mr-c

# Courtesy Chulalongkorn University Systems Biology Center
# CWL workshop 2019-08-30
FROM debian
RUN apt-get update && apt-get install -y r-base-core
RUN apt-get install r-bioc-preprocesscore r-cran-nnls
RUN R -e "install.packages('https://github.com/cran/FARDEEP/archive/1.0.1.tar.gz')"

mr-c

{
    "$graph": [
        {
            "requirements": [
                {
                    "class": "DockerRequirement",
                    "dockerPull": "quay.io/ncigdc/bam_readgroup_to_json:7cb045ba57c027e283fbf42ea566f39b5f4846b1381e69b9e36e32bb978f0c9a"
                },
                {
                    "class": "InlineJavascriptRequirement"

mr-c

#
# This file was autogenerated using schema-salad-tool --codegen=python
#
from __future__ import absolute_import
import ruamel.yaml
from ruamel.yaml.comments import CommentedBase, CommentedMap, CommentedSeq
import re
import os
import traceback

mr-c

#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: CommandLineTool

hints:
  DockerRequirement:
    dockerPull: mgibio/mixcr
  SoftwareRequirement:
    packages:
      mixcr:

mr-c

empty

mr-c

# -*- mode: ruby -*-
# vi: set ft=ruby :

Vagrant.configure("2") do |config|
  config.vm.box = "centos/7"
  config.vm.provider "virtualbox" do |v|
	  v.linked_clone = true
  end
  config.vm.provision "shell", inline: <<-SHELL
sudo yum install -y gcc python-setuptools squashfs-tools git

mr-c

<?xml version="1.0" encoding="UTF-8"?>
<rdf:RDF
   xmlns:CommandLineBinding="https://w3id.org/cwl/cwl#CommandLineBinding/"
   xmlns:cwl="https://w3id.org/cwl/cwl#"
   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
   xmlns:sld="https://w3id.org/cwl/salad#"
>
  <rdf:Description rdf:nodeID="N4ef640f378484c3e91d651024cbb7202">
    <rdf:first>mem</rdf:first>
    <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>

mr-c

Michael,

Your project may be a good candidate for Conservancy.  The only item
that gives me some pause is that we're typically a home for software
projects, not for standards, although I do see you have a reference
implementation.  Nevertheless, I think it's worth applying to
Conservancy.  Our application process is relatively informal.  The
materials are below:

######################################################################

mr-c

rgiuly@ubuntu:~/cwl-workflows/workflows/lobSTR$ sudo
./lobSTR-workflow.cwl lobSTR-demo.json
/usr/local/bin/cwl-runner 1.0.20150929170517
Unhandled exception
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/cwltool/workflow.py",
line 202, in try_make_job
    for j in jobs:
  File "/usr/local/lib/python2.7/dist-packages/cwltool/workflow.py",
line 126, in job

mr-c

# Rackspace Ubuntu 14.04
# 500 MB too slow
# Trying 1 GB General Purpose v1

ssh -L 8080:localhost:8080 root@${host}
su ubuntu

cd
sudo apt-get update
sudo apt-get dist-upgrade