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

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

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

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

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

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

mr-c

#!/usr/bin/env cwl-runner
class: Workflow
id: file:///home/michael/common-workflow-language/v1.0/v1.0.orig/count-lines3-wf.cwl
inputs:
- id: file1
  type:
    items: File
    type: array
outputs:
- id: count_output

mr-c

FAILED: search/CMakeFiles/search_test.dir/search_test.cpp.o 
/usr/bin/ccache /usr/lib/ccache/c++  -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -Ivendor/googletest/googletest/include -I/build/seqan3-3.0.0+ds2/test/include -I/build/seqan3-3.0.0+ds2/include -isystem /build/seqan3-3.0.0+ds2/submodules/sdsl-lite/include -isystem /build/seqan3-3.0.0+ds2/submodules/range-v3/include -g -O2 -fdebug-prefix-map=/build/seqan3-3.0.0+ds2=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2   -pedantic -Wall -Wextra -Werror -std=c++17 -fconcepts -MD -MT search/CMakeFiles/search_test.dir/search_test.cpp.o -MF search/CMakeFiles/search_test.dir/search_test.cpp.o.d -o search/CMakeFiles/search_test.dir/search_test.cpp.o -c /build/seqan3-3.0.0+ds2/test/unit/search/search_test.cpp
In file included from /build/seqan3-3.0.0+ds2/include/seqan3/search/fm_index/fm_index.hpp:24,
                 from /build/seqan3-3.0.0+ds2/include/seqan3/search/fm_index/bi_fm_index.hpp:20,
               

mr-c

I: Running in no-targz mode
I: pbuilder: network access will be disabled during build
I: Current time: Fri Dec  6 19:44:44 CET 2019
I: pbuilder-time-stamp: 1575657884
I: copying local configuration
W: No local /etc/mailname to copy, relying on /var/cache/pbuilder/build/cow.30182/etc/mailname to be correct
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm