allisonheath

{
  "id": 1,
  "gender": "Male",
  "race": ["White", "Asian"],
  "ethnicity": "Not Hispanic or Latino",
  "age": 230,
  "diagnosis_pathology": ["Medulloblastoma", "PNET"],
  "diagnosis_other": "Unknown",
  "diagnosis_comments": null,
  "has_chemo": "Not Reported",

allisonheath

#!/bin/bash
wget http://download.asperasoft.com/download/sw/ascp-client/3.5.4/ascp-install-3.5.4.102989-linux-64.sh
sh ascp-install-3.5.4.102989-linux-64.sh

pip install awscli

curl -o /usr/bin/s3md5 https://raw.githubusercontent.com/antespi/s3md5/master/s3md5
chmod +x /usr/bin/s3md5

allisonheath

Using perl v5.14.2 on fairly vanilla Ubuntu 12.04.1 LTS

In order that they appear:

Can't locate Const/Fast.pm in @INC (@INC contains: lib /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at lib/PCAP.pm line 24.

Building BioPerl-1.006923 ... Module::Build version 0.42 required--this is only version 0.38 at ./Build line 43.

Error:  Can't locate Data/UUID.pm in @INC (@INC contains: /opt/PCAP-core/blib/lib /opt/PCAP-core/blib/arch /opt/ICGC/lib/perl5/x86_64-linux-gnu-thread-multi /opt/ICGC/lib/perl5/x86_64-linux-gnu-thread-multi /opt/ICGC/lib/perl5 /opt/ICGC/lib/perl5/x86_64-linux-gnu-thread-multi /opt/ICGC/lib/perl5 /opt/ICGC/lib/perl5/x86_64-linux-gnu-thread-multi /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at /opt/PCAP-core/blib/lib/PCAP/SRA.pm line 36.

allisonheath

PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/1_pm_compile.t ...... ok
t/2_pl_compile.t ...... ok
    
    #   Failed test 'Expect version 0.0.125 for bamcollate2'
    #   at t/3_external_progs.t line 51.
    
    #   Failed test 'Expect version 0.0.125 for bammarkduplicates'
    #   at t/3_external_progs.t line 51.