[ARVADOS] updated: c5be0c3abd926adc54e0c1de65e8dfdd25a84ea1

[git at public.curoverse.com]

Summary of changes:
 crunch_scripts/collection-merge       |  39 ++++------
 crunch_scripts/decompress-all.py      |  62 +++++++++++++++
 crunch_scripts/run-command            | 143 +++++++++++++++++++++++++++-------
 crunch_scripts/split-fastq.py         | 128 ++++++++++++++++++++++++++++++
 crunch_scripts/subst.py               |   6 +-
 docker/jobs/Dockerfile                |   4 +-
 sdk/cli/bin/arv-run-pipeline-instance |  12 +--
 7 files changed, 334 insertions(+), 60 deletions(-)
 create mode 100755 crunch_scripts/decompress-all.py
 create mode 100755 crunch_scripts/split-fastq.py

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commit c5be0c3abd926adc54e0c1de65e8dfdd25a84ea1
Merge: 57ee969 0a53423
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Tue Aug 12 11:42:55 2014 -0400

    Merge branch '3373-improve-gatk3-snv-pipeline' closes #3373


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