admin Variant Calling 03

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インストール方法

http://goo.gl/QzSfdm
からHOSOMICHI_HLA_tools2内のファイルを入手

  • Galaxy-Workflow-imported__HLA2_Workflow_(alpha3).ga はワークフロー
  • Seq-reads_for_TEST.tar.gz はサンプルのリード配列
  • To_disk-reference.tar.gz は解凍後 /disk/reference 下に置く。
  • To_galaxy-dist_tools.tar.gz は解凍後 galaxy-dist/tools 下に置く。

パスの設定は hlaconf.pm

  • hlaconf.pm はgalaxy-dist/tools/workflow/hla2 の下に
  • hlaconf.pm の20行めまでにパス周り集中。要確認!

tool_data_table_conf.xml

    <!-- for HOSOMICHI HLA tools, NOTE: "value" field is required.-->
    <table name="HOSOMICHI_HLA_TOOLS_DATA" comment_char="#">
        <columns>value, locus, ref, nuc, int</columns>
        <file path="tool-data/HOSOMICHI_HLA_TOOLS_DATA.loc" />
    </table>

HOSOMICHI_HLA_TOOLS_DATA.loc

  • HOSOMICHI_HLA_TOOLS_DATA.loc はgalaxy-dist/tool-dataの下に
#All datas are into galaxy-refs/hosomichi directory.
#Value	Locus	Reference(Bwa index)	Nucleotid	Intervals
#value	locus	ref	nuc	int
HLA-A	A	ref/HLA-A.fasta	db/A_nuc_HAC.fasta	db/HLA-A_gene_start_end.intervals
HLA-B	B	ref/HLA-B.fasta	db/B_nuc_HAC.fasta	db/HLA-B_gene_start_end.intervals
HLA-C	C	ref/HLA-C.fasta	db/C_nuc_HAC.fasta	db/HLA-C_gene_start_end.intervals
HLA-DPB1	DPB1	ref/HLA-DPB1.fasta	db/DPB1_nuc_HAC.fasta	db/HLA-DPB1_gene_start_end.intervals
HLA-DQB1	DQB1	ref/HLA-DQB1.fasta	db/DQB1_nuc_HAC.fasta	db/HLA-DQB1_gene_start_end.intervals
HLA-DRB1	DRB1	ref/HLA-DRB1.fasta	db/DRB1_nuc_HAC.fasta	db/HLA-DRB1_gene_start_end.intervals

tool_conf.xml

  • tool_conf-HLA-Part.xml galaxy-dist下のtool_conf.xmlのHLAtoolsについての記載部分
  <section name="HLA2 wf test" id="hla2_wf">
    <label text="HLA2 test" id="hla2"/>
       <tool file="workflow/hla2/fastq_quality_trimmerM.xml"/>
       <tool file="workflow/hla2/pairedread.xml"/>
       <tool file="workflow/hla2/bwa/bwa_wrapper.xml"/>
       <tool file="workflow/hla2/bwa/bwa4hla.xml"/>
       <tool file="workflow/hla2/samtools/samtools_HOSO.xml"/>
       <tool file="workflow/hla2/gatkFastaAltRefMaker.xml"/>
       <tool file="workflow/hla2/gatkUnifiedGenotyper.xml"/>
       <tool file="workflow/hla2/picardadd.xml"/>
       <tool file="workflow/hla2/bam2cds.xml"/>
       <tool file="workflow/hla2/rewritevcf.xml"/>
       <tool file="workflow/hla2/awkSam300.xml"/>
       <tool file="workflow/hla2/awkSam500.xml"/>
       <tool file="workflow/hla2/grepvariant.xml"/>
       <tool file="workflow/hla2/awk_cds_closest.xml"/>
       <tool file="workflow/hla2/awk_cds_perfect.xml"/>
       <tool file="workflow/hla2/blat_haplo.xml"/>
       <tool file="workflow/hla2/haplo.xml"/>
       <tool file="workflow/hla2/hoso_zip_archive.xml"/>
       <tool file="workflow/hla2/remove_minor_reads_samtools_sam.xml"/>
       <tool file="workflow/hla2/remove_minor_reads_samtools_bam.xml"/>
       <tool file="workflow/hla2/filter_hetero_reads.xml"/>
       <tool file="workflow/hla2/rmread3.xml"/>
       <tool file="workflow/hla2/hoso_param.xml"/>
  </section>