[DOCKTESTERS] Thanks!

[George Mihaiescu]

Hi,

I had problems installing the gtdownload cline, so I changed your scripts to use the icgc-storage client and downloaded the BAMs from Collaboratory, but I think this caused more harm in the end because I diverted from the good known testing path.

This is the content of the Dockstore.json file:

root at dockstore4-dkfz:~/PCAWG-Docker-Test# cat tests/DKFZ/DO218695/Dockstore.json
{
  "run-id": "run_id",
  "tumor-bam":
  {
    "path":"/root/PCAWG-Docker-Test/data/DO218695/tumor.bam",
    "class":"File"
  },
  "normal-bam":
  {
    "path":"/root/PCAWG-Docker-Test/data/DO218695/normal.bam",
    "class":"File"
  },
  "reference-gz":
  {
    "path": "/root/PCAWG-Docker-Test/resources//dkfz-workflow-dependencies_150318_0951.tar.gz",
    "class": "File"
  },
  "delly-bedpe":
  {
    "path":"/root/PCAWG-Docker-Test/tests/Delly/DO218695/output//DO218695.delly.somatic.sv.bedpe.txt",
    "class":"File"
  },
  "germline_indel_vcf_gz": {
    "path": "/root/PCAWG-Docker-Test/tests/DKFZ/DO218695//output//DO218695.germline.indel.vcf.gz",
    "class": "File"
  },
  "somatic_snv_mnv_vcf_gz": {
    "path": "/root/PCAWG-Docker-Test/tests/DKFZ/DO218695//output//DO218695.somatic.snv.mnv.vcf.gz",
    "class": "File"
  },
  "germline_snv_mnv_vcf_gz": {
    "path": "/root/PCAWG-Docker-Test/tests/DKFZ/DO218695//output//DO218695.germline.snv.mnv.vcf.gz",
    "class": "File"
  },
  "somatic_cnv_tar_gz": {
    "path": "/root/PCAWG-Docker-Test/tests/DKFZ/DO218695//output//DO218695.somatic.cnv.tar.gz",
    "class": "File"
  },
  "somatic_cnv_vcf_gz": {
    "path": "/root/PCAWG-Docker-Test/tests/DKFZ/DO218695//output//DO218695.somatic.cnv.vcf.gz",
    "class": "File"
  },
  "somatic_indel_tar_gz": {
    "path": "/root/PCAWG-Docker-Test/tests/DKFZ/DO218695//output//DO218695.somatic.indel.tar.gz",
    "class": "File"
  },
  "somatic_snv_mnv_tar_gz": {
    "path": "/root/PCAWG-Docker-Test/tests/DKFZ/DO218695//output//DO218695.somatic.snv.mnv.tar.gz",
    "class": "File"
  },
  "somatic_indel_vcf_gz": {
    "path": "/root/PCAWG-Docker-Test/tests/DKFZ/DO218695//output//DO218695.somatic.indel.vcf.gz",
    "class": "File"
  }
}

Thank you,
George

From: Miguel Vazquez <mikisvaz at gmail.com<mailto:mikisvaz at gmail.com>>
Date: Wednesday, March 29, 2017 at 4:09 AM
To: George Mihaiescu <George.Mihaiescu at oicr.on.ca<mailto:George.Mihaiescu at oicr.on.ca>>
Cc: Jonas Demeulemeester <Jonas.Demeulemeester at crick.ac.uk<mailto:Jonas.Demeulemeester at crick.ac.uk>>, Junjun Zhang <Junjun.Zhang at oicr.on.ca<mailto:Junjun.Zhang at oicr.on.ca>>, "docktesters at lists.icgc.org<mailto:docktesters at lists.icgc.org>" <docktesters at lists.icgc.org<mailto:docktesters at lists.icgc.org>>
Subject: Re: [DOCKTESTERS] Thanks!

tests/DKFZ/DO218695/Dockstore.json
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